def clean_reference_alignment(region, refname, VERBOSE=0, subtype='B', ): '''Clean reference alignment''' from hivwholeseq.reference import load_custom_reference from Bio import SeqIO from Bio.Align import MultipleSeqAlignment from hivwholeseq.cross_sectional.filenames import ( get_subtype_reference_alignment_filename) fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, VERBOSE=VERBOSE) ali = AlignIO.read(fn, 'fasta') nseqs = len(ali) ali = MultipleSeqAlignment(filter(filter_sequence, ali)) nseqsnew = len(ali) if VERBOSE >= 2: print refname, region, subtype+':', nseqsnew, 'of', nseqs, 'seqs kept' return ali
def clean_reference_alignment( region, refname, VERBOSE=0, subtype='B', ): '''Clean reference alignment''' from hivwholeseq.reference import load_custom_reference from Bio import SeqIO from Bio.Align import MultipleSeqAlignment from hivwholeseq.cross_sectional.filenames import ( get_subtype_reference_alignment_filename) fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, VERBOSE=VERBOSE) ali = AlignIO.read(fn, 'fasta') nseqs = len(ali) ali = MultipleSeqAlignment(filter(filter_sequence, ali)) nseqsnew = len(ali) if VERBOSE >= 2: print refname, region, subtype + ':', nseqsnew, 'of', nseqs, 'seqs kept' return ali
def get_subtype_reference_alignment(region, subtype='B', refname='HXB2', type='nuc', VERBOSE=0): '''Get the observables from subtype B reference alignments''' from Bio import AlignIO ali_fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, type=type, VERBOSE=VERBOSE) ali = AlignIO.read(ali_fn, 'fasta') return ali
def get_subtype_reference_alignment(region, subtype='B', refname='HXB2', type='nuc', VERBOSE=0): '''Get the observables from subtype B reference alignments''' from Bio import AlignIO ali_fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, type=type, VERBOSE=VERBOSE) ali = AlignIO.read(ali_fn, 'fasta') return ali
# Script if __name__ == '__main__': parser = argparse.ArgumentParser(description='Align to reference', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('--region', required=True, help='Region to anign (e.g. V3)') parser.add_argument('--reference', default='HXB2', help='Reference to use for alignment') parser.add_argument('--verbose', type=int, default=0, help='Verbosity level [0-4]') parser.add_argument('--subtype', default='B', help='Subtype to analyze') args = parser.parse_args() region = args.region refname = args.reference VERBOSE = args.verbose subtype = args.subtype ali = clean_reference_alignment(region, refname, subtype=subtype, VERBOSE=VERBOSE) fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, VERBOSE=VERBOSE) AlignIO.write(ali, fn, 'fasta')
description='Align to reference', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('--region', required=True, help='Region to anign (e.g. V3)') parser.add_argument('--reference', default='HXB2', help='Reference to use for alignment') parser.add_argument('--verbose', type=int, default=0, help='Verbosity level [0-4]') parser.add_argument('--subtype', default='B', help='Subtype to analyze') args = parser.parse_args() region = args.region refname = args.reference VERBOSE = args.verbose subtype = args.subtype ali = clean_reference_alignment(region, refname, subtype=subtype, VERBOSE=VERBOSE) fn = get_subtype_reference_alignment_filename(region, subtype=subtype, refname=refname, VERBOSE=VERBOSE) AlignIO.write(ali, fn, 'fasta')