xi_covutils.msa module
from Bio import SeqIO
from xi_covutils.pdbmapper import align_sequence_to_sequence
def map_reference_to_sequence(msa_file, sequence, start=1, end=None):
'''
Align the reference sequence of a substring from it to a another given sequence.
Substring alignment is useful for paired MSA.
:param msa_file: Path to a fasta file.
:param start: Index of the starting position of the MSA which will be mapped. Starting at 1.
:param end: Index of the last position of the MSA which will be mapped. Starting at 1.
:param sequence: An ungapped protein sequence to be used as destination of mapping.
'''
ref = str(SeqIO.parse(msa_file, "fasta").next().seq)
end = end if end else len(ref)
ref = ref[start-1: end].replace("-", "")
return align_sequence_to_sequence(ref, sequence)
Functions
def map_reference_to_sequence(
msa_file, sequence, start=1, end=None)
Align the reference sequence of a substring from it to a another given sequence. Substring alignment is useful for paired MSA. :param msa_file: Path to a fasta file. :param start: Index of the starting position of the MSA which will be mapped. Starting at 1. :param end: Index of the last position of the MSA which will be mapped. Starting at 1. :param sequence: An ungapped protein sequence to be used as destination of mapping.
def map_reference_to_sequence(msa_file, sequence, start=1, end=None):
'''
Align the reference sequence of a substring from it to a another given sequence.
Substring alignment is useful for paired MSA.
:param msa_file: Path to a fasta file.
:param start: Index of the starting position of the MSA which will be mapped. Starting at 1.
:param end: Index of the last position of the MSA which will be mapped. Starting at 1.
:param sequence: An ungapped protein sequence to be used as destination of mapping.
'''
ref = str(SeqIO.parse(msa_file, "fasta").next().seq)
end = end if end else len(ref)
ref = ref[start-1: end].replace("-", "")
return align_sequence_to_sequence(ref, sequence)