def analyse_coh(args):
import seq_manager as sm
import os
query = sm.WorkSeq(args['name'][:4], args['name'], sm.read_multi_fastas('all_cohs.txt')[args['name']+'.A']['seq'])
print args
print query
strands = get_strands_seq(query.name, query.fasta)
all_coh_fastas = sm.read_multi_fastas('Coh_All_Setup-Oct2014-d-for-lizi.txt')
pass_threshold = [{'name': query.name, 'seq': query.fasta}]
for hit_name, hit_val in all_coh_fastas.items():
# print hit_val
pw_aln = sm.pair_wise_aln_from_seqs(query.fasta, hit_val['seq'].upper())
if sm.aln_identity(pw_aln[0], pw_aln[1]) >= 0.4 and not gap_in_essential(strands, pw_aln[1], 4) \
and not gap_in_essential(strands, pw_aln[0], 4):
pass_threshold.append(hit_val)
# else:
# print 'not accepted'
# print pw_aln[0]
# print pw_aln[1]
# print ''.join(a if i in strands else '_' for i, a in enumerate(query.fasta))
print 'found %i seqs that passed the thresholds' % len(pass_threshold)
# import sys
# sys.exit()
pass_thresh_fasta_name = args['path']+args['name']+'_passed_thresholds.fasta'
sm.write_multi_seqs_to_file(pass_threshold, pass_thresh_fasta_name)
os.system('muscle -in ' + pass_thresh_fasta_name + ' -out ' + args['path']+args['name']+'_passed_thresholds.aln')
aln_fastas = sm.read_multi_fastas(args['path']+args['name']+'_passed_thresholds.aln')
os.system('weblogo -f %s -o %s --annotate %s' % (args['path']+args['name']+'_passed_thresholds.aln',
args['path']+args['name']+'_passed_thresholds.eps',
','.join(a for a in aln_fastas[args['name']]['seq'].replace('-', '-'))))
sm.write_seq_from_seq(args['name'], args['path'], query.fasta)
sm.run_psi_blast_for_pssm(args['path']+args['name']+'.fasta', args['path']+args['name']+'_passed_thresholds.aln',
args['path']+args['name']+'.pssm')
def analyse_doc(args):
import seq_manager as sm
import os
query = sm.WorkSeq(args['name'][:4], args['name'], sm.read_multi_fastas('all_docs.fasta')[args['name']+'.B']['seq'])
helices = get_helices_seq(args['name'][:4], query.fasta)
all_doc_fastas = sm.read_multi_fastas('all_dockerins_May2015.txt')
pass_thresh = [{'name': args['name'], 'seq': query.fasta}]
for hit_name, hit_val in all_doc_fastas.items():
pw_aln = sm.pair_wise_aln_from_seqs(query.fasta, hit_val['seq'].upper())
if sm.aln_identity(pw_aln[0], pw_aln[1]) >= 0.4 and not gap_in_essential(helices, pw_aln[1]) \
and not gap_in_essential(helices, pw_aln[0]):
pass_thresh.append(hit_val)
pass_thresh_fasta_name = args['path']+args['name']+'_passed_thresholds.fasta'
sm.write_multi_seqs_to_file({a['name']: a for a in pass_thresh}, pass_thresh_fasta_name)
os.system('muscle -in ' + pass_thresh_fasta_name + ' -out ' + args['path']+args['name']+'_passed_thresholds.aln')
aln_fastas = sm.read_multi_fastas(args['path']+args['name']+'_passed_thresholds.aln')
os.system('weblogo -f %s -o %s --annotate %s' % (args['path']+args['name']+'_passed_thresholds.aln',
args['path']+args['name']+'_passed_thresholds.eps',
','.join(a for a in aln_fastas[args['name']]['seq'].replace('-', '-'))))
print 'aln_fastas', aln_fastas
sm.write_seq_from_seq(args['name'], args['path'], query.fasta)
sm.write_multi_seqs_to_file(aln_fastas, args['path']+args['name']+'_passed_thresholds.aln', args['name'])
sm.run_psi_blast_for_pssm(args['path']+args['name']+'.fasta', args['path']+args['name']+'_passed_thresholds.aln',
args['path']+args['name']+'.pssm')
def analyse_coh(args):
import seq_manager as sm
import os
query = sm.WorkSeq(
args['name'][:4], args['name'],
sm.read_multi_fastas('all_cohs.txt')[args['name'] + '.A']['seq'])
print args
print query
strands = get_strands_seq(query.name, query.fasta)
all_coh_fastas = sm.read_multi_fastas(
'Coh_All_Setup-Oct2014-d-for-lizi.txt')
pass_threshold = [{'name': query.name, 'seq': query.fasta}]
for hit_name, hit_val in all_coh_fastas.items():
# print hit_val
pw_aln = sm.pair_wise_aln_from_seqs(query.fasta,
hit_val['seq'].upper())
if sm.aln_identity(pw_aln[0], pw_aln[1]) >= 0.4 and not gap_in_essential(strands, pw_aln[1], 4) \
and not gap_in_essential(strands, pw_aln[0], 4):
pass_threshold.append(hit_val)
# else:
# print 'not accepted'
# print pw_aln[0]
# print pw_aln[1]
# print ''.join(a if i in strands else '_' for i, a in enumerate(query.fasta))
print 'found %i seqs that passed the thresholds' % len(pass_threshold)
# import sys
# sys.exit()
pass_thresh_fasta_name = args['path'] + args[
'name'] + '_passed_thresholds.fasta'
sm.write_multi_seqs_to_file(pass_threshold, pass_thresh_fasta_name)
os.system('muscle -in ' + pass_thresh_fasta_name + ' -out ' +
args['path'] + args['name'] + '_passed_thresholds.aln')
aln_fastas = sm.read_multi_fastas(args['path'] + args['name'] +
'_passed_thresholds.aln')
os.system(
'weblogo -f %s -o %s --annotate %s' %
(args['path'] + args['name'] + '_passed_thresholds.aln',
args['path'] + args['name'] + '_passed_thresholds.eps', ','.join(
a for a in aln_fastas[args['name']]['seq'].replace('-', '-'))))
sm.write_seq_from_seq(args['name'], args['path'], query.fasta)
sm.run_psi_blast_for_pssm(
args['path'] + args['name'] + '.fasta',
args['path'] + args['name'] + '_passed_thresholds.aln',
args['path'] + args['name'] + '.pssm')
def analyse_doc(args):
import seq_manager as sm
import os
query = sm.WorkSeq(
args['name'][:4], args['name'],
sm.read_multi_fastas('all_docs.fasta')[args['name'] + '.B']['seq'])
helices = get_helices_seq(args['name'][:4], query.fasta)
all_doc_fastas = sm.read_multi_fastas('all_dockerins_May2015.txt')
pass_thresh = [{'name': args['name'], 'seq': query.fasta}]
for hit_name, hit_val in all_doc_fastas.items():
pw_aln = sm.pair_wise_aln_from_seqs(query.fasta,
hit_val['seq'].upper())
if sm.aln_identity(pw_aln[0], pw_aln[1]) >= 0.4 and not gap_in_essential(helices, pw_aln[1]) \
and not gap_in_essential(helices, pw_aln[0]):
pass_thresh.append(hit_val)
pass_thresh_fasta_name = args['path'] + args[
'name'] + '_passed_thresholds.fasta'
sm.write_multi_seqs_to_file({a['name']: a
for a in pass_thresh}, pass_thresh_fasta_name)
os.system('muscle -in ' + pass_thresh_fasta_name + ' -out ' +
args['path'] + args['name'] + '_passed_thresholds.aln')
aln_fastas = sm.read_multi_fastas(args['path'] + args['name'] +
'_passed_thresholds.aln')
os.system(
'weblogo -f %s -o %s --annotate %s' %
(args['path'] + args['name'] + '_passed_thresholds.aln',
args['path'] + args['name'] + '_passed_thresholds.eps', ','.join(
a for a in aln_fastas[args['name']]['seq'].replace('-', '-'))))
print 'aln_fastas', aln_fastas
sm.write_seq_from_seq(args['name'], args['path'], query.fasta)
sm.write_multi_seqs_to_file(
aln_fastas, args['path'] + args['name'] + '_passed_thresholds.aln',
args['name'])
sm.run_psi_blast_for_pssm(
args['path'] + args['name'] + '.fasta',
args['path'] + args['name'] + '_passed_thresholds.aln',
args['path'] + args['name'] + '.pssm')