def all_by_all(species_1, species_2):
# results = fasta_blast(species_1, species_2)
results = 'pairwise_blast/{}_{}-blast_results.xml'.format(species_1, species_2)
if results:
with open(results, 'r') as result_handle:
blast_records = NCBIXML.parse(result_handle)
hits_list = []
for blast_record in blast_records:
qsp, qid = kv.fasta_id_parse(blast_record.query)
query_record = kv.get_mongo_record(qsp, qid)
for alignment in blast_record.alignments:
asp, aid = kv.fasta_id_parse(alignment.hit_def)
alignment_record = kv.get_mongo_record(asp, aid)
for hsp in alignment.hsps:
if hsp.align_length > 100:
pident = float(hsp.positives)/float(hsp.align_length)
length = hsp.align_length
hits_list.append((query_record, alignment_record))
break
break
return hits_list
else:
print "Blast didn't work for some reason"
def group_hits(core=False):
all_species = kv.get_collection('core').distinct('species')
if not core:
all_species.extend(kv.get_collection('other').distinct('species'))
hits_db = kv.get_collection('hits')
species_index = sorted(all_species)
print species_index
df = pd.DataFrame()
core_groups = sorted(core_hgt_groups(), key=len, reverse=True)
for group in sorted(hits_db.distinct('group')):
recorded = []
s = {sp:0.0 for sp in species_index}
for hit in core_groups[group-1]:
if not hit in recorded:
s[hit[0]] += len(kv.get_mongo_record(*hit)['dna_seq'])
recorded.append(hit)
for hit in hits_db.find_one({'group':group})['group_hits']:
if float(hit[2]) > 90 and float(hit[3]) > 100:
if hit[1] not in recorded:
s[kv.fasta_id_parse(hit[1])[0]] += float(hit[2])*float(hit[3])/100
recorded.append(hit[1])
s = pd.Series(s, name='group_{}'.format(group))
df['group_{}'.format(group)] = s
df.to_csv('group_hits_other.csv')
# if __name__ == '__main__':
# import os
# kv.mongo_init('pacbio2')
# os.chdir('/Users/KBLaptop/computation/kvasir/data/output/pacbio2/')
# # group_hits(core=True)
# # output_groups()
# # core_hgt_stats()
# output_hits_csv()
'-dbtype', 'nucl',
'-out', 'pairwise_blast/{}_blastdb'.format(species_2),
'-title', os.path.basename(species_2),
]
).wait()
indexed_blast = blast_one(s1, 'pairwise_blast/{}_blastdb'.format(species_2))
concatenated_subject = kv.concat_contigs(kv.get_collection(species_1))
xys = []
last_end = 0
for i in range(len(indexed_blast))[0::4]:
# print indexed_blast[i:i+4]
subject = concatenated_subject[ObjectId(kv.fasta_id_parse(indexed_blast[i])[1])]
query = kv.get_mongo_record(*kv.fasta_id_parse(indexed_blast[i+1]))
x1 = subject['location']['start']
if x1 <= last_end:
x1 = last_end + 1
x2 = subject['location']['end']
last_end = x2
y = float(indexed_blast[i+2])
print [(x1-0.1, 0), (x1, y), (x2, y), (x2+0.1, 0)]
xys.extend([(x1-0.1, 0), (x1, y), (x2, y), (x2+0.1, 0)])
xys.sort(key=lambda xy:xy[0])
x, y = zip(*xys)
