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# Copyright 2007-2010 by Peter Cock.  All rights reserved. 

# Revisions copyright 2010 by Uri Laserson.  All rights reserved. 

# This code is part of the Biopython distribution and governed by its 

# license.  Please see the LICENSE file that should have been included 

# as part of this package. 

"""Internal code for parsing GenBank and EMBL files (PRIVATE). 

 

This code is NOT intended for direct use.  It provides a basic scanner 

(for use with a event consumer such as Bio.GenBank._FeatureConsumer) 

to parse a GenBank or EMBL file (with their shared INSDC feature table). 

 

It is used by Bio.GenBank to parse GenBank files 

It is also used by Bio.SeqIO to parse GenBank and EMBL files 

 

Feature Table Documentation: 

http://www.insdc.org/files/feature_table.html 

http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html 

ftp://ftp.ncbi.nih.gov/genbank/docs/ 

""" 

# 17-MAR-2009: added wgs, wgs_scafld for GenBank whole genome shotgun master records. 

# These are GenBank files that summarize the content of a project, and provide lists of 

# scaffold and contig files in the project. These will be in annotations['wgs'] and 

# annotations['wgs_scafld']. These GenBank files do not have sequences. See 

# http://groups.google.com/group/bionet.molbio.genbank/browse_thread/thread/51fb88bf39e7dc36 

# http://is.gd/nNgk 

# for more details of this format, and an example. 

# Added by Ying Huang & Iddo Friedberg 

 

from __future__ import print_function 

 

import warnings 

import re 

from Bio.Seq import Seq 

from Bio.SeqRecord import SeqRecord 

from Bio.Alphabet import generic_protein 

from Bio import BiopythonParserWarning 

 

 

class InsdcScanner(object): 

    """Basic functions for breaking up a GenBank/EMBL file into sub sections. 

 

    The International Nucleotide Sequence Database Collaboration (INSDC) 

    between the DDBJ, EMBL, and GenBank.  These organisations all use the 

    same "Feature Table" layout in their plain text flat file formats. 

 

    However, the header and sequence sections of an EMBL file are very 

    different in layout to those produced by GenBank/DDBJ.""" 

 

    #These constants get redefined with sensible values in the sub classes: 

    RECORD_START = "XXX"  # "LOCUS       " or "ID   " 

    HEADER_WIDTH = 3   # 12 or 5 

    FEATURE_START_MARKERS = ["XXX***FEATURES***XXX"] 

    FEATURE_END_MARKERS = ["XXX***END FEATURES***XXX"] 

    FEATURE_QUALIFIER_INDENT = 0 

    FEATURE_QUALIFIER_SPACER = "" 

    SEQUENCE_HEADERS = ["XXX"]  # with right hand side spaces removed 

 

    def __init__(self, debug=0): 

        assert len(self.RECORD_START) == self.HEADER_WIDTH 

        for marker in self.SEQUENCE_HEADERS: 

            assert marker == marker.rstrip() 

        assert len(self.FEATURE_QUALIFIER_SPACER) == self.FEATURE_QUALIFIER_INDENT 

        self.debug = debug 

        self.line = None 

 

    def set_handle(self, handle): 

        self.handle = handle 

        self.line = "" 

 

    def find_start(self): 

        """Read in lines until find the ID/LOCUS line, which is returned. 

 

        Any preamble (such as the header used by the NCBI on *.seq.gz archives) 

        will we ignored.""" 

        while True: 

            if self.line: 

                line = self.line 

                self.line = "" 

            else: 

                line = self.handle.readline() 

            if not line: 

                if self.debug: 

                    print("End of file") 

                return None 

            if line[:self.HEADER_WIDTH] == self.RECORD_START: 

                if self.debug > 1: 

                    print("Found the start of a record:\n" + line) 

                break 

            line = line.rstrip() 

            if line == "//": 

                if self.debug > 1: 

                    print("Skipping // marking end of last record") 

            elif line == "": 

                if self.debug > 1: 

                    print("Skipping blank line before record") 

            else: 

                #Ignore any header before the first ID/LOCUS line. 

                if self.debug > 1: 

                        print("Skipping header line before record:\n" + line) 

        self.line = line 

        return line 

 

    def parse_header(self): 

        """Return list of strings making up the header 

 

        New line characters are removed. 

 

        Assumes you have just read in the ID/LOCUS line. 

        """ 

        assert self.line[:self.HEADER_WIDTH] == self.RECORD_START, \ 

            "Not at start of record" 

 

        header_lines = [] 

        while True: 

            line = self.handle.readline() 

            if not line: 

                raise ValueError("Premature end of line during sequence data") 

            line = line.rstrip() 

            if line in self.FEATURE_START_MARKERS: 

                if self.debug: 

                    print("Found feature table") 

                break 

            #if line[:self.HEADER_WIDTH]==self.FEATURE_START_MARKER[:self.HEADER_WIDTH]: 

            #    if self.debug : print("Found header table (?)") 

            #    break 

            if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS: 

                if self.debug: 

                    print("Found start of sequence") 

                break 

            if line == "//": 

                raise ValueError("Premature end of sequence data marker '//' found") 

            header_lines.append(line) 

        self.line = line 

        return header_lines 

 

    def parse_features(self, skip=False): 

        """Return list of tuples for the features (if present) 

 

        Each feature is returned as a tuple (key, location, qualifiers) 

        where key and location are strings (e.g. "CDS" and 

        "complement(join(490883..490885,1..879))") while qualifiers 

        is a list of two string tuples (feature qualifier keys and values). 

 

        Assumes you have already read to the start of the features table. 

        """ 

        if self.line.rstrip() not in self.FEATURE_START_MARKERS: 

            if self.debug: 

                print("Didn't find any feature table") 

            return [] 

 

        while self.line.rstrip() in self.FEATURE_START_MARKERS: 

            self.line = self.handle.readline() 

 

        features = [] 

        line = self.line 

        while True: 

            if not line: 

                raise ValueError("Premature end of line during features table") 

            if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS: 

                if self.debug: 

                    print("Found start of sequence") 

                break 

            line = line.rstrip() 

            if line == "//": 

                raise ValueError("Premature end of features table, marker '//' found") 

            if line in self.FEATURE_END_MARKERS: 

                if self.debug: 

                    print("Found end of features") 

                line = self.handle.readline() 

                break 

            if line[2:self.FEATURE_QUALIFIER_INDENT].strip() == "": 

                #This is an empty feature line between qualifiers. Empty 

                #feature lines within qualifiers are handled below (ignored). 

                line = self.handle.readline() 

                continue 

            if len(line) < self.FEATURE_QUALIFIER_INDENT: 

                warnings.warn("line too short to contain a feature: %r" % line, 

                              BiopythonParserWarning) 

                line = self.handle.readline() 

                continue 

 

            if skip: 

                line = self.handle.readline() 

                while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER: 

                    line = self.handle.readline() 

            else: 

                #Build up a list of the lines making up this feature: 

                if line[self.FEATURE_QUALIFIER_INDENT] != " " \ 

                        and " " in line[self.FEATURE_QUALIFIER_INDENT:]: 

                    #The feature table design enforces a length limit on the feature keys. 

                    #Some third party files (e.g. IGMT's EMBL like files) solve this by 

                    #over indenting the location and qualifiers. 

                    feature_key, line = line[2:].strip().split(None, 1) 

                    feature_lines = [line] 

                    warnings.warn("Overindented %s feature?" % feature_key, 

                                  BiopythonParserWarning) 

                else: 

                    feature_key = line[2:self.FEATURE_QUALIFIER_INDENT].strip() 

                    feature_lines = [line[self.FEATURE_QUALIFIER_INDENT:]] 

                line = self.handle.readline() 

                while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER \ 

                        or line.rstrip() == "":  # cope with blank lines in the midst of a feature 

                    #Use strip to remove any harmless trailing white space AND and leading 

                    #white space (e.g. out of spec files with too much indentation) 

                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].strip()) 

                    line = self.handle.readline() 

                features.append(self.parse_feature(feature_key, feature_lines)) 

        self.line = line 

        return features 

 

    def parse_feature(self, feature_key, lines): 

        """Expects a feature as a list of strings, returns a tuple (key, location, qualifiers) 

 

        For example given this GenBank feature: 

 

             CDS             complement(join(490883..490885,1..879)) 

                             /locus_tag="NEQ001" 

                             /note="conserved hypothetical [Methanococcus jannaschii]; 

                             COG1583:Uncharacterized ACR; IPR001472:Bipartite nuclear 

                             localization signal; IPR002743: Protein of unknown 

                             function DUF57" 

                             /codon_start=1 

                             /transl_table=11 

                             /product="hypothetical protein" 

                             /protein_id="NP_963295.1" 

                             /db_xref="GI:41614797" 

                             /db_xref="GeneID:2732620" 

                             /translation="MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK 

                             EKYFNFTLIPKKDIIENKRYYLIISSPDKRFIEVLHNKIKDLDIITIGLAQFQLRKTK 

                             KFDPKLRFPWVTITPIVLREGKIVILKGDKYYKVFVKRLEELKKYNLIKKKEPILEEP 

                             IEISLNQIKDGWKIIDVKDRYYDFRNKSFSAFSNWLRDLKEQSLRKYNNFCGKNFYFE 

                             EAIFEGFTFYKTVSIRIRINRGEAVYIGTLWKELNVYRKLDKEEREFYKFLYDCGLGS 

                             LNSMGFGFVNTKKNSAR" 

 

        Then should give input key="CDS" and the rest of the data as a list of strings 

        lines=["complement(join(490883..490885,1..879))", ..., "LNSMGFGFVNTKKNSAR"] 

        where the leading spaces and trailing newlines have been removed. 

 

        Returns tuple containing: (key as string, location string, qualifiers as list) 

        as follows for this example: 

 

        key = "CDS", string 

        location = "complement(join(490883..490885,1..879))", string 

        qualifiers = list of string tuples: 

 

        [('locus_tag', '"NEQ001"'), 

         ('note', '"conserved hypothetical [Methanococcus jannaschii];\nCOG1583:..."'), 

         ('codon_start', '1'), 

         ('transl_table', '11'), 

         ('product', '"hypothetical protein"'), 

         ('protein_id', '"NP_963295.1"'), 

         ('db_xref', '"GI:41614797"'), 

         ('db_xref', '"GeneID:2732620"'), 

         ('translation', '"MRLLLELKALNSIDKKQLSNYLIQGFIYNILKNTEYSWLHNWKK\nEKYFNFT..."')] 

 

        In the above example, the "note" and "translation" were edited for compactness, 

        and they would contain multiple new line characters (displayed above as \n) 

 

        If a qualifier is quoted (in this case, everything except codon_start and 

        transl_table) then the quotes are NOT removed. 

 

        Note that no whitespace is removed. 

        """ 

        #Skip any blank lines 

        iterator = (x for x in lines if x) 

        try: 

            line = next(iterator) 

 

            feature_location = line.strip() 

            while feature_location[-1:] == ",": 

                #Multiline location, still more to come! 

                line = next(iterator) 

                feature_location += line.strip() 

 

            qualifiers = [] 

 

            for line_number, line in enumerate(iterator): 

                # check for extra wrapping of the location closing parentheses 

                if line_number == 0 and line.startswith(")"): 

                    feature_location += line.strip() 

                elif line[0] == "/": 

                    #New qualifier 

                    i = line.find("=") 

                    key = line[1:i]  # does not work if i==-1 

                    value = line[i + 1:]  # we ignore 'value' if i==-1 

                    if i == -1: 

                        #Qualifier with no key, e.g. /pseudo 

                        key = line[1:] 

                        qualifiers.append((key, None)) 

                    elif not value: 

                        #ApE can output /note= 

                        qualifiers.append((key, "")) 

                    elif value == '"': 

                        #One single quote 

                        if self.debug: 

                            print("Single quote %s:%s" % (key, value)) 

                        #DO NOT remove the quote... 

                        qualifiers.append((key, value)) 

                    elif value[0] == '"': 

                        #Quoted... 

                        value_list = [value] 

                        while value_list[-1][-1] != '"': 

                            value_list.append(next(iterator)) 

                        value = '\n'.join(value_list) 

                        #DO NOT remove the quotes... 

                        qualifiers.append((key, value)) 

                    else: 

                        #Unquoted 

                        #if debug : print("Unquoted line %s:%s" % (key,value)) 

                        qualifiers.append((key, value)) 

                else: 

                    #Unquoted continuation 

                    assert len(qualifiers) > 0 

                    assert key == qualifiers[-1][0] 

                    #if debug : print("Unquoted Cont %s:%s" % (key, line)) 

                    if qualifiers[-1][1] is None: 

                        raise StopIteration 

                    qualifiers[-1] = (key, qualifiers[-1][1] + "\n" + line) 

            return (feature_key, feature_location, qualifiers) 

        except StopIteration: 

            #Bummer 

            raise ValueError("Problem with '%s' feature:\n%s" 

                             % (feature_key, "\n".join(lines))) 

 

    def parse_footer(self): 

        """returns a tuple containing a list of any misc strings, and the sequence""" 

        #This is a basic bit of code to scan and discard the sequence, 

        #which was useful when developing the sub classes. 

        if self.line in self.FEATURE_END_MARKERS: 

            while self.line[:self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS: 

                self.line = self.handle.readline() 

                if not self.line: 

                    raise ValueError("Premature end of file") 

                self.line = self.line.rstrip() 

 

        assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \ 

            "Not at start of sequence" 

        while True: 

            line = self.handle.readline() 

            if not line: 

                raise ValueError("Premature end of line during sequence data") 

            line = line.rstrip() 

            if line == "//": 

                break 

        self.line = line 

        return ([], "")  # Dummy values! 

 

    def _feed_first_line(self, consumer, line): 

        """Handle the LOCUS/ID line, passing data to the comsumer 

 

        This should be implemented by the EMBL / GenBank specific subclass 

 

        Used by the parse_records() and parse() methods. 

        """ 

        pass 

 

    def _feed_header_lines(self, consumer, lines): 

        """Handle the header lines (list of strings), passing data to the comsumer 

 

        This should be implemented by the EMBL / GenBank specific subclass 

 

        Used by the parse_records() and parse() methods. 

        """ 

        pass 

 

    def _feed_feature_table(self, consumer, feature_tuples): 

        """Handle the feature table (list of tuples), passing data to the comsumer 

 

        Used by the parse_records() and parse() methods. 

        """ 

        consumer.start_feature_table() 

        for feature_key, location_string, qualifiers in feature_tuples: 

            consumer.feature_key(feature_key) 

            consumer.location(location_string) 

            for q_key, q_value in qualifiers: 

                if q_value is None: 

                    consumer.feature_qualifier(q_key, q_value) 

                else: 

                    consumer.feature_qualifier(q_key, q_value.replace("\n", " ")) 

 

    def _feed_misc_lines(self, consumer, lines): 

        """Handle any lines between features and sequence (list of strings), passing data to the consumer 

 

        This should be implemented by the EMBL / GenBank specific subclass 

 

        Used by the parse_records() and parse() methods. 

        """ 

        pass 

 

    def feed(self, handle, consumer, do_features=True): 

        """Feed a set of data into the consumer. 

 

        This method is intended for use with the "old" code in Bio.GenBank 

 

        Arguments: 

        handle - A handle with the information to parse. 

        consumer - The consumer that should be informed of events. 

        do_features - Boolean, should the features be parsed? 

                      Skipping the features can be much faster. 

 

        Return values: 

        true  - Passed a record 

        false - Did not find a record 

        """ 

        #Should work with both EMBL and GenBank files provided the 

        #equivalent Bio.GenBank._FeatureConsumer methods are called... 

        self.set_handle(handle) 

        if not self.find_start(): 

            #Could not find (another) record 

            consumer.data = None 

            return False 

 

        #We use the above class methods to parse the file into a simplified format. 

        #The first line, header lines and any misc lines after the features will be 

        #dealt with by GenBank / EMBL specific derived classes. 

 

        #First line and header: 

        self._feed_first_line(consumer, self.line) 

        self._feed_header_lines(consumer, self.parse_header()) 

 

        #Features (common to both EMBL and GenBank): 

        if do_features: 

            self._feed_feature_table(consumer, self.parse_features(skip=False)) 

        else: 

            self.parse_features(skip=True)  # ignore the data 

 

        #Footer and sequence 

        misc_lines, sequence_string = self.parse_footer() 

        self._feed_misc_lines(consumer, misc_lines) 

 

        consumer.sequence(sequence_string) 

        #Calls to consumer.base_number() do nothing anyway 

        consumer.record_end("//") 

 

        assert self.line == "//" 

 

        #And we are done 

        return True 

 

    def parse(self, handle, do_features=True): 

        """Returns a SeqRecord (with SeqFeatures if do_features=True) 

 

        See also the method parse_records() for use on multi-record files. 

        """ 

        from Bio.GenBank import _FeatureConsumer 

        from Bio.GenBank.utils import FeatureValueCleaner 

 

        consumer = _FeatureConsumer(use_fuzziness=1, 

                                    feature_cleaner=FeatureValueCleaner()) 

 

        if self.feed(handle, consumer, do_features): 

            return consumer.data 

        else: 

            return None 

 

    def parse_records(self, handle, do_features=True): 

        """Returns a SeqRecord object iterator 

 

        Each record (from the ID/LOCUS line to the // line) becomes a SeqRecord 

 

        The SeqRecord objects include SeqFeatures if do_features=True 

 

        This method is intended for use in Bio.SeqIO 

        """ 

        #This is a generator function 

        while True: 

            record = self.parse(handle, do_features) 

            if record is None: 

                break 

            if record.id is None: 

                raise ValueError("Failed to parse the record's ID. Invalid ID line?") 

            if record.name == "<unknown name>": 

                raise ValueError("Failed to parse the record's name. Invalid ID line?") 

            if record.description == "<unknown description>": 

                raise ValueError("Failed to parse the record's description") 

            yield record 

 

    def parse_cds_features(self, handle, 

                           alphabet=generic_protein, 

                           tags2id=('protein_id', 'locus_tag', 'product')): 

        """Returns SeqRecord object iterator 

 

        Each CDS feature becomes a SeqRecord. 

 

        alphabet - Used for any sequence found in a translation field. 

        tags2id  - Tupple of three strings, the feature keys to use 

                   for the record id, name and description, 

 

        This method is intended for use in Bio.SeqIO 

        """ 

        self.set_handle(handle) 

        while self.find_start(): 

            #Got an EMBL or GenBank record... 

            self.parse_header()  # ignore header lines! 

            feature_tuples = self.parse_features() 

            #self.parse_footer() # ignore footer lines! 

            while True: 

                line = self.handle.readline() 

                if not line: 

                    break 

                if line[:2] == "//": 

                    break 

            self.line = line.rstrip() 

 

            #Now go though those features... 

            for key, location_string, qualifiers in feature_tuples: 

                if key == "CDS": 

                    #Create SeqRecord 

                    #================ 

                    #SeqRecord objects cannot be created with annotations, they 

                    #must be added afterwards.  So create an empty record and 

                    #then populate it: 

                    record = SeqRecord(seq=None) 

                    annotations = record.annotations 

 

                    #Should we add a location object to the annotations? 

                    #I *think* that only makes sense for SeqFeatures with their 

                    #sub features... 

                    annotations['raw_location'] = location_string.replace(' ', '') 

 

                    for (qualifier_name, qualifier_data) in qualifiers: 

                        if qualifier_data is not None \ 

                                and qualifier_data[0] == '"' and qualifier_data[-1] == '"': 

                            #Remove quotes 

                            qualifier_data = qualifier_data[1:-1] 

                        #Append the data to the annotation qualifier... 

                        if qualifier_name == "translation": 

                            assert record.seq is None, "Multiple translations!" 

                            record.seq = Seq(qualifier_data.replace("\n", ""), alphabet) 

                        elif qualifier_name == "db_xref": 

                            #its a list, possibly empty.  Its safe to extend 

                            record.dbxrefs.append(qualifier_data) 

                        else: 

                            if qualifier_data is not None: 

                                qualifier_data = qualifier_data.replace("\n", " ").replace("  ", " ") 

                            try: 

                                annotations[qualifier_name] += " " + qualifier_data 

                            except KeyError: 

                                #Not an addition to existing data, its the first bit 

                                annotations[qualifier_name] = qualifier_data 

 

                    #Fill in the ID, Name, Description 

                    #================================= 

                    try: 

                        record.id = annotations[tags2id[0]] 

                    except KeyError: 

                        pass 

                    try: 

                        record.name = annotations[tags2id[1]] 

                    except KeyError: 

                        pass 

                    try: 

                        record.description = annotations[tags2id[2]] 

                    except KeyError: 

                        pass 

 

                    yield record 

 

 

class EmblScanner(InsdcScanner): 

    """For extracting chunks of information in EMBL files""" 

 

    RECORD_START = "ID   " 

    HEADER_WIDTH = 5 

    FEATURE_START_MARKERS = ["FH   Key             Location/Qualifiers", "FH"] 

    FEATURE_END_MARKERS = ["XX"]  # XX can also mark the end of many things! 

    FEATURE_QUALIFIER_INDENT = 21 

    FEATURE_QUALIFIER_SPACER = "FT" + " " * (FEATURE_QUALIFIER_INDENT - 2) 

    SEQUENCE_HEADERS = ["SQ", "CO"]  # Remove trailing spaces 

 

    def parse_footer(self): 

        """returns a tuple containing a list of any misc strings, and the sequence""" 

        assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \ 

            "Eh? '%s'" % self.line 

 

        #Note that the SQ line can be split into several lines... 

        misc_lines = [] 

        while self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS: 

            misc_lines.append(self.line) 

            self.line = self.handle.readline() 

            if not self.line: 

                raise ValueError("Premature end of file") 

            self.line = self.line.rstrip() 

 

        assert self.line[:self.HEADER_WIDTH] == " " * self.HEADER_WIDTH \ 

            or self.line.strip() == '//', repr(self.line) 

 

        seq_lines = [] 

        line = self.line 

        while True: 

            if not line: 

                raise ValueError("Premature end of file in sequence data") 

            line = line.strip() 

            if not line: 

                raise ValueError("Blank line in sequence data") 

            if line == '//': 

                break 

            assert self.line[:self.HEADER_WIDTH] == " " * self.HEADER_WIDTH, \ 

                repr(self.line) 

            #Remove tailing number now, remove spaces later 

            seq_lines.append(line.rsplit(None, 1)[0]) 

            line = self.handle.readline() 

        self.line = line 

        return (misc_lines, "".join(seq_lines).replace(" ", "")) 

 

    def _feed_first_line(self, consumer, line): 

        assert line[:self.HEADER_WIDTH].rstrip() == "ID" 

        if line[self.HEADER_WIDTH:].count(";") == 6: 

            #Looks like the semi colon separated style introduced in 2006 

            self._feed_first_line_new(consumer, line) 

        elif line[self.HEADER_WIDTH:].count(";") == 3: 

            if line.rstrip().endswith(" SQ"): 

                #EMBL-bank patent data 

                self._feed_first_line_patents(consumer,line) 

            else: 

                #Looks like the pre 2006 style 

                self._feed_first_line_old(consumer, line) 

        else: 

            raise ValueError('Did not recognise the ID line layout:\n' + line) 

 

    def _feed_first_line_patents(self, consumer, line): 

        #Either Non-Redundant Level 1 database records, 

        #ID <accession>; <molecule type>; <non-redundant level 1>; <cluster size L1> 

        #e.g. ID   NRP_AX000635; PRT; NR1; 15 SQ 

        # 

        #Or, Non-Redundant Level 2 database records: 

        #ID <L2-accession>; <molecule type>; <non-redundant level 2>; <cluster size L2> 

        #e.g. ID   NRP0000016E; PRT; NR2; 5 SQ 

        fields = line[self.HEADER_WIDTH:].rstrip()[:-3].split(";") 

        assert len(fields) == 4 

        consumer.locus(fields[0]) 

        consumer.residue_type(fields[1]) 

        consumer.data_file_division(fields[2]) 

        #TODO - Record cluster size? 

 

    def _feed_first_line_old(self, consumer, line): 

        #Expects an ID line in the style before 2006, e.g. 

        #ID   SC10H5 standard; DNA; PRO; 4870 BP. 

        #ID   BSUB9999   standard; circular DNA; PRO; 4214630 BP. 

        assert line[:self.HEADER_WIDTH].rstrip() == "ID" 

        fields = [line[self.HEADER_WIDTH:].split(None, 1)[0]] 

        fields.extend(line[self.HEADER_WIDTH:].split(None, 1)[1].split(";")) 

        fields = [entry.strip() for entry in fields] 

        """ 

        The tokens represent: 

           0. Primary accession number 

           (space sep) 

           1. ??? (e.g. standard) 

           (semi-colon) 

           2. Topology and/or Molecule type (e.g. 'circular DNA' or 'DNA') 

           3. Taxonomic division (e.g. 'PRO') 

           4. Sequence length (e.g. '4639675 BP.') 

        """ 

        consumer.locus(fields[0])  # Should we also call the accession consumer? 

        consumer.residue_type(fields[2]) 

        consumer.data_file_division(fields[3]) 

        self._feed_seq_length(consumer, fields[4]) 

 

    def _feed_first_line_new(self, consumer, line): 

        #Expects an ID line in the style introduced in 2006, e.g. 

        #ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP. 

        #ID   CD789012; SV 4; linear; genomic DNA; HTG; MAM; 500 BP. 

        assert line[:self.HEADER_WIDTH].rstrip() == "ID" 

        fields = [data.strip() for data in line[self.HEADER_WIDTH:].strip().split(";")] 

        assert len(fields) == 7 

        """ 

        The tokens represent: 

           0. Primary accession number 

           1. Sequence version number 

           2. Topology: 'circular' or 'linear' 

           3. Molecule type (e.g. 'genomic DNA') 

           4. Data class (e.g. 'STD') 

           5. Taxonomic division (e.g. 'PRO') 

           6. Sequence length (e.g. '4639675 BP.') 

        """ 

 

        consumer.locus(fields[0]) 

 

        #Call the accession consumer now, to make sure we record 

        #something as the record.id, in case there is no AC line 

        consumer.accession(fields[0]) 

 

        #TODO - How to deal with the version field?  At the moment the consumer 

        #will try and use this for the ID which isn't ideal for EMBL files. 

        version_parts = fields[1].split() 

        if len(version_parts) == 2 \ 

            and version_parts[0] == "SV" \ 

                and version_parts[1].isdigit(): 

            consumer.version_suffix(version_parts[1]) 

 

        #Based on how the old GenBank parser worked, merge these two: 

        consumer.residue_type(" ".join(fields[2:4]))  # TODO - Store as two fields? 

 

        #consumer.xxx(fields[4]) #TODO - What should we do with the data class? 

 

        consumer.data_file_division(fields[5]) 

 

        self._feed_seq_length(consumer, fields[6]) 

 

    def _feed_seq_length(self, consumer, text): 

        length_parts = text.split() 

        assert len(length_parts) == 2, "Invalid sequence length string %r" % text 

        assert length_parts[1].upper() in ["BP", "BP.", "AA", "AA."] 

        consumer.size(length_parts[0]) 

 

    def _feed_header_lines(self, consumer, lines): 

        EMBL_INDENT = self.HEADER_WIDTH 

        EMBL_SPACER = " " * EMBL_INDENT 

        consumer_dict = { 

            'AC': 'accession', 

            'SV': 'version',  # SV line removed in June 2006, now part of ID line 

            'DE': 'definition', 

            #'RN' : 'reference_num', 

            #'RC' : reference comment... TODO 

            #'RP' : 'reference_bases', 

            #'RX' : reference cross reference... DOI or Pubmed 

            'RG': 'consrtm',  # optional consortium 

            #'RA' : 'authors', 

            #'RT' : 'title', 

            'RL': 'journal', 

            'OS': 'organism', 

            'OC': 'taxonomy', 

            #'DR' : data reference 

            'CC': 'comment', 

            #'XX' : splitter 

        } 

        #We have to handle the following specially: 

        #RX (depending on reference type...) 

        for line in lines: 

            line_type = line[:EMBL_INDENT].strip() 

            data = line[EMBL_INDENT:].strip() 

            if line_type == 'XX': 

                pass 

            elif line_type == 'RN': 

                # Reformat reference numbers for the GenBank based consumer 

                # e.g. '[1]' becomes '1' 

                if data[0] == "[" and data[-1] == "]": 

                    data = data[1:-1] 

                consumer.reference_num(data) 

            elif line_type == 'RP': 

                # Reformat reference numbers for the GenBank based consumer 

                # e.g. '1-4639675' becomes '(bases 1 to 4639675)' 

                # and '160-550, 904-1055' becomes '(bases 160 to 550; 904 to 1055)' 

                # Note could be multi-line, and end with a comma 

                parts = [bases.replace("-", " to ").strip() for bases in data.split(",") if bases.strip()] 

                consumer.reference_bases("(bases %s)" % "; ".join(parts)) 

            elif line_type == 'RT': 

                #Remove the enclosing quotes and trailing semi colon. 

                #Note the title can be split over multiple lines. 

                if data.startswith('"'): 

                    data = data[1:] 

                if data.endswith('";'): 

                    data = data[:-2] 

                consumer.title(data) 

            elif line_type == 'RX': 

                # EMBL support three reference types at the moment: 

                # - PUBMED    PUBMED bibliographic database (NLM) 

                # - DOI       Digital Object Identifier (International DOI Foundation) 

                # - AGRICOLA  US National Agriculture Library (NAL) of the US Department 

                #             of Agriculture (USDA) 

                # 

                # Format: 

                # RX  resource_identifier; identifier. 

                # 

                # e.g. 

                # RX   DOI; 10.1016/0024-3205(83)90010-3. 

                # RX   PUBMED; 264242. 

                # 

                # Currently our reference object only supports PUBMED and MEDLINE 

                # (as these were in GenBank files?). 

                key, value = data.split(";", 1) 

                if value.endswith("."): 

                    value = value[:-1] 

                value = value.strip() 

                if key == "PUBMED": 

                    consumer.pubmed_id(value) 

                #TODO - Handle other reference types (here and in BioSQL bindings) 

            elif line_type == 'CC': 

                # Have to pass a list of strings for this one (not just a string) 

                consumer.comment([data]) 

            elif line_type == 'DR': 

                # Database Cross-reference, format: 

                # DR   database_identifier; primary_identifier; secondary_identifier. 

                # 

                # e.g. 

                # DR   MGI; 98599; Tcrb-V4. 

                # 

                # TODO - How should we store any secondary identifier? 

                parts = data.rstrip(".").split(";") 

                #Turn it into "database_identifier:primary_identifier" to 

                #mimic the GenBank parser. e.g. "MGI:98599" 

                consumer.dblink("%s:%s" % (parts[0].strip(), 

                                           parts[1].strip())) 

            elif line_type == 'RA': 

                # Remove trailing ; at end of authors list 

                consumer.authors(data.rstrip(";")) 

            elif line_type == 'PR': 

                # Remove trailing ; at end of the project reference 

                # In GenBank files this corresponds to the old PROJECT 

                # line which is being replaced with the DBLINK line. 

                consumer.project(data.rstrip(";")) 

            elif line_type == 'KW': 

                consumer.keywords(data.rstrip(";")) 

            elif line_type in consumer_dict: 

                #Its a semi-automatic entry! 

                getattr(consumer, consumer_dict[line_type])(data) 

            else: 

                if self.debug: 

                    print("Ignoring EMBL header line:\n%s" % line) 

 

    def _feed_misc_lines(self, consumer, lines): 

        #TODO - Should we do something with the information on the SQ line(s)? 

        lines.append("") 

        line_iter = iter(lines) 

        try: 

            for line in line_iter: 

                if line.startswith("CO   "): 

                    line = line[5:].strip() 

                    contig_location = line 

                    while True: 

                        line = next(line_iter) 

                        if not line: 

                            break 

                        elif line.startswith("CO   "): 

                            #Don't need to preseve the whitespace here. 

                            contig_location += line[5:].strip() 

                        else: 

                            raise ValueError('Expected CO (contig) continuation line, got:\n' + line) 

                    consumer.contig_location(contig_location) 

                if line.startswith("SQ   Sequence "): 

                    #e.g. 

                    #SQ   Sequence 219 BP; 82 A; 48 C; 33 G; 45 T; 11 other; 

                    # 

                    #Or, EMBL-bank patent, e.g. 

                    #SQ   Sequence 465 AA; 3963407aa91d3a0d622fec679a4524e0; MD5; 

                    self._feed_seq_length(consumer, line[14:].rstrip().rstrip(";").split(";", 1)[0]) 

                    #TODO - Record the checksum etc? 

            return 

        except StopIteration: 

            raise ValueError("Problem in misc lines before sequence") 

 

 

class _ImgtScanner(EmblScanner): 

    """For extracting chunks of information in IMGT (EMBL like) files (PRIVATE). 

 

    IMGT files are like EMBL files but in order to allow longer feature types 

    the features should be indented by 25 characters not 21 characters. In 

    practice the IMGT flat files tend to use either 21 or 25 characters, so we 

    must cope with both. 

 

    This is private to encourage use of Bio.SeqIO rather than Bio.GenBank. 

    """ 

 

    FEATURE_START_MARKERS = ["FH   Key             Location/Qualifiers", 

                             "FH   Key             Location/Qualifiers (from EMBL)", 

                             "FH   Key                 Location/Qualifiers", 

                             "FH"] 

 

    def parse_features(self, skip=False): 

        """Return list of tuples for the features (if present) 

 

        Each feature is returned as a tuple (key, location, qualifiers) 

        where key and location are strings (e.g. "CDS" and 

        "complement(join(490883..490885,1..879))") while qualifiers 

        is a list of two string tuples (feature qualifier keys and values). 

 

        Assumes you have already read to the start of the features table. 

        """ 

        if self.line.rstrip() not in self.FEATURE_START_MARKERS: 

            if self.debug: 

                print("Didn't find any feature table") 

            return [] 

 

        while self.line.rstrip() in self.FEATURE_START_MARKERS: 

            self.line = self.handle.readline() 

 

        bad_position_re = re.compile(r'([0-9]+)>{1}') 

 

        features = [] 

        line = self.line 

        while True: 

            if not line: 

                raise ValueError("Premature end of line during features table") 

            if line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS: 

                if self.debug: 

                    print("Found start of sequence") 

                break 

            line = line.rstrip() 

            if line == "//": 

                raise ValueError("Premature end of features table, marker '//' found") 

            if line in self.FEATURE_END_MARKERS: 

                if self.debug: 

                    print("Found end of features") 

                line = self.handle.readline() 

                break 

            if line[2:self.FEATURE_QUALIFIER_INDENT].strip() == "": 

                #This is an empty feature line between qualifiers. Empty 

                #feature lines within qualifiers are handled below (ignored). 

                line = self.handle.readline() 

                continue 

 

            if skip: 

                line = self.handle.readline() 

                while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER: 

                    line = self.handle.readline() 

            else: 

                assert line[:2] == "FT" 

                try: 

                    feature_key, location_start = line[2:].strip().split() 

                except ValueError: 

                    #e.g. "FT   TRANSMEMBRANE-REGION2163..2240\n" 

                    #Assume indent of 25 as per IMGT spec, with the location 

                    #start in column 26 (one-based). 

                    feature_key = line[2:25].strip() 

                    location_start = line[25:].strip() 

                feature_lines = [location_start] 

                line = self.handle.readline() 

                while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER \ 

                        or line.rstrip() == "":  # cope with blank lines in the midst of a feature 

                    #Use strip to remove any harmless trailing white space AND and leading 

                    #white space (copes with 21 or 26 indents and orther variants) 

                    assert line[:2] == "FT" 

                    feature_lines.append(line[self.FEATURE_QUALIFIER_INDENT:].strip()) 

                    line = self.handle.readline() 

                feature_key, location, qualifiers = \ 

                    self.parse_feature(feature_key, feature_lines) 

                #Try to handle known problems with IMGT locations here: 

                if ">" in location: 

                    #Nasty hack for common IMGT bug, should be >123 not 123> 

                    #in a location string. At least here the meaning is clear, 

                    #and since it is so common I don't want to issue a warning 

                    #warnings.warn("Feature location %s is invalid, " 

                    #              "moving greater than sign before position" 

                    #              % location, BiopythonParserWarning) 

                    location = bad_position_re.sub(r'>\1', location) 

                features.append((feature_key, location, qualifiers)) 

        self.line = line 

        return features 

 

 

class GenBankScanner(InsdcScanner): 

    """For extracting chunks of information in GenBank files""" 

 

    RECORD_START = "LOCUS       " 

    HEADER_WIDTH = 12 

    FEATURE_START_MARKERS = ["FEATURES             Location/Qualifiers", "FEATURES"] 

    FEATURE_END_MARKERS = [] 

    FEATURE_QUALIFIER_INDENT = 21 

    FEATURE_QUALIFIER_SPACER = " " * FEATURE_QUALIFIER_INDENT 

    SEQUENCE_HEADERS = ["CONTIG", "ORIGIN", "BASE COUNT", "WGS"]  # trailing spaces removed 

 

    def parse_footer(self): 

        """returns a tuple containing a list of any misc strings, and the sequence""" 

        assert self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS, \ 

            "Eh? '%s'" % self.line 

 

        misc_lines = [] 

        while self.line[:self.HEADER_WIDTH].rstrip() in self.SEQUENCE_HEADERS \ 

            or self.line[:self.HEADER_WIDTH] == " " * self.HEADER_WIDTH \ 

                or "WGS" == self.line[:3]: 

            misc_lines.append(self.line.rstrip()) 

            self.line = self.handle.readline() 

            if not self.line: 

                raise ValueError("Premature end of file") 

            self.line = self.line 

 

        assert self.line[:self.HEADER_WIDTH].rstrip() not in self.SEQUENCE_HEADERS, \ 

            "Eh? '%s'" % self.line 

 

        #Now just consume the sequence lines until reach the // marker 

        #or a CONTIG line 

        seq_lines = [] 

        line = self.line 

        while True: 

            if not line: 

                warnings.warn("Premature end of file in sequence data", 

                              BiopythonParserWarning) 

                line = '//' 

                break 

            line = line.rstrip() 

            if not line: 

                warnings.warn("Blank line in sequence data", 

                              BiopythonParserWarning) 

                line = self.handle.readline() 

                continue 

            if line == '//': 

                break 

            if line.startswith('CONTIG'): 

                break 

            if len(line) > 9 and line[9:10] != ' ': 

                # Some broken programs indent the sequence by one space too many 

                # so try to get rid of that and test again. 

                warnings.warn("Invalid indentation for sequence line", 

                              BiopythonParserWarning) 

                line = line[1:] 

                if len(line) > 9 and line[9:10] != ' ': 

                    raise ValueError("Sequence line mal-formed, '%s'" % line) 

            seq_lines.append(line[10:])  # remove spaces later 

            line = self.handle.readline() 

 

        self.line = line 

        #Seq("".join(seq_lines), self.alphabet) 

        return (misc_lines, "".join(seq_lines).replace(" ", "")) 

 

    def _feed_first_line(self, consumer, line): 

        """Scan over and parse GenBank LOCUS line (PRIVATE). 

 

        This must cope with several variants, primarily the old and new column 

        based standards from GenBank. Additionally EnsEMBL produces GenBank 

        files where the LOCUS line is space separated rather that following 

        the column based layout. 

 

        We also try to cope with GenBank like files with partial LOCUS lines. 

        """ 

        ##################################### 

        # LOCUS line                        # 

        ##################################### 

        GENBANK_INDENT = self.HEADER_WIDTH 

        GENBANK_SPACER = " " * GENBANK_INDENT 

        assert line[0:GENBANK_INDENT] == 'LOCUS       ', \ 

            'LOCUS line does not start correctly:\n' + line 

 

        #Have to break up the locus line, and handle the different bits of it. 

        #There are at least two different versions of the locus line... 

        if line[29:33] in [' bp ', ' aa ', ' rc '] and line[55:62] == '       ': 

            #Old... note we insist on the 55:62 being empty to avoid trying 

            #to parse space separated LOCUS lines from Ensembl etc, see below. 

            # 

            #    Positions  Contents 

            #    ---------  -------- 

            #    00:06      LOCUS 

            #    06:12      spaces 

            #    12:??      Locus name 

            #    ??:??      space 

            #    ??:29      Length of sequence, right-justified 

            #    29:33      space, bp, space 

            #    33:41      strand type 

            #    41:42      space 

            #    42:51      Blank (implies linear), linear or circular 

            #    51:52      space 

            #    52:55      The division code (e.g. BCT, VRL, INV) 

            #    55:62      space 

            #    62:73      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991) 

            # 

            #assert line[29:33] in [' bp ', ' aa ',' rc '] , \ 

            #       'LOCUS line does not contain size units at expected position:\n' + line 

            assert line[41:42] == ' ', \ 

                'LOCUS line does not contain space at position 42:\n' + line 

            assert line[42:51].strip() in ['', 'linear', 'circular'], \ 

                'LOCUS line does not contain valid entry (linear, circular, ...):\n' + line 

            assert line[51:52] == ' ', \ 

                'LOCUS line does not contain space at position 52:\n' + line 

            #assert line[55:62] == '       ', \ 

            #      'LOCUS line does not contain spaces from position 56 to 62:\n' + line 

            if line[62:73].strip(): 

                assert line[64:65] == '-', \ 

                    'LOCUS line does not contain - at position 65 in date:\n' + line 

                assert line[68:69] == '-', \ 

                    'LOCUS line does not contain - at position 69 in date:\n' + line 

 

            name_and_length_str = line[GENBANK_INDENT:29] 

            while '  ' in name_and_length_str: 

                name_and_length_str = name_and_length_str.replace('  ', ' ') 

            name_and_length = name_and_length_str.split(' ') 

            assert len(name_and_length) <= 2, \ 

                'Cannot parse the name and length in the LOCUS line:\n' + line 

            assert len(name_and_length) != 1, \ 

                'Name and length collide in the LOCUS line:\n' + line 

                   #Should be possible to split them based on position, if 

                   #a clear definition of the standard exists THAT AGREES with 

                   #existing files. 

            consumer.locus(name_and_length[0]) 

            consumer.size(name_and_length[1]) 

            #consumer.residue_type(line[33:41].strip()) 

 

            if line[33:51].strip() == "" and line[29:33] == ' aa ': 

                #Amino acids -> protein (even if there is no residue type given) 

                #We want to use a protein alphabet in this case, rather than a 

                #generic one. Not sure if this is the best way to achieve this, 

                #but it works because the scanner checks for this: 

                consumer.residue_type("PROTEIN") 

            else: 

                consumer.residue_type(line[33:51].strip()) 

 

            consumer.data_file_division(line[52:55]) 

            if line[62:73].strip(): 

                consumer.date(line[62:73]) 

        elif line[40:44] in [' bp ', ' aa ', ' rc '] \ 

                and line[54:64].strip() in ['', 'linear', 'circular']: 

            #New... linear/circular/big blank test should avoid EnsEMBL style 

            #LOCUS line being treated like a proper column based LOCUS line. 

            # 

            #    Positions  Contents 

            #    ---------  -------- 

            #    00:06      LOCUS 

            #    06:12      spaces 

            #    12:??      Locus name 

            #    ??:??      space 

            #    ??:40      Length of sequence, right-justified 

            #    40:44      space, bp, space 

            #    44:47      Blank, ss-, ds-, ms- 

            #    47:54      Blank, DNA, RNA, tRNA, mRNA, uRNA, snRNA, cDNA 

            #    54:55      space 

            #    55:63      Blank (implies linear), linear or circular 

            #    63:64      space 

            #    64:67      The division code (e.g. BCT, VRL, INV) 

            #    67:68      space 

            #    68:79      Date, in the form dd-MMM-yyyy (e.g., 15-MAR-1991) 

            # 

            assert line[40:44] in [' bp ', ' aa ', ' rc '], \ 

                'LOCUS line does not contain size units at expected position:\n' + line 

            assert line[44:47] in ['   ', 'ss-', 'ds-', 'ms-'], \ 

                'LOCUS line does not have valid strand type (Single stranded, ...):\n' + line 

            assert line[47:54].strip() == "" \ 

                or 'DNA' in line[47:54].strip().upper() \ 

                or 'RNA' in line[47:54].strip().upper(), \ 

                   'LOCUS line does not contain valid sequence type (DNA, RNA, ...):\n' + line 

            assert line[54:55] == ' ', \ 

                'LOCUS line does not contain space at position 55:\n' + line 

            assert line[55:63].strip() in ['', 'linear', 'circular'], \ 

                'LOCUS line does not contain valid entry (linear, circular, ...):\n' + line 

            assert line[63:64] == ' ', \ 

                'LOCUS line does not contain space at position 64:\n' + line 

            assert line[67:68] == ' ', \ 

                'LOCUS line does not contain space at position 68:\n' + line 

            if line[68:79].strip(): 

                assert line[70:71] == '-', \ 

                    'LOCUS line does not contain - at position 71 in date:\n' + line 

                assert line[74:75] == '-', \ 

                    'LOCUS line does not contain - at position 75 in date:\n' + line 

 

            name_and_length_str = line[GENBANK_INDENT:40] 

            while '  ' in name_and_length_str: 

                name_and_length_str = name_and_length_str.replace('  ', ' ') 

            name_and_length = name_and_length_str.split(' ') 

            assert len(name_and_length) <= 2, \ 

                'Cannot parse the name and length in the LOCUS line:\n' + line 

            assert len(name_and_length) != 1, \ 

                'Name and length collide in the LOCUS line:\n' + line 

                   #Should be possible to split them based on position, if 

                   #a clear definition of the stand exists THAT AGREES with 

                   #existing files. 

            consumer.locus(name_and_length[0]) 

            consumer.size(name_and_length[1]) 

 

            if line[44:54].strip() == "" and line[40:44] == ' aa ': 

                #Amino acids -> protein (even if there is no residue type given) 

                #We want to use a protein alphabet in this case, rather than a 

                #generic one. Not sure if this is the best way to achieve this, 

                #but it works because the scanner checks for this: 

                consumer.residue_type(("PROTEIN " + line[54:63]).strip()) 

            else: 

                consumer.residue_type(line[44:63].strip()) 

 

            consumer.data_file_division(line[64:67]) 

            if line[68:79].strip(): 

                consumer.date(line[68:79]) 

        elif line[GENBANK_INDENT:].strip().count(" ") == 0: 

            #Truncated LOCUS line, as produced by some EMBOSS tools - see bug 1762 

            # 

            #e.g. 

            # 

            #    "LOCUS       U00096" 

            # 

            #rather than: 

            # 

            #    "LOCUS       U00096               4639675 bp    DNA     circular BCT" 

            # 

            #    Positions  Contents 

            #    ---------  -------- 

            #    00:06      LOCUS 

            #    06:12      spaces 

            #    12:??      Locus name 

            if line[GENBANK_INDENT:].strip() != "": 

                consumer.locus(line[GENBANK_INDENT:].strip()) 

            else: 

                #Must just have just "LOCUS       ", is this even legitimate? 

                #We should be able to continue parsing... we need real world testcases! 

                warnings.warn("Minimal LOCUS line found - is this " 

                              "correct?\n:%r" % line, BiopythonParserWarning) 

        elif len(line.split()) == 8 and line.split()[3] in ("aa", "bp") and \ 

             line.split()[5] in ('linear', 'circular'): 

            # Cope with invalidly spaced GenBank LOCUS lines like 

            #LOCUS       AB070938          6497 bp    DNA     linear   BCT 11-OCT-2001 

            splitline = line.split() 

            consumer.locus(splitline[1]) 

            consumer.size(splitline[2]) 

            consumer.residue_type(splitline[4]) 

            consumer.data_file_division(splitline[6]) 

            consumer.date(splitline[7]) 

            warnings.warn("Attempting to parse malformed locus line:\n%r\n" 

                          "Found locus %r size %r residue_type %r\n" 

                          "Some fields may be wrong." % (line, splitline[1], 

                          splitline[2], splitline[4]), BiopythonParserWarning) 

        elif len(line.split()) == 7 and line.split()[3] in ["aa", "bp"]: 

            #Cope with EnsEMBL genbank files which use space separation rather 

            #than the expected column based layout. e.g. 

            #LOCUS       HG531_PATCH 1000000 bp DNA HTG 18-JUN-2011 

            #LOCUS       HG531_PATCH 759984 bp DNA HTG 18-JUN-2011 

            #LOCUS       HG506_HG1000_1_PATCH 814959 bp DNA HTG 18-JUN-2011 

            #LOCUS       HG506_HG1000_1_PATCH 1219964 bp DNA HTG 18-JUN-2011 

            #Notice that the 'bp' can occur in the position expected by either 

            #the old or the new fixed column standards (parsed above). 

            splitline = line.split() 

            consumer.locus(splitline[1]) 

            consumer.size(splitline[2]) 

            consumer.residue_type(splitline[4]) 

            consumer.data_file_division(splitline[5]) 

            consumer.date(splitline[6]) 

        elif len(line.split()) >= 4 and line.split()[3] in ["aa", "bp"]: 

            #Cope with EMBOSS seqret output where it seems the locus id can cause 

            #the other fields to overflow.  We just IGNORE the other fields! 

            warnings.warn("Malformed LOCUS line found - is this " 

                          "correct?\n:%r" % line, BiopythonParserWarning) 

            consumer.locus(line.split()[1]) 

            consumer.size(line.split()[2]) 

        elif len(line.split()) >= 4 and line.split()[-1] in ["aa", "bp"]: 

            #Cope with pseudo-GenBank files like this: 

            #   "LOCUS       RNA5 complete       1718 bp" 

            #Treat everything between LOCUS and the size as the identifier. 

            warnings.warn("Malformed LOCUS line found - is this " 

                          "correct?\n:%r" % line, BiopythonParserWarning) 

            consumer.locus(line[5:].rsplit(None, 2)[0].strip()) 

            consumer.size(line.split()[-2]) 

        else: 

            raise ValueError('Did not recognise the LOCUS line layout:\n' + line) 

 

    def _feed_header_lines(self, consumer, lines): 

        #Following dictionary maps GenBank lines to the associated 

        #consumer methods - the special cases like LOCUS where one 

        #genbank line triggers several consumer calls have to be 

        #handled individually. 

        GENBANK_INDENT = self.HEADER_WIDTH 

        GENBANK_SPACER = " " * GENBANK_INDENT 

        consumer_dict = { 

            'DEFINITION': 'definition', 

            'ACCESSION': 'accession', 

            'NID': 'nid', 

            'PID': 'pid', 

            'DBSOURCE': 'db_source', 

            'KEYWORDS': 'keywords', 

            'SEGMENT': 'segment', 

            'SOURCE': 'source', 

            'AUTHORS': 'authors', 

            'CONSRTM': 'consrtm', 

            'PROJECT': 'project', 

            'DBLINK': 'dblink', 

            'TITLE': 'title', 

            'JOURNAL': 'journal', 

            'MEDLINE': 'medline_id', 

            'PUBMED': 'pubmed_id', 

            'REMARK': 'remark'} 

        #We have to handle the following specially: 

        #ORIGIN (locus, size, residue_type, data_file_division and date) 

        #COMMENT (comment) 

        #VERSION (version and gi) 

        #REFERENCE (eference_num and reference_bases) 

        #ORGANISM (organism and taxonomy) 

        lines = [_f for _f in lines if _f] 

        lines.append("")  # helps avoid getting StopIteration all the time 

        line_iter = iter(lines) 

        try: 

            line = next(line_iter) 

            while True: 

                if not line: 

                    break 

                line_type = line[:GENBANK_INDENT].strip() 

                data = line[GENBANK_INDENT:].strip() 

 

                if line_type == 'VERSION': 

                    #Need to call consumer.version(), and maybe also consumer.gi() as well. 

                    #e.g. 

                    # VERSION     AC007323.5  GI:6587720 

                    while '  ' in data: 

                        data = data.replace('  ', ' ') 

                    if ' GI:' not in data: 

                        consumer.version(data) 

                    else: 

                        if self.debug: 

                            print("Version [" + data.split(' GI:')[0] + "], gi [" + data.split(' GI:')[1] + "]") 

                        consumer.version(data.split(' GI:')[0]) 

                        consumer.gi(data.split(' GI:')[1]) 

                    #Read in the next line! 

                    line = next(line_iter) 

                elif line_type == 'REFERENCE': 

                    if self.debug > 1: 

                        print("Found reference [" + data + "]") 

                    #Need to call consumer.reference_num() and consumer.reference_bases() 

                    #e.g. 

                    # REFERENCE   1  (bases 1 to 86436) 

                    # 

                    #Note that this can be multiline, see Bug 1968, e.g. 

                    # 

                    # REFERENCE   42 (bases 1517 to 1696; 3932 to 4112; 17880 to 17975; 21142 to 

                    #             28259) 

                    # 

                    #For such cases we will call the consumer once only. 

                    data = data.strip() 

 

                    #Read in the next line, and see if its more of the reference: 

                    while True: 

                        line = next(line_iter) 

                        if line[:GENBANK_INDENT] == GENBANK_SPACER: 

                            #Add this continuation to the data string 

                            data += " " + line[GENBANK_INDENT:] 

                            if self.debug > 1: 

                                print("Extended reference text [" + data + "]") 

                        else: 

                            #End of the reference, leave this text in the variable "line" 

                            break 

 

                    #We now have all the reference line(s) stored in a string, data, 

                    #which we pass to the consumer 

                    while '  ' in data: 

                        data = data.replace('  ', ' ') 

                    if ' ' not in data: 

                        if self.debug > 2: 

                            print('Reference number \"' + data + '\"') 

                        consumer.reference_num(data) 

                    else: 

                        if self.debug > 2: 

                            print('Reference number \"' + data[:data.find(' ')] + '\", \"' + data[data.find(' ') + 1:] + '\"') 

                        consumer.reference_num(data[:data.find(' ')]) 

                        consumer.reference_bases(data[data.find(' ') + 1:]) 

                elif line_type == 'ORGANISM': 

                    #Typically the first line is the organism, and subsequent lines 

                    #are the taxonomy lineage.  However, given longer and longer 

                    #species names (as more and more strains and sub strains get 

                    #sequenced) the oragnism name can now get wrapped onto multiple 

                    #lines.  The NCBI say we have to recognise the lineage line by 

                    #the presence of semi-colon delimited entries.  In the long term, 

                    #they are considering adding a new keyword (e.g. LINEAGE). 

                    #See Bug 2591 for details. 

                    organism_data = data 

                    lineage_data = "" 

                    while True: 

                        line = next(line_iter) 

                        if line[0:GENBANK_INDENT] == GENBANK_SPACER: 

                            if lineage_data or ";" in line: 

                                lineage_data += " " + line[GENBANK_INDENT:] 

                            else: 

                                organism_data += " " + line[GENBANK_INDENT:].strip() 

                        else: 

                            #End of organism and taxonomy 

                            break 

                    consumer.organism(organism_data) 

                    if lineage_data.strip() == "" and self.debug > 1: 

                        print("Taxonomy line(s) missing or blank") 

                    consumer.taxonomy(lineage_data.strip()) 

                    del organism_data, lineage_data 

                elif line_type == 'COMMENT': 

                    if self.debug > 1: 

                        print("Found comment") 

                    #This can be multiline, and should call consumer.comment() once 

                    #with a list where each entry is a line. 

                    comment_list = [] 

                    comment_list.append(data) 

                    while True: 

                        line = next(line_iter) 

                        if line[0:GENBANK_INDENT] == GENBANK_SPACER: 

                            data = line[GENBANK_INDENT:] 

                            comment_list.append(data) 

                            if self.debug > 2: 

                                print("Comment continuation [" + data + "]") 

                        else: 

                            #End of the comment 

                            break 

                    consumer.comment(comment_list) 

                    del comment_list 

                elif line_type in consumer_dict: 

                    #Its a semi-automatic entry! 

                    #Now, this may be a multi line entry... 

                    while True: 

                        line = next(line_iter) 

                        if line[0:GENBANK_INDENT] == GENBANK_SPACER: 

                            data += ' ' + line[GENBANK_INDENT:] 

                        else: 

                            #We now have all the data for this entry: 

                            getattr(consumer, consumer_dict[line_type])(data) 

                            #End of continuation - return to top of loop! 

                            break 

                else: 

                    if self.debug: 

                        print("Ignoring GenBank header line:\n" % line) 

                    #Read in next line 

                    line = next(line_iter) 

        except StopIteration: 

            raise ValueError("Problem in header") 

 

    def _feed_misc_lines(self, consumer, lines): 

        #Deals with a few misc lines between the features and the sequence 

        GENBANK_INDENT = self.HEADER_WIDTH 

        GENBANK_SPACER = " " * GENBANK_INDENT 

        lines.append("") 

        line_iter = iter(lines) 

        try: 

            for line in line_iter: 

                if line.startswith('BASE COUNT'): 

                    line = line[10:].strip() 

                    if line: 

                        if self.debug: 

                            print("base_count = " + line) 

                        consumer.base_count(line) 

                if line.startswith('ORIGIN'): 

                    line = line[6:].strip() 

                    if line: 

                        if self.debug: 

                            print("origin_name = " + line) 

                        consumer.origin_name(line) 

                if line.startswith('WGS '): 

                    line = line[3:].strip() 

                    consumer.wgs(line) 

                if line.startswith('WGS_SCAFLD'): 

                    line = line[10:].strip() 

                    consumer.add_wgs_scafld(line) 

                if line.startswith('CONTIG'): 

                    line = line[6:].strip() 

                    contig_location = line 

                    while True: 

                        line = next(line_iter) 

                        if not line: 

                            break 

                        elif line[:GENBANK_INDENT] == GENBANK_SPACER: 

                            #Don't need to preseve the whitespace here. 

                            contig_location += line[GENBANK_INDENT:].rstrip() 

                        elif line.startswith('ORIGIN'): 

                            #Strange, seen this in GenPept files via Entrez gbwithparts 

                            line = line[6:].strip() 

                            if line: 

                                consumer.origin_name(line) 

                            break 

                        else: 

                            raise ValueError('Expected CONTIG continuation line, got:\n' + line) 

                    consumer.contig_location(contig_location) 

            return 

        except StopIteration: 

            raise ValueError("Problem in misc lines before sequence") 

 

if __name__ == "__main__": 

    from Bio._py3k import StringIO 

 

    gbk_example = \ 

        """LOCUS       SCU49845     5028 bp    DNA             PLN       21-JUN-1999 

DEFINITION  Saccharomyces cerevisiae TCP1-beta gene, partial cds, and Axl2p 

            (AXL2) and Rev7p (REV7) genes, complete cds. 

ACCESSION   U49845 

VERSION     U49845.1  GI:1293613 

KEYWORDS    . 

SOURCE      Saccharomyces cerevisiae (baker's yeast) 

  ORGANISM  Saccharomyces cerevisiae 

            Eukaryota; Fungi; Ascomycota; Saccharomycotina; Saccharomycetes; 

            Saccharomycetales; Saccharomycetaceae; Saccharomyces. 

REFERENCE   1  (bases 1 to 5028) 

  AUTHORS   Torpey,L.E., Gibbs,P.E., Nelson,J. and Lawrence,C.W. 

  TITLE     Cloning and sequence of REV7, a gene whose function is required for 

            DNA damage-induced mutagenesis in Saccharomyces cerevisiae 

  JOURNAL   Yeast 10 (11), 1503-1509 (1994) 

  PUBMED    7871890 

REFERENCE   2  (bases 1 to 5028) 

  AUTHORS   Roemer,T., Madden,K., Chang,J. and Snyder,M. 

  TITLE     Selection of axial growth sites in yeast requires Axl2p, a novel 

            plasma membrane glycoprotein 

  JOURNAL   Genes Dev. 10 (7), 777-793 (1996) 

  PUBMED    8846915 

REFERENCE   3  (bases 1 to 5028) 

  AUTHORS   Roemer,T. 

  TITLE     Direct Submission 

  JOURNAL   Submitted (22-FEB-1996) Terry Roemer, Biology, Yale University, New 

            Haven, CT, USA 

FEATURES             Location/Qualifiers 

     source          1..5028 

                     /organism="Saccharomyces cerevisiae" 

                     /db_xref="taxon:4932" 

                     /chromosome="IX" 

                     /map="9" 

     CDS             <1..206 

                     /codon_start=3 

                     /product="TCP1-beta" 

                     /protein_id="AAA98665.1" 

                     /db_xref="GI:1293614" 

                     /translation="SSIYNGISTSGLDLNNGTIADMRQLGIVESYKLKRAVVSSASEA 

                     AEVLLRVDNIIRARPRTANRQHM" 

     gene            687..3158 

                     /gene="AXL2" 

     CDS             687..3158 

                     /gene="AXL2" 

                     /note="plasma membrane glycoprotein" 

                     /codon_start=1 

                     /function="required for axial budding pattern of S. 

                     cerevisiae" 

                     /product="Axl2p" 

                     /protein_id="AAA98666.1" 

                     /db_xref="GI:1293615" 

                     /translation="MTQLQISLLLTATISLLHLVVATPYEAYPIGKQYPPVARVNESF 

                     TFQISNDTYKSSVDKTAQITYNCFDLPSWLSFDSSSRTFSGEPSSDLLSDANTTLYFN 

                     VILEGTDSADSTSLNNTYQFVVTNRPSISLSSDFNLLALLKNYGYTNGKNALKLDPNE 

                     VFNVTFDRSMFTNEESIVSYYGRSQLYNAPLPNWLFFDSGELKFTGTAPVINSAIAPE 

                     TSYSFVIIATDIEGFSAVEVEFELVIGAHQLTTSIQNSLIINVTDTGNVSYDLPLNYV 

                     YLDDDPISSDKLGSINLLDAPDWVALDNATISGSVPDELLGKNSNPANFSVSIYDTYG 

                     DVIYFNFEVVSTTDLFAISSLPNINATRGEWFSYYFLPSQFTDYVNTNVSLEFTNSSQ 

                     DHDWVKFQSSNLTLAGEVPKNFDKLSLGLKANQGSQSQELYFNIIGMDSKITHSNHSA 

                     NATSTRSSHHSTSTSSYTSSTYTAKISSTSAAATSSAPAALPAANKTSSHNKKAVAIA 

                     CGVAIPLGVILVALICFLIFWRRRRENPDDENLPHAISGPDLNNPANKPNQENATPLN 

                     NPFDDDASSYDDTSIARRLAALNTLKLDNHSATESDISSVDEKRDSLSGMNTYNDQFQ 

                     SQSKEELLAKPPVQPPESPFFDPQNRSSSVYMDSEPAVNKSWRYTGNLSPVSDIVRDS 

                     YGSQKTVDTEKLFDLEAPEKEKRTSRDVTMSSLDPWNSNISPSPVRKSVTPSPYNVTK 

                     HRNRHLQNIQDSQSGKNGITPTTMSTSSSDDFVPVKDGENFCWVHSMEPDRRPSKKRL 

                     VDFSNKSNVNVGQVKDIHGRIPEML" 

     gene            complement(3300..4037) 

                     /gene="REV7" 

     CDS             complement(3300..4037) 

                     /gene="REV7" 

                     /codon_start=1 

                     /product="Rev7p" 

                     /protein_id="AAA98667.1" 

                     /db_xref="GI:1293616" 

                     /translation="MNRWVEKWLRVYLKCYINLILFYRNVYPPQSFDYTTYQSFNLPQ 

                     FVPINRHPALIDYIEELILDVLSKLTHVYRFSICIINKKNDLCIEKYVLDFSELQHVD 

                     KDDQIITETEVFDEFRSSLNSLIMHLEKLPKVNDDTITFEAVINAIELELGHKLDRNR 

                     RVDSLEEKAEIERDSNWVKCQEDENLPDNNGFQPPKIKLTSLVGSDVGPLIIHQFSEK 

                     LISGDDKILNGVYSQYEEGESIFGSLF" 

ORIGIN       

        1 gatcctccat atacaacggt atctccacct caggtttaga tctcaacaac ggaaccattg 

       61 ccgacatgag acagttaggt atcgtcgaga gttacaagct aaaacgagca gtagtcagct 

      121 ctgcatctga agccgctgaa gttctactaa gggtggataa catcatccgt gcaagaccaa 

      181 gaaccgccaa tagacaacat atgtaacata tttaggatat acctcgaaaa taataaaccg 

      241 ccacactgtc attattataa ttagaaacag aacgcaaaaa ttatccacta tataattcaa 

      301 agacgcgaaa aaaaaagaac aacgcgtcat agaacttttg gcaattcgcg tcacaaataa 

      361 attttggcaa cttatgtttc ctcttcgagc agtactcgag ccctgtctca agaatgtaat 

      421 aatacccatc gtaggtatgg ttaaagatag catctccaca acctcaaagc tccttgccga 

      481 gagtcgccct cctttgtcga gtaattttca cttttcatat gagaacttat tttcttattc 

      541 tttactctca catcctgtag tgattgacac tgcaacagcc accatcacta gaagaacaga 

      601 acaattactt aatagaaaaa ttatatcttc ctcgaaacga tttcctgctt ccaacatcta 

      661 cgtatatcaa gaagcattca cttaccatga cacagcttca gatttcatta ttgctgacag 

      721 ctactatatc actactccat ctagtagtgg ccacgcccta tgaggcatat cctatcggaa 

      781 aacaataccc cccagtggca agagtcaatg aatcgtttac atttcaaatt tccaatgata 

      841 cctataaatc gtctgtagac aagacagctc aaataacata caattgcttc gacttaccga 

      901 gctggctttc gtttgactct agttctagaa cgttctcagg tgaaccttct tctgacttac 

      961 tatctgatgc gaacaccacg ttgtatttca atgtaatact cgagggtacg gactctgccg 

     1021 acagcacgtc tttgaacaat acataccaat ttgttgttac aaaccgtcca tccatctcgc 

     1081 tatcgtcaga tttcaatcta ttggcgttgt taaaaaacta tggttatact aacggcaaaa 

     1141 acgctctgaa actagatcct aatgaagtct tcaacgtgac ttttgaccgt tcaatgttca 

     1201 ctaacgaaga atccattgtg tcgtattacg gacgttctca gttgtataat gcgccgttac 

     1261 ccaattggct gttcttcgat tctggcgagt tgaagtttac tgggacggca ccggtgataa 

     1321 actcggcgat tgctccagaa acaagctaca gttttgtcat catcgctaca gacattgaag 

     1381 gattttctgc cgttgaggta gaattcgaat tagtcatcgg ggctcaccag ttaactacct 

     1441 ctattcaaaa tagtttgata atcaacgtta ctgacacagg taacgtttca tatgacttac 

     1501 ctctaaacta tgtttatctc gatgacgatc ctatttcttc tgataaattg ggttctataa 

     1561 acttattgga tgctccagac tgggtggcat tagataatgc taccatttcc gggtctgtcc 

     1621 cagatgaatt actcggtaag aactccaatc ctgccaattt ttctgtgtcc atttatgata 

     1681 cttatggtga tgtgatttat ttcaacttcg aagttgtctc cacaacggat ttgtttgcca 

     1741 ttagttctct tcccaatatt aacgctacaa ggggtgaatg gttctcctac tattttttgc 

     1801 cttctcagtt tacagactac gtgaatacaa acgtttcatt agagtttact aattcaagcc 

     1861 aagaccatga ctgggtgaaa ttccaatcat ctaatttaac attagctgga gaagtgccca 

     1921 agaatttcga caagctttca ttaggtttga aagcgaacca aggttcacaa tctcaagagc 

     1981 tatattttaa catcattggc atggattcaa agataactca ctcaaaccac agtgcgaatg 

     2041 caacgtccac aagaagttct caccactcca cctcaacaag ttcttacaca tcttctactt 

     2101 acactgcaaa aatttcttct acctccgctg ctgctacttc ttctgctcca gcagcgctgc 

     2161 cagcagccaa taaaacttca tctcacaata aaaaagcagt agcaattgcg tgcggtgttg 

     2221 ctatcccatt aggcgttatc ctagtagctc tcatttgctt cctaatattc tggagacgca 

     2281 gaagggaaaa tccagacgat gaaaacttac cgcatgctat tagtggacct gatttgaata 

     2341 atcctgcaaa taaaccaaat caagaaaacg ctacaccttt gaacaacccc tttgatgatg 

     2401 atgcttcctc gtacgatgat acttcaatag caagaagatt ggctgctttg aacactttga 

     2461 aattggataa ccactctgcc actgaatctg atatttccag cgtggatgaa aagagagatt 

     2521 ctctatcagg tatgaataca tacaatgatc agttccaatc ccaaagtaaa gaagaattat 

     2581 tagcaaaacc cccagtacag cctccagaga gcccgttctt tgacccacag aataggtctt 

     2641 cttctgtgta tatggatagt gaaccagcag taaataaatc ctggcgatat actggcaacc 

     2701 tgtcaccagt ctctgatatt gtcagagaca gttacggatc acaaaaaact gttgatacag 

     2761 aaaaactttt cgatttagaa gcaccagaga aggaaaaacg tacgtcaagg gatgtcacta 

     2821 tgtcttcact ggacccttgg aacagcaata ttagcccttc tcccgtaaga aaatcagtaa 

     2881 caccatcacc atataacgta acgaagcatc gtaaccgcca cttacaaaat attcaagact 

     2941 ctcaaagcgg taaaaacgga atcactccca caacaatgtc aacttcatct tctgacgatt 

     3001 ttgttccggt taaagatggt gaaaattttt gctgggtcca tagcatggaa ccagacagaa 

     3061 gaccaagtaa gaaaaggtta gtagattttt caaataagag taatgtcaat gttggtcaag 

     3121 ttaaggacat tcacggacgc atcccagaaa tgctgtgatt atacgcaacg atattttgct 

     3181 taattttatt ttcctgtttt attttttatt agtggtttac agatacccta tattttattt 

     3241 agtttttata cttagagaca tttaatttta attccattct tcaaatttca tttttgcact 

     3301 taaaacaaag atccaaaaat gctctcgccc tcttcatatt gagaatacac tccattcaaa 

     3361 attttgtcgt caccgctgat taatttttca ctaaactgat gaataatcaa aggccccacg 

     3421 tcagaaccga ctaaagaagt gagttttatt ttaggaggtt gaaaaccatt attgtctggt 

     3481 aaattttcat cttcttgaca tttaacccag tttgaatccc tttcaatttc tgctttttcc 

     3541 tccaaactat cgaccctcct gtttctgtcc aacttatgtc ctagttccaa ttcgatcgca 

     3601 ttaataactg cttcaaatgt tattgtgtca tcgttgactt taggtaattt ctccaaatgc 

     3661 ataatcaaac tatttaagga agatcggaat tcgtcgaaca cttcagtttc cgtaatgatc 

     3721 tgatcgtctt tatccacatg ttgtaattca ctaaaatcta aaacgtattt ttcaatgcat 

     3781 aaatcgttct ttttattaat aatgcagatg gaaaatctgt aaacgtgcgt taatttagaa 

     3841 agaacatcca gtataagttc ttctatatag tcaattaaag caggatgcct attaatggga 

     3901 acgaactgcg gcaagttgaa tgactggtaa gtagtgtagt cgaatgactg aggtgggtat 

     3961 acatttctat aaaataaaat caaattaatg tagcatttta agtataccct cagccacttc 

     4021 tctacccatc tattcataaa gctgacgcaa cgattactat tttttttttc ttcttggatc 

     4081 tcagtcgtcg caaaaacgta taccttcttt ttccgacctt ttttttagct ttctggaaaa 

     4141 gtttatatta gttaaacagg gtctagtctt agtgtgaaag ctagtggttt cgattgactg 

     4201 atattaagaa agtggaaatt aaattagtag tgtagacgta tatgcatatg tatttctcgc 

     4261 ctgtttatgt ttctacgtac ttttgattta tagcaagggg aaaagaaata catactattt 

     4321 tttggtaaag gtgaaagcat aatgtaaaag ctagaataaa atggacgaaa taaagagagg 

     4381 cttagttcat cttttttcca aaaagcaccc aatgataata actaaaatga aaaggatttg 

     4441 ccatctgtca gcaacatcag ttgtgtgagc aataataaaa tcatcacctc cgttgccttt 

     4501 agcgcgtttg tcgtttgtat cttccgtaat tttagtctta tcaatgggaa tcataaattt 

     4561 tccaatgaat tagcaatttc gtccaattct ttttgagctt cttcatattt gctttggaat 

     4621 tcttcgcact tcttttccca ttcatctctt tcttcttcca aagcaacgat ccttctaccc 

     4681 atttgctcag agttcaaatc ggcctctttc agtttatcca ttgcttcctt cagtttggct 

     4741 tcactgtctt ctagctgttg ttctagatcc tggtttttct tggtgtagtt ctcattatta 

     4801 gatctcaagt tattggagtc ttcagccaat tgctttgtat cagacaattg actctctaac 

     4861 ttctccactt cactgtcgag ttgctcgttt ttagcggaca aagatttaat ctcgttttct 

     4921 ttttcagtgt tagattgctc taattctttg agctgttctc tcagctcctc atatttttct 

     4981 tgccatgact cagattctaa ttttaagcta ttcaatttct ctttgatc 

//""" 

 

    # GenBank format protein (aka GenPept) file from: 

    # http://www.molecularevolution.org/resources/fileformats/ 

    gbk_example2 = \ 

        """LOCUS       AAD51968                 143 aa            linear   BCT 21-AUG-2001 

DEFINITION  transcriptional regulator RovA [Yersinia enterocolitica]. 

ACCESSION   AAD51968 

VERSION     AAD51968.1  GI:5805369 

DBSOURCE    locus AF171097 accession AF171097.1 

KEYWORDS    . 

SOURCE      Yersinia enterocolitica 

  ORGANISM  Yersinia enterocolitica 

            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; 

            Enterobacteriaceae; Yersinia. 

REFERENCE   1  (residues 1 to 143) 

  AUTHORS   Revell,P.A. and Miller,V.L. 

  TITLE     A chromosomally encoded regulator is required for expression of the 

            Yersinia enterocolitica inv gene and for virulence 

  JOURNAL   Mol. Microbiol. 35 (3), 677-685 (2000) 

  MEDLINE   20138369 

   PUBMED   10672189 

REFERENCE   2  (residues 1 to 143) 

  AUTHORS   Revell,P.A. and Miller,V.L. 

  TITLE     Direct Submission 

  JOURNAL   Submitted (22-JUL-1999) Molecular Microbiology, Washington 

            University School of Medicine, Campus Box 8230, 660 South Euclid, 

            St. Louis, MO 63110, USA 

COMMENT     Method: conceptual translation. 

FEATURES             Location/Qualifiers 

     source          1..143 

                     /organism="Yersinia enterocolitica" 

                     /mol_type="unassigned DNA" 

                     /strain="JB580v" 

                     /serotype="O:8" 

                     /db_xref="taxon:630" 

     Protein         1..143 

                     /product="transcriptional regulator RovA" 

                     /name="regulates inv expression" 

     CDS             1..143 

                     /gene="rovA" 

                     /coded_by="AF171097.1:380..811" 

                     /note="regulator of virulence" 

                     /transl_table=11 

ORIGIN 

        1 mestlgsdla rlvrvwrali dhrlkplelt qthwvtlhni nrlppeqsqi qlakaigieq 

       61 pslvrtldql eekglitrht candrrakri klteqsspii eqvdgvicst rkeilggisp 

      121 deiellsgli dklerniiql qsk 

// 

""" 

 

    embl_example = """ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP. 

XX 

AC   X56734; S46826; 

XX 

DT   12-SEP-1991 (Rel. 29, Created) 

DT   25-NOV-2005 (Rel. 85, Last updated, Version 11) 

XX 

DE   Trifolium repens mRNA for non-cyanogenic beta-glucosidase 

XX 

KW   beta-glucosidase. 

XX 

OS   Trifolium repens (white clover) 

OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; 

OC   Spermatophyta; Magnoliophyta; eudicotyledons; core eudicotyledons; rosids; 

OC   eurosids I; Fabales; Fabaceae; Papilionoideae; Trifolieae; Trifolium. 

XX 

RN   [5] 

RP   1-1859 

RX   PUBMED; 1907511. 

RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.; 

RT   "Nucleotide and derived amino acid sequence of the cyanogenic 

RT   beta-glucosidase (linamarase) from white clover (Trifolium repens L.)"; 

RL   Plant Mol. Biol. 17(2):209-219(1991). 

XX 

RN   [6] 

RP   1-1859 

RA   Hughes M.A.; 

RT   ; 

RL   Submitted (19-NOV-1990) to the EMBL/GenBank/DDBJ databases. 

RL   Hughes M.A., University of Newcastle Upon Tyne, Medical School, Newcastle 

RL   Upon Tyne, NE2 4HH, UK 

XX 

FH   Key             Location/Qualifiers 

FH 

FT   source          1..1859 

FT                   /organism="Trifolium repens" 

FT                   /mol_type="mRNA" 

FT                   /clone_lib="lambda gt10" 

FT                   /clone="TRE361" 

FT                   /tissue_type="leaves" 

FT                   /db_xref="taxon:3899" 

FT   CDS             14..1495 

FT                   /product="beta-glucosidase" 

FT                   /EC_number="3.2.1.21" 

FT                   /note="non-cyanogenic" 

FT                   /db_xref="GOA:P26204" 

FT                   /db_xref="InterPro:IPR001360" 

FT                   /db_xref="InterPro:IPR013781" 

FT                   /db_xref="UniProtKB/Swiss-Prot:P26204" 

FT                   /protein_id="CAA40058.1" 

FT                   /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRSSFPRGFI 

FT                   FGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITVDQYHRYKEDVGIMK 

FT                   DQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLINELLANGIQPFVTLFHWDLPQ 

FT                   VLEDEYGGFLNSGVINDFRDYTDLCFKEFGDRVRYWSTLNEPWVFSNSGYALGTNAPGR 

FT                   CSASNVAKPGDSGTGPYIVTHNQILAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLD 

FT                   DNSIPDIKAAERSLDFQFGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDF 

FT                   IGINYYSSSYISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQ 

FT                   EDFEIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYYIRSA 

FT                   IRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD" 

FT   mRNA            1..1859 

FT                   /experiment="experimental evidence, no additional details 

FT                   recorded" 

XX 

SQ   Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other; 

     aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt        60 

     cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag       120 

     tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga       180 

     aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata       240 

     tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta       300 

     caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc       360 

     ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa       420 

     atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct       480 

     ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg       540 

     tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt       600 

     gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg       660 

     aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac       720 

     aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta       780 

     taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg       840 

     gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga       900 

     cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg       960 

     gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg      1020 

     ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc      1080 

     acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa      1140 

     acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat      1200 

     gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct      1260 

     gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga      1320 

     agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg      1380 

     ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg      1440 

     taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga      1500 

     tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa      1560 

     ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt      1620 

     tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg      1680 

     aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc      1740 

     agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac      1800 

     tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa       1859 

// 

""" 

 

    print("GenBank CDS Iteration") 

    print("=====================") 

 

    g = GenBankScanner() 

    for record in g.parse_cds_features(StringIO(gbk_example)): 

        print(record) 

 

    g = GenBankScanner() 

    for record in g.parse_cds_features(StringIO(gbk_example2), 

                                       tags2id=('gene', 'locus_tag', 'product')): 

        print(record) 

 

    g = GenBankScanner() 

    for record in g.parse_cds_features(StringIO(gbk_example + "\n" + gbk_example2), 

                                       tags2id=('gene', 'locus_tag', 'product')): 

        print(record) 

 

    print("") 

    print("GenBank Iteration") 

    print("=================") 

    g = GenBankScanner() 

    for record in g.parse_records(StringIO(gbk_example), do_features=False): 

        print("%s %s %s" % (record.id, record.name, record.description)) 

        print(record.seq) 

 

    g = GenBankScanner() 

    for record in g.parse_records(StringIO(gbk_example), do_features=True): 

        print("%s %s %s" % (record.id, record.name, record.description)) 

        print(record.seq) 

 

    g = GenBankScanner() 

    for record in g.parse_records(StringIO(gbk_example2), do_features=False): 

        print("%s %s %s" % (record.id, record.name, record.description)) 

        print(record.seq) 

 

    g = GenBankScanner() 

    for record in g.parse_records(StringIO(gbk_example2), do_features=True): 

        print("%s %s %s" % (record.id, record.name, record.description)) 

        print(record.seq) 

 

    print("") 

    print("EMBL CDS Iteration") 

    print("==================") 

 

    e = EmblScanner() 

    for record in e.parse_cds_features(StringIO(embl_example)): 

        print(record) 

 

    print("") 

    print("EMBL Iteration") 

    print("==============") 

    e = EmblScanner() 

    for record in e.parse_records(StringIO(embl_example), do_features=True): 

        print("%s %s %s" % (record.id, record.name, record.description)) 

        print(record.seq)