Module xi_covutils.msa

MSA functions

Expand source code
"""
MSA functions
"""
from xi_covutils.msa._msa import get_terminal_gaps
from xi_covutils.msa._msa import map_reference_to_sequence
from xi_covutils.msa._msa import map_ref_to_sequence
from xi_covutils.msa._msa import _count_mismatches
from xi_covutils.msa._msa import _count_gaps
from xi_covutils.msa._msa import map_sequence_to_reference
from xi_covutils.msa._msa import _gapstrip_template
from xi_covutils.msa._msa import gapstrip_sequences
from xi_covutils.msa._msa import pop_reference
from xi_covutils.msa._msa import gapstrip
from xi_covutils.msa._msa import _download_pfam
from xi_covutils.msa._msa import _extract_pfam
from xi_covutils.msa._msa import from_pfam
from xi_covutils.msa._msa import subset
from xi_covutils.msa._msa import pairwise_aln_stats
from xi_covutils.msa._msa import strip_terminal_gaps
from xi_covutils.msa._msa import default_aligner
from xi_covutils.msa._msa import pick_reference
from xi_covutils.msa._msa import msa_to_list
from xi_covutils.msa._msa import columns_to_rows
from xi_covutils.msa._msa import shuffle_without_gaps
from xi_covutils.msa._msa import shuffle_with_gaps
from xi_covutils.msa._msa import shuffle_msa
from xi_covutils.msa._msa import gap_content
from xi_covutils.msa._msa import gap_content_by_column
from xi_covutils.msa._msa import compare_two_msa
from xi_covutils.msa._msa import print_dict
from xi_covutils.msa._msa import compare_msas
from xi_covutils.msa._msa import extract_subsequences
from xi_covutils.msa._msa import pad
from xi_covutils.msa._msa import cut
from xi_covutils.msa._types import MsaTypes
from xi_covutils.msa._types import MsaSequenceList
from xi_covutils.msa._types import MsaDescSeqDict
from xi_covutils.msa._types import MsaDescSeqList
from xi_covutils.msa._types import MsaFilename
from xi_covutils.msa._io import read_msa
from xi_covutils.msa._io import write_msa
from xi_covutils.msa._io import as_sequence_list
from xi_covutils.msa._io import as_desc_seq_dict
from xi_covutils.msa._io import as_desc_seq_tuple
from xi_covutils.msa._pssm import build_dna_pssm
from xi_covutils.msa._pssm import build_rna_pssm
from xi_covutils.msa._pssm import build_protein_pssm
from xi_covutils.msa._patterns import build_dna_consensus
from xi_covutils.msa._patterns import build_dna_pattern
from xi_covutils.msa._patterns import build_rna_consensus
from xi_covutils.msa._patterns import build_rna_pattern
from xi_covutils.msa._patterns import build_protein_consensus
from xi_covutils.msa._patterns import build_protein_pattern
from xi_covutils.msa._cigar import generate_cigar_string