def _main(self): alifile = '/home/allis/Documents/INMI/Fervidicoccales-signature/arb-silva.de_2016-04-06_id331139.fasta' group_names = ['Fervidicoccales', 'Acidilobales', 'Desulfurococcales', 'Thermoproteales:Sulfolobales', 'Other'] predefined_positions = [34, 501, 544, 1244, 1293] ref_name = 'Escherichia' reference = None groups = ListDB() with user_message('Loadding initial alignment...', '\n'): ali = AlignmentUtils.load_first(alifile) if not ali: return 1 with user_message('Sorting alignment into subgroups...', '\n'): for rec in ali: if ref_name in rec.description: reference = rec continue found = False for g in group_names: for k in g.split(':'): if k in rec.description: groups[g] = rec found = True break if not found: groups['Other'] = rec groups = dict((n, AlignmentExt(groups[n])) for n in groups) ali_len = ali.get_alignment_length() predefined_positions = [self._col_index(i, reference) for i in predefined_positions] print ('\nReference sequence:\n>%s\n%s' % (reference.description, str(reference.seq).replace('.', '').replace('-', ''))) print '\nAlignment: %d seqs, %d columns' % (len(ali), ali_len) print print_table([(g, '%d sequences' % len(groups[g])) for g in group_names]) print main_group = group_names[0] main_ali = groups[main_group] others = group_names[1:] for ci in xrange(ali_len): main_letter = self.LetterStats(main_ali[:,ci]) predef = ci in predefined_positions if predef or main_letter.freq_no_gaps >= 0.95 and main_letter.freq > 0.5: other_letters = [self.LetterStats(groups[g][:,ci]) for g in others] if predef or any(l.letter != main_letter.letter for l in other_letters): print ('------------------ E.coli position: %d ---------------------' % (self._ref_index(ci, reference)+1)) print print_table([(main_group, str(main_letter))]+ [(g, str(l)) for g, l in zip(others, other_letters)]) print print 'Done'
def _main(self): min_prod = 400 silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva.fasta' alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta' add_filename = FilenameParser.strip_ext(alifile)+'.with_additions.fasta' outgroups = ['Thermococcus_chitonophagus', 'SMTZ1-55', 'contig72135_1581_sunspring_meta'] add = ['KF836721.1.1270','EU635905.1.1323'] exclude = []#['Thermococcus_chitonophagus', 'SMTZ1-55', 'BA1-16S', 'contig72135_1581_sunspring_meta'] #load alignment if os.path.isfile(add_filename): alifile = add_filename add_filename = '' with user_message('Loadding initial alignment...', '\n'): orig_ali = AlignmentUtils.load_first(alifile) if not orig_ali: return 1 #load homologs if add_filename: with user_message('Loadding additional sequences...', '\n'): add_seqs = [] db = SeqView() if db.load(silva_db): for sid in add: seq = db.get(sid) if seq: add_seqs.append(seq) else: print '%s not found in %s' % (sid, silva_db) #realign data if needed if add_seqs: with user_message('Realigning data...', '\n'): add_filename = FilenameParser.strip_ext(alifile)+'.with_additions.fasta' AlignmentUtils.align(list(orig_ali)+add_seqs, add_filename) orig_ali = AlignmentUtils.load_first(add_filename) if not orig_ali: return 2 #process the alignment ali = orig_ali.remove(*exclude).trim() for out in outgroups: if not ali.index(out): print '%s not found in the alignment' % out return 3 ali.sort(key=lambda r: 'zzzzzzzz' if r.id in outgroups else r.id) ali_len = ali.get_alignment_length() AlignmentUtils.save(ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.trimmed.fasta') args = dict(plen = (20,40), max_mismatches = 8, min_match_mismatches = 1, first_match_mismatches = 1, first_may_match = 1, AT_first=True, outgroup=len(outgroups)) fprimers = self._find_primers(ali, **args) rprimers = self._find_primers(ali.reverse_complement(), **args) pairs = [] for i, (fs, fp) in enumerate(fprimers): start = fs fprimer = Primer.from_sequences(fp[:-1], 1, 'SSBaF%d' % fs) for _j, (rs, rp) in enumerate(rprimers): end = ali_len-rs if end-start <= min_prod: continue pairs.append((fprimer, Primer.from_sequences(rp[:-1], 1, 'SSBaR%d' % (ali_len-rs+1)))) if not pairs: print '\nNo suitable primer pairs found' return 3 added = set() for i, (fp, rp) in enumerate(pairs): print '\npair %d' % (i+1) print '%s: %s' % (fp.id, fp) print '%s: %s' % (rp.id, rp) if fp.id not in added: orig_ali.append(fp.master_sequence+'-'*(orig_ali.get_alignment_length()-len(fp))) added.add(fp.id) if rp.id not in added: orig_ali.append(copy_attrs(rp.master_sequence, rp.master_sequence.reverse_complement())+ '-'*(orig_ali.get_alignment_length()-len(rp))) added.add(rp.id) print orig_ali = AlignmentUtils.align(orig_ali) AlignmentUtils.save(orig_ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.with_primers.aln.fasta') print 'Done'
def _main(self): min_prod = 400 silva_db = '/home/allis/Documents/INMI/SILVA-DB/SILVA_123_SSURef_Nr99_tax_silva.fasta' alifile = '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.fasta' add_filename = FilenameParser.strip_ext( alifile) + '.with_additions.fasta' outgroups = [ 'Thermococcus_chitonophagus', 'SMTZ1-55', 'contig72135_1581_sunspring_meta' ] add = ['KF836721.1.1270', 'EU635905.1.1323'] exclude = [ ] #['Thermococcus_chitonophagus', 'SMTZ1-55', 'BA1-16S', 'contig72135_1581_sunspring_meta'] #load alignment if os.path.isfile(add_filename): alifile = add_filename add_filename = '' with user_message('Loadding initial alignment...', '\n'): orig_ali = AlignmentUtils.load_first(alifile) if not orig_ali: return 1 #load homologs if add_filename: with user_message('Loadding additional sequences...', '\n'): add_seqs = [] db = SeqView() if db.load(silva_db): for sid in add: seq = db.get(sid) if seq: add_seqs.append(seq) else: print '%s not found in %s' % (sid, silva_db) #realign data if needed if add_seqs: with user_message('Realigning data...', '\n'): add_filename = FilenameParser.strip_ext( alifile) + '.with_additions.fasta' AlignmentUtils.align( list(orig_ali) + add_seqs, add_filename) orig_ali = AlignmentUtils.load_first(add_filename) if not orig_ali: return 2 #process the alignment ali = orig_ali.remove(*exclude).trim() for out in outgroups: if not ali.index(out): print '%s not found in the alignment' % out return 3 ali.sort(key=lambda r: 'zzzzzzzz' if r.id in outgroups else r.id) AlignmentUtils.save( ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.aln.trimmed.fasta' ) args = dict(plen=(20, 40), max_mismatches=8, min_match_mismatches=1, first_match_mismatches=1, first_may_match=1, AT_first=True, outgroup=len(outgroups)) fprimers = PrimerFinder.find_discriminating_primers(ali, **args) rprimers = PrimerFinder.find_discriminating_primers(ali, reverse=True, **args) pairs = PrimerFinder.compile_pairs(fprimers, rprimers, min_prod, 'SSBa') if not pairs: print '\nNo suitable primer pairs found' return 3 PrimerFinder.print_pairs(pairs) orig_ali = PrimerFinder.add_pairs_to_alignment(pairs, orig_ali) AlignmentUtils.save( orig_ali, '/home/allis/Documents/INMI/SunS-metagenome/Bathy/BA2_SunS_16S.with_primers.aln.fasta' ) print 'Done'