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# Copyright 2006-2013 by Peter Cock.  All rights reserved. 

# Revisions copyright 2011 Brandon Invergo. 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. 

"""AlignIO support for "phylip" format from Joe Felsenstein's PHYLIP tools. 

 

You are expected to use this module via the Bio.AlignIO functions (or the 

Bio.SeqIO functions if you want to work directly with the gapped sequences). 

 

Support for "relaxed phylip" format is also provided. Relaxed phylip differs 

from standard phylip format in the following ways: 

 

* No whitespace is allowed in the sequence ID. 

* No truncation is performed. Instead, sequence IDs are padded to the longest 

   ID length, rather than 10 characters. A space separates the sequence 

   identifier from the sequence. 

 

Relaxed phylip is supported by RAxML and PHYML. 

 

Note 

==== 

In TREE_PUZZLE (Schmidt et al. 2003) and PHYML (Guindon and Gascuel 2003) 

a dot/period (".") in a sequence is interpreted as meaning the same 

character as in the first sequence.  The PHYLIP documentation from 3.3 to 3.69 

http://evolution.genetics.washington.edu/phylip/doc/sequence.html says: 

 

   "a period was also previously allowed but it is no longer allowed, 

   because it sometimes is used in different senses in other programs" 

 

Biopython 1.58 or later treats dots/periods in the sequence as invalid, both 

for reading and writing. Older versions did nothing special with a dot/period. 

""" 

from __future__ import print_function 

 

import string 

 

from Bio._py3k import range 

 

from Bio.Seq import Seq 

from Bio.SeqRecord import SeqRecord 

from Bio.Align import MultipleSeqAlignment 

from .Interfaces import AlignmentIterator, SequentialAlignmentWriter 

 

_PHYLIP_ID_WIDTH = 10 

 

 

class PhylipWriter(SequentialAlignmentWriter): 

    """Phylip alignment writer.""" 

 

    def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH): 

        """Use this to write (another) single alignment to an open file. 

 

        This code will write interlaced alignments (when the sequences are 

        longer than 50 characters). 

 

        Note that record identifiers are strictly truncated to id_width, 

        defaulting to the value required to comply with the PHYLIP standard. 

 

        For more information on the file format, please see: 

        http://evolution.genetics.washington.edu/phylip/doc/sequence.html 

        http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles 

        """ 

        handle = self.handle 

 

        if len(alignment) == 0: 

            raise ValueError("Must have at least one sequence") 

        length_of_seqs = alignment.get_alignment_length() 

        for record in alignment: 

            if length_of_seqs != len(record.seq): 

                raise ValueError("Sequences must all be the same length") 

        if length_of_seqs <= 0: 

            raise ValueError("Non-empty sequences are required") 

 

        # Check for repeated identifiers... 

        # Apply this test *after* cleaning the identifiers 

        names = [] 

        seqs = [] 

        for record in alignment: 

            """ 

            Quoting the PHYLIP version 3.6 documentation: 

 

            The name should be ten characters in length, filled out to 

            the full ten characters by blanks if shorter. Any printable 

            ASCII/ISO character is allowed in the name, except for 

            parentheses ("(" and ")"), square brackets ("[" and "]"), 

            colon (":"), semicolon (";") and comma (","). If you forget 

            to extend the names to ten characters in length by blanks, 

            the program [i.e. PHYLIP] will get out of synchronization 

            with the contents of the data file, and an error message will 

            result. 

 

            Note that Tab characters count as only one character in the 

            species names. Their inclusion can cause trouble. 

            """ 

            name = record.id.strip() 

            #Either remove the banned characters, or map them to something 

            #else like an underscore "_" or pipe "|" character... 

            for char in "[](),": 

                name = name.replace(char, "") 

            for char in ":;": 

                name = name.replace(char, "|") 

            name = name[:id_width] 

            if name in names: 

                raise ValueError("Repeated name %r (originally %r), " 

                                 "possibly due to truncation" 

                                 % (name, record.id)) 

            names.append(name) 

            sequence = str(record.seq) 

            if "." in sequence: 

                # Do this check here (once per record, not once per block) 

                raise ValueError("PHYLIP format no longer allows dots in " 

                                 "sequence") 

            seqs.append(sequence) 

 

        # From experimentation, the use of tabs is not understood by the 

        # EMBOSS suite.  The nature of the expected white space is not 

        # defined in the PHYLIP documentation, simply "These are in free 

        # format, separated by blanks".  We'll use spaces to keep EMBOSS 

        # happy. 

        handle.write(" %i %s\n" % (len(alignment), length_of_seqs)) 

        block = 0 

        while True: 

            for name, sequence in zip(names, seqs): 

                if block == 0: 

                    #Write name (truncated/padded to id_width characters) 

                    #Now truncate and right pad to expected length. 

                    handle.write(name[:id_width].ljust(id_width)) 

                else: 

                    #write indent 

                    handle.write(" " * id_width) 

                #Write five chunks of ten letters per line... 

                for chunk in range(0, 5): 

                    i = block*50 + chunk*10 

                    seq_segment = sequence[i:i+10] 

                    #TODO - Force any gaps to be '-' character?  Look at the 

                    #alphabet... 

                    #TODO - How to cope with '?' or '.' in the sequence? 

                    handle.write(" %s" % seq_segment) 

                    if i+10 > length_of_seqs: 

                        break 

                handle.write("\n") 

            block = block+1 

            if block*50 > length_of_seqs: 

                break 

            handle.write("\n") 

 

 

class PhylipIterator(AlignmentIterator): 

    """Reads a Phylip alignment file returning a MultipleSeqAlignment iterator. 

 

    Record identifiers are limited to at most 10 characters. 

 

    It only copes with interlaced phylip files!  Sequential files won't work 

    where the sequences are split over multiple lines. 

 

    For more information on the file format, please see: 

    http://evolution.genetics.washington.edu/phylip/doc/sequence.html 

    http://evolution.genetics.washington.edu/phylip/doc/main.html#inputfiles 

    """ 

 

    # Default truncation length 

    id_width = _PHYLIP_ID_WIDTH 

 

    def _is_header(self, line): 

        line = line.strip() 

        parts = [x for x in line.split() if x] 

        if len(parts) != 2: 

            return False  # First line should have two integers 

        try: 

            number_of_seqs = int(parts[0]) 

            length_of_seqs = int(parts[1]) 

            return True 

        except ValueError: 

            return False  # First line should have two integers 

 

    def _split_id(self, line): 

        """ 

        Extracts the sequence ID from a Phylip line, returning a tuple 

        containing: 

 

            (sequence_id, sequence_residues) 

 

        The first 10 characters in the line are are the sequence id, the 

        remainder are sequence data. 

        """ 

        seq_id = line[:self.id_width].strip() 

        seq = line[self.id_width:].strip().replace(' ', '') 

        return seq_id, seq 

 

    def __next__(self): 

        handle = self.handle 

 

        try: 

            #Header we saved from when we were parsing 

            #the previous alignment. 

            line = self._header 

            del self._header 

        except AttributeError: 

            line = handle.readline() 

 

        if not line: 

            raise StopIteration 

        line = line.strip() 

        parts = [x for x in line.split() if x] 

        if len(parts) != 2: 

            raise ValueError("First line should have two integers") 

        try: 

            number_of_seqs = int(parts[0]) 

            length_of_seqs = int(parts[1]) 

        except ValueError: 

            raise ValueError("First line should have two integers") 

 

        assert self._is_header(line) 

 

        if self.records_per_alignment is not None \ 

        and self.records_per_alignment != number_of_seqs: 

            raise ValueError("Found %i records in this alignment, told to expect %i" 

                             % (number_of_seqs, self.records_per_alignment)) 

 

        ids = [] 

        seqs = [] 

 

        # By default, expects STRICT truncation / padding to 10 characters. 

        # Does not require any whitespace between name and seq. 

        for i in range(number_of_seqs): 

            line = handle.readline().rstrip() 

            sequence_id, s = self._split_id(line) 

            ids.append(sequence_id) 

            if "." in s: 

                raise ValueError("PHYLIP format no longer allows dots in sequence") 

            seqs.append([s]) 

 

        #Look for further blocks 

        line = "" 

        while True: 

            #Skip any blank lines between blocks... 

            while "" == line.strip(): 

                line = handle.readline() 

                if not line: 

                    break  # end of file 

            if not line: 

                break  # end of file 

 

            if self._is_header(line): 

                #Looks like the start of a concatenated alignment 

                self._header = line 

                break 

 

            #print "New block..." 

            for i in range(number_of_seqs): 

                s = line.strip().replace(" ", "") 

                if "." in s: 

                    raise ValueError("PHYLIP format no longer allows dots in sequence") 

                seqs[i].append(s) 

                line = handle.readline() 

                if (not line) and i+1 < number_of_seqs: 

                    raise ValueError("End of file mid-block") 

            if not line: 

                break  # end of file 

 

        records = (SeqRecord(Seq("".join(s), self.alphabet), 

                             id=i, name=i, description=i) 

                   for (i, s) in zip(ids, seqs)) 

        return MultipleSeqAlignment(records, self.alphabet) 

 

 

# Relaxed Phylip 

class RelaxedPhylipWriter(PhylipWriter): 

    """ 

    Relaxed Phylip format writer 

    """ 

 

    def write_alignment(self, alignment): 

        """ 

        Write a relaxed phylip alignment 

        """ 

        # Check inputs 

        for name in (s.id.strip() for s in alignment): 

            if any(c in name for c in string.whitespace): 

                raise ValueError("Whitespace not allowed in identifier: %s" 

                        % name) 

 

        # Calculate a truncation length - maximum length of sequence ID plus a 

        # single character for padding 

        # If no sequences, set id_width to 1. super(...) call will raise a 

        # ValueError 

        if len(alignment) == 0: 

            id_width = 1 

        else: 

            id_width = max((len(s.id.strip()) for s in alignment)) + 1 

        super(RelaxedPhylipWriter, self).write_alignment(alignment, id_width) 

 

 

class RelaxedPhylipIterator(PhylipIterator): 

    """ 

    Relaxed Phylip format Iterator 

    """ 

 

    def _split_id(self, line): 

        """Returns the ID, sequence data from a line 

        Extracts the sequence ID from a Phylip line, returning a tuple 

        containing: 

 

            (sequence_id, sequence_residues) 

 

        For relaxed format - split at the first whitespace character 

        """ 

        seq_id, sequence = line.split(None, 1) 

        sequence = sequence.strip().replace(" ", "") 

        return seq_id, sequence 

 

 

class SequentialPhylipWriter(SequentialAlignmentWriter): 

    """ 

    Sequential Phylip format Writer 

    """ 

    def write_alignment(self, alignment, id_width=_PHYLIP_ID_WIDTH): 

        handle = self.handle 

 

        if len(alignment) == 0: 

            raise ValueError("Must have at least one sequence") 

        length_of_seqs = alignment.get_alignment_length() 

        for record in alignment: 

            if length_of_seqs != len(record.seq): 

                raise ValueError("Sequences must all be the same length") 

        if length_of_seqs <= 0: 

            raise ValueError("Non-empty sequences are required") 

 

        # Check for repeated identifiers... 

        # Apply this test *after* cleaning the identifiers 

        names = [] 

        for record in alignment: 

            name = record.id.strip() 

            #Either remove the banned characters, or map them to something 

            #else like an underscore "_" or pipe "|" character... 

            for char in "[](),": 

                name = name.replace(char, "") 

            for char in ":;": 

                name = name.replace(char, "|") 

            name = name[:id_width] 

            if name in names: 

                raise ValueError("Repeated name %r (originally %r), " 

                                 "possibly due to truncation" 

                                 % (name, record.id)) 

            names.append(name) 

 

        # From experimentation, the use of tabs is not understood by the 

        # EMBOSS suite.  The nature of the expected white space is not 

        # defined in the PHYLIP documentation, simply "These are in free 

        # format, separated by blanks".  We'll use spaces to keep EMBOSS 

        # happy. 

        handle.write(" %i %s\n" % (len(alignment), length_of_seqs)) 

        for name, record in zip(names, alignment): 

            sequence = str(record.seq) 

            if "." in sequence: 

                raise ValueError("PHYLIP format no longer allows dots in " 

                                 "sequence") 

            handle.write(name[:id_width].ljust(id_width)) 

            # Write the entire sequence to one line (see sequential format 

            # notes in the SequentialPhylipIterator docstring 

            handle.write(sequence) 

            handle.write("\n") 

 

 

class SequentialPhylipIterator(PhylipIterator): 

    """ 

    Sequential Phylip format Iterator 

 

    The sequential format carries the same restrictions as the normal 

    interleaved one, with the difference being that the sequences are listed 

    sequentially, each sequence written in its entirety before the start of 

    the next. According to the PHYLIP documentation for input file formatting, 

    newlines and spaces may optionally be entered at any point in the sequences. 

    """ 

    def __next__(self): 

        handle = self.handle 

 

        try: 

            #Header we saved from when we were parsing 

            #the previous alignment. 

            line = self._header 

            del self._header 

        except AttributeError: 

            line = handle.readline() 

 

        if not line: 

            raise StopIteration 

        line = line.strip() 

        parts = [x for x in line.split() if x] 

        if len(parts) != 2: 

            raise ValueError("First line should have two integers") 

        try: 

            number_of_seqs = int(parts[0]) 

            length_of_seqs = int(parts[1]) 

        except ValueError: 

            raise ValueError("First line should have two integers") 

 

        assert self._is_header(line) 

 

        if self.records_per_alignment is not None \ 

        and self.records_per_alignment != number_of_seqs: 

            raise ValueError("Found %i records in this alignment, told to expect %i" 

                             % (number_of_seqs, self.records_per_alignment)) 

 

        ids = [] 

        seqs = [] 

 

        # By default, expects STRICT truncation / padding to 10 characters. 

        # Does not require any whitespace between name and seq. 

        for i in range(number_of_seqs): 

            line = handle.readline().rstrip() 

            sequence_id, s = self._split_id(line) 

            ids.append(sequence_id) 

            while len(s) < length_of_seqs: 

                # The sequence may be split into multiple lines 

                line = handle.readline().strip() 

                if not line: 

                    break 

                if line == "": 

                    continue 

                s = "".join([s, line.strip().replace(" ", "")]) 

                if len(s) > length_of_seqs: 

                    raise ValueError("Found a record of length %i, should be %i" 

                            % (len(s), length_of_seqs)) 

            if "." in s: 

                raise ValueError("PHYLIP format no longer allows dots in sequence") 

            seqs.append(s) 

        while True: 

            # Find other alignments in the file 

            line = handle.readline() 

            if not line: 

                break 

            if self._is_header(line): 

                self._header = line 

                break 

 

        records = (SeqRecord(Seq(s, self.alphabet), 

                             id=i, name=i, description=i) 

                   for (i, s) in zip(ids, seqs)) 

        return MultipleSeqAlignment(records, self.alphabet) 

 

 

if __name__ == "__main__": 

    print("Running short mini-test") 

 

    phylip_text = """     8    286 

V_Harveyi_ --MKNWIKVA VAAIA--LSA A--------- ---------T VQAATEVKVG 

B_subtilis MKMKKWTVLV VAALLAVLSA CG-------- ----NGNSSS KEDDNVLHVG 

B_subtilis MKKALLALFM VVSIAALAAC GAGNDNQSKD NAKDGDLWAS IKKKGVLTVG 

YA80_HAEIN MKKLLFTTAL LTGAIAFSTF ---------- -SHAGEIADR VEKTKTLLVG 

FLIY_ECOLI MKLAHLGRQA LMGVMAVALV AG---MSVKS FADEG-LLNK VKERGTLLVG 

E_coli_Gln --MKSVLKVS LAALTLAFAV S--------- ---------S HAADKKLVVA 

Deinococcu -MKKSLLSLK LSGLLVPSVL ALS------- -LSACSSPSS TLNQGTLKIA 

HISJ_E_COL MKKLVLSLSL VLAFSSATAA F--------- ---------- AAIPQNIRIG 

 

           MSGRYFPFTF VKQ--DKLQG FEVDMWDEIG KRNDYKIEYV TANFSGLFGL 

           ATGQSYPFAY KEN--GKLTG FDVEVMEAVA KKIDMKLDWK LLEFSGLMGE 

           TEGTYEPFTY HDKDTDKLTG YDVEVITEVA KRLGLKVDFK ETQWGSMFAG 

           TEGTYAPFTF HDK-SGKLTG FDVEVIRKVA EKLGLKVEFK ETQWDAMYAG 

           LEGTYPPFSF QGD-DGKLTG FEVEFAQQLA KHLGVEASLK PTKWDGMLAS 

           TDTAFVPFEF KQG--DKYVG FDVDLWAAIA KELKLDYELK PMDFSGIIPA 

           MEGTYPPFTS KNE-QGELVG FDVDIAKAVA QKLNLKPEFV LTEWSGILAG 

           TDPTYAPFES KNS-QGELVG FDIDLAKELC KRINTQCTFV ENPLDALIPS 

 

           LETGRIDTIS NQITMTDARK AKYLFADPYV VDG-AQITVR KGNDSIQGVE 

           LQTGKLDTIS NQVAVTDERK ETYNFTKPYA YAG-TQIVVK KDNTDIKSVD 

           LNSKRFDVVA NQVG-KTDRE DKYDFSDKYT TSR-AVVVTK KDNNDIKSEA 

           LNAKRFDVIA NQTNPSPERL KKYSFTTPYN YSG-GVIVTK SSDNSIKSFE 

           LDSKRIDVVI NQVTISDERK KKYDFSTPYT ISGIQALVKK GNEGTIKTAD 

           LQTKNVDLAL AGITITDERK KAIDFSDGYY KSG-LLVMVK ANNNDVKSVK 

           LQANKYDVIV NQVGITPERQ NSIGFSQPYA YSRPEIIVAK NNTFNPQSLA 

           LKAKKIDAIM SSLSITEKRQ QEIAFTDKLY AADSRLVVAK NSDIQP-TVE 

 

           DLAGKTVAVN LGSNFEQLLR DYDKDGKINI KTYDT--GIE HDVALGRADA 

           DLKGKTVAAV LGSNHAKNLE SKDPDKKINI KTYETQEGTL KDVAYGRVDA 

           DVKGKTSAQS LTSNYNKLAT N----AGAKV EGVEGMAQAL QMIQQARVDM 

           DLKGRKSAQS ATSNWGKDAK A----AGAQI LVVDGLAQSL ELIKQGRAEA 

           DLKGKKVGVG LGTNYEEWLR QNV--QGVDV RTYDDDPTKY QDLRVGRIDA 

           DLDGKVVAVK SGTGSVDYAK AN--IKTKDL RQFPNIDNAY MELGTNRADA 

           DLKGKRVGST LGSNYEKQLI DTG---DIKI VTYPGAPEIL ADLVAGRIDA 

           SLKGKRVGVL QGTTQETFGN EHWAPKGIEI VSYQGQDNIY SDLTAGRIDA 

 

           FIMDRLSALE -LIKKT-GLP LQLAGEPFET I-----QNAW PFVDNEKGRK 

           YVNSRTVLIA -QIKKT-GLP LKLAGDPIVY E-----QVAF PFAKDDAHDK 

           TYNDKLAVLN -YLKTSGNKN VKIAFETGEP Q-----STYF TFRKGS--GE 

           TINDKLAVLD -YFKQHPNSG LKIAYDRGDK T-----PTAF AFLQGE--DA 

           ILVDRLAALD -LVKKT-NDT LAVTGEAFSR Q-----ESGV ALRKGN--ED 

           VLHDTPNILY -FIKTAGNGQ FKAVGDSLEA Q-----QYGI AFPKGS--DE 

           AYNDRLVVNY -IINDQ-KLP VRGAGQIGDA A-----PVGI ALKKGN--SA 

           AFQDEVAASE GFLKQPVGKD YKFGGPSVKD EKLFGVGTGM GLRKED--NE 

 

           LQAEVNKALA EMRADGTVEK ISVKWFGADI TK---- 

           LRKKVNKALD ELRKDGTLKK LSEKYFNEDI TVEQKH 

           VVDQVNKALK EMKEDGTLSK ISKKWFGEDV SK---- 

           LITKFNQVLE ALRQDGTLKQ ISIEWFGYDI TQ---- 

           LLKAVNDAIA EMQKDGTLQA LSEKWFGADV TK---- 

           LRDKVNGALK TLRENGTYNE IYKKWFGTEP K----- 

           LKDQIDKALT EMRSDGTFEK ISQKWFGQDV GQP--- 

           LREALNKAFA EMRADGTYEK LAKKYFDFDV YGG--- 

""" 

 

    from Bio._py3k import StringIO 

    handle = StringIO(phylip_text) 

    count = 0 

    for alignment in PhylipIterator(handle): 

        for record in alignment: 

            count = count+1 

            print(record.id) 

            #print str(record.seq) 

    assert count == 8 

 

    expected = """mkklvlslsl vlafssataa faaipqniri gtdptyapfe sknsqgelvg 

    fdidlakelc krintqctfv enpldalips lkakkidaim sslsitekrq qeiaftdkly 

    aadsrlvvak nsdiqptves lkgkrvgvlq gttqetfgne hwapkgieiv syqgqdniys 

    dltagridaafqdevaaseg flkqpvgkdy kfggpsvkde klfgvgtgmg lrkednelre 

    alnkafaemradgtyeklak kyfdfdvygg""".replace(" ", "").replace("\n", "").upper() 

    assert str(record.seq).replace("-", "") == expected 

 

    #From here: 

    #http://atgc.lirmm.fr/phyml/usersguide.html 

    phylip_text2 = """5 60 

Tax1        CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAG 

Tax2        CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGG 

Tax3        CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGG 

Tax4        TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGG 

Tax5        CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGG 

 

GAAATGGTCAATATTACAAGGT 

GAAATGGTCAACATTAAAAGAT 

GAAATCGTCAATATTAAAAGGT 

GAAATGGTCAATCTTAAAAGGT 

GAAATGGTCAATATTAAAAGGT""" 

 

    phylip_text3 = """5 60 

Tax1        CCATCTCACGGTCGGTACGATACACCTGCTTTTGGCAGGAAATGGTCAATATTACAAGGT 

Tax2        CCATCTCACGGTCAGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAACATTAAAAGAT 

Tax3        CCATCTCCCGCTCAGTAAGATACCCCTGCTGTTGGCGGGAAATCGTCAATATTAAAAGGT 

Tax4        TCATCTCATGGTCAATAAGATACTCCTGCTTTTGGCGGGAAATGGTCAATCTTAAAAGGT 

Tax5        CCATCTCACGGTCGGTAAGATACACCTGCTTTTGGCGGGAAATGGTCAATATTAAAAGGT""" 

 

    handle = StringIO(phylip_text2) 

    list2 = list(PhylipIterator(handle)) 

    handle.close() 

    assert len(list2) == 1 

    assert len(list2[0]) == 5 

 

    handle = StringIO(phylip_text3) 

    list3 = list(PhylipIterator(handle)) 

    handle.close() 

    assert len(list3) == 1 

    assert len(list3[0]) == 5 

 

    for i in range(0, 5): 

        list2[0][i].id == list3[0][i].id 

        str(list2[0][i].seq) == str(list3[0][i].seq) 

 

    #From here: 

    #http://evolution.genetics.washington.edu/phylip/doc/sequence.html 

    #Note the lack of any white space between names 2 and 3 and their seqs. 

    phylip_text4 = """  5    42 

Turkey    AAGCTNGGGC ATTTCAGGGT 

Salmo gairAAGCCTTGGC AGTGCAGGGT 

H. SapiensACCGGTTGGC CGTTCAGGGT 

Chimp     AAACCCTTGC CGTTACGCTT 

Gorilla   AAACCCTTGC CGGTACGCTT 

 

GAGCCCGGGC AATACAGGGT AT 

GAGCCGTGGC CGGGCACGGT AT 

ACAGGTTGGC CGTTCAGGGT AA 

AAACCGAGGC CGGGACACTC AT 

AAACCATTGC CGGTACGCTT AA""" 

 

    #From here: 

    #http://evolution.genetics.washington.edu/phylip/doc/sequence.html 

    phylip_text5 = """  5    42 

Turkey    AAGCTNGGGC ATTTCAGGGT 

GAGCCCGGGC AATACAGGGT AT 

Salmo gairAAGCCTTGGC AGTGCAGGGT 

GAGCCGTGGC CGGGCACGGT AT 

H. SapiensACCGGTTGGC CGTTCAGGGT 

ACAGGTTGGC CGTTCAGGGT AA 

Chimp     AAACCCTTGC CGTTACGCTT 

AAACCGAGGC CGGGACACTC AT 

Gorilla   AAACCCTTGC CGGTACGCTT 

AAACCATTGC CGGTACGCTT AA""" 

 

    phylip_text5a = """  5    42 

Turkey    AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT 

Salmo gairAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT 

H. SapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA 

Chimp     AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT 

Gorilla   AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA""" 

 

    handle = StringIO(phylip_text4) 

    list4 = list(PhylipIterator(handle)) 

    handle.close() 

    assert len(list4) == 1 

    assert len(list4[0]) == 5 

 

    handle = StringIO(phylip_text5) 

    try: 

        list5 = list(PhylipIterator(handle)) 

        assert len(list5) == 1 

        assert len(list5[0]) == 5 

        print("That should have failed...") 

    except ValueError: 

        print("Evil multiline non-interlaced example failed as expected") 

    handle.close() 

 

    handle = StringIO(phylip_text5a) 

    list5 = list(PhylipIterator(handle)) 

    handle.close() 

    assert len(list5) == 1 

    assert len(list4[0]) == 5 

 

    print("Concatenation") 

    handle = StringIO(phylip_text4 + "\n" + phylip_text4) 

    assert len(list(PhylipIterator(handle))) == 2 

 

    handle = StringIO(phylip_text3 + "\n" + phylip_text4 + "\n\n\n" + phylip_text) 

    assert len(list(PhylipIterator(handle))) == 3 

 

    print("OK") 

 

    print("Checking write/read") 

    handle = StringIO() 

    PhylipWriter(handle).write_file(list5) 

    handle.seek(0) 

    list6 = list(PhylipIterator(handle)) 

    assert len(list5) == len(list6) 

    for a1, a2 in zip(list5, list6): 

        assert len(a1) == len(a2) 

        for r1, r2 in zip(a1, a2): 

            assert r1.id == r2.id 

            assert str(r1.seq) == str(r2.seq) 

    print("Done")