### MAIN ###
### fill tables by org
for org in orgs:
c.execute('insert into org (short) values ("%s")' % org)
con.commit()
orgid = c.execute('select id from org where short="%s"' %
org).fetchone()[0]
print('%i %s' % (orgid, org))
# genomic contig sequences
gen = '%s.genome.fa' % org
if not os.path.exists(gen): continue
gs = Fasta.FastaSeqs()
gs.loadseqs([gen])
print('%i genomic contig seqs' % len(gs.seqs))
for s in gs.seqs.values():
ex = 'insert into genomic(org,name,seq) values(%i,"%s","%s")' % (
orgid, s.name, s.seq)
c.execute(ex)
con.commit()
gff = '%s.gff' % org
features = read_gff(gff)
# CDS models (seems to be present and usable in all gffs)
for cds in features['CDS'].values():
ex = 'insert into cds (org,seq,pid,start,end,strand) values (%i,"%s","%s","%s","%s","%s")' % (
orgid, cds.seq, cds.fid, cds.start, cds.end, cds.strand)
f = sys.argv[2]
def expandprimer(primer):
seqs = []
choices = [degen_nucs[n] for n in primer]
all_combinations_gen(0, len(primer), [], seqs, choices)
return seqs
primers = expandprimer(primer)
print('%i primers' % len(primers))
for p in primers:
print p
fs = Fasta.FastaSeqs()
fs.loadseqs([f])
#primers.append('A')
seqmatches = {}
for s in fs.seqs:
seqmatches[s] = []
for p in primers:
prgx = re.compile(p, re.IGNORECASE)
for match in prgx.finditer(fs.seqs[s].seq):
seqmatches[s].append([p, match.start(), ''])
rvscmp = re.compile(rvs_comp_str(p), re.IGNORECASE)
if __name__ == "__main__":
import sys
app = BLAST_nr()
# args are blasttable, minpident, minalen
bfnm = sys.argv[1]
minpident = float(sys.argv[2])
minalnlen = int(sys.argv[3])
app.parseBLAST(bfnm,minpident,minalnlen)
# print(app)
# print(app.non_uni_clusters())
# print('\n'.join(app.keys()))
grp_path = 'BLASTn_grps'
if not os.path.exists(grp_path): os.mkdir(grp_path)
import Fasta
fa = Fasta.FastaSeqs()
fa.loadseqs([sys.argv[4]])
sfx = '%i.%i' %(int(minpident),minalnlen)
lngf = open('%s.lng.%s.fa' %(bfnm,sfx),'w')
for k,mates in app.items():
lngf.write('>%s\n%s\n' %(k,fa.seqs[k].seq))
f = open('%s/%s.grp.%s.fa' %(grp_path,k,sfx),'w')
f.write('>%s\n%s\n' %(k,fa.seqs[k].seq))
for m in mates:
f.write('>%s\n%s\n' %(m,fa.seqs[m].seq))
f.close()
lngf.close()
exf = open('%s.extras.%s.fa' %(bfnm,sfx),'w')
incids = app.allids()
for k in fa.seqs:
if not k in incids: