def main():
inFile = plausi()
fo = open(inFile)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
name = o.get_name()
geneHash = o.get_gene_hash()
for geneid, species in geneHash.iteritems(): print geneid + "\t" + name
def main():
inFile = plausi()
fo = open(inFile)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
name = o.get_name()
geneHash = o.get_gene_hash()
for geneid, species in geneHash.iteritems():
print geneid + "\t" + name
def main():
args = plausi()
in_orthomcl = args[0]
EVALUE = float('1e-20')
IDENTITY = 30.0
if len(args) == 4:
in_fasta, in_gg, in_blast = args[1:4]
gene2species, speciesArray = read_gg(in_gg)
gene2length = get_seq_lengths(in_fasta)
dbmfile = in_blast + ".add.dbm"
dbm = anydbm.open(dbmfile, "c")
fo = open(in_blast)
for line in fo:
line = line.rstrip()
cols = line.split("\t")
qid, hid, evalue, identity = cols[0], cols[1], float(
cols[10]), float(cols[2])
# ignore self-hits and between-species hits, check e-value threshold
if qid == hid: continue
if gene2species[qid] != gene2species[hid]: continue
if evalue > EVALUE: continue
if identity < IDENTITY: continue
# check that blast alignment spans at least 75% of the longer sequence
alnlength, qlength, hlength = int(
cols[3]), gene2length[qid], gene2length[hid]
lengthcutoff = 0.80 * max([qlength, hlength])
if alnlength < lengthcutoff: continue
if not dbm.has_key(qid): dbm[qid] = ""
else: dbm[qid] += " "
dbm[qid] += hid
fo.close()
dbm.close()
else:
dbmfile = args[1]
dbm = anydbm.open(dbmfile)
fo = open(in_orthomcl)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
oldsize = o.get_count()
additions = []
for geneid, species in o.get_gene_hash().iteritems():
if not dbm.has_key(geneid): continue
[additions.append([x, species]) for x in dbm[geneid].split()]
for x, species in additions:
o.add_gene(x, species)
o.to_s()
newsize = o.get_count()
print >> sys.stderr, "%s\t%s\t%s" % (o.get_name(), oldsize, newsize)
def main():
args = plausi()
in_orthomcl = args[0]
EVALUE = float('1e-20')
IDENTITY = 30.0
if len(args) == 4:
in_fasta, in_gg, in_blast = args[1:4]
gene2species, speciesArray = read_gg(in_gg)
gene2length = get_seq_lengths(in_fasta)
dbmfile = in_blast + ".add.dbm"
dbm = anydbm.open(dbmfile, "c")
fo = open(in_blast)
for line in fo:
line = line.rstrip()
cols = line.split("\t")
qid, hid, evalue, identity = cols[0], cols[1], float(cols[10]), float(cols[2])
# ignore self-hits and between-species hits, check e-value threshold
if qid == hid: continue
if gene2species[qid] != gene2species[hid]: continue
if evalue > EVALUE: continue
if identity < IDENTITY: continue
# check that blast alignment spans at least 75% of the longer sequence
alnlength, qlength, hlength = int(cols[3]), gene2length[qid], gene2length[hid]
lengthcutoff = 0.80 * max([qlength, hlength])
if alnlength < lengthcutoff: continue
if not dbm.has_key(qid): dbm[qid] = ""
else: dbm[qid] += " "
dbm[qid] += hid
fo.close()
dbm.close()
else: dbmfile = args[1]
dbm = anydbm.open(dbmfile)
fo = open(in_orthomcl)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
oldsize = o.get_count()
additions = []
for geneid, species in o.get_gene_hash().iteritems():
if not dbm.has_key(geneid): continue
[additions.append([x, species]) for x in dbm[geneid].split()]
for x, species in additions: o.add_gene(x,species)
o.to_s()
newsize = o.get_count()
print >> sys.stderr, "%s\t%s\t%s" %(o.get_name(), oldsize, newsize)
def main():
inFile = plausi()
fo = open(inFile)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
print o.get_name() + "\t" + o.get_species_hash()['Arath'][0]
def main():
inFile = plausi()
fo = open(inFile)
for line in fo:
o = OrthoMCLCluster(line.rstrip())
print o.get_name() + "\t" + o.get_species_hash()['Arath'][0]