def make_index(gff_file):
"""
Make a sqlite database for fast retrieval of features.
"""
import GFFutils
db_file = gff_file + ".db"
if need_update(gff_file, db_file):
if op.exists(db_file):
os.remove(db_file)
GFFutils.create_gffdb(gff_file, db_file)
return GFFutils.GFFDB(db_file)
def make_index(gff_file):
"""
Make a sqlite database for fast retrieval of features.
"""
import GFFutils
db_file = gff_file + ".db"
if need_update(gff_file, db_file):
if op.exists(db_file):
os.remove(db_file)
GFFutils.create_gffdb(gff_file, db_file)
return GFFutils.GFFDB(db_file)
def main(gff_file, fasta_file, parents, children):
db_file = gff_file + ".db"
if not op.exists(db_file):
GFFutils.create_gffdb(gff_file, db_file)
f = Fasta(fasta_file)
g = GFFutils.GFFDB(db_file)
parents = set(parents.split(','))
parents_iter = [g.features_of_type(x) for x in parents]
parents_list = itertools.chain(*parents_iter)
children_list = set(children.split(','))
for feat in parents_list:
children = []
for c in g.children(feat.id, 1):
if c.featuretype not in children_list: continue
child = f.sequence(dict(chr=c.chrom, start=c.start, stop=c.stop,
strand=c.strand))
children.append((child, c))
if not children:
print >>sys.stderr, "[warning] %s has no children with type %s" \
% (feat.id, ','.join(children_list))
continue
# sort children in incremental position
children.sort(key=lambda x: x[1].start)
# reverse children if negative strand
if feat.strand=='-': children.reverse()
feat_seq = ''.join(x[0] for x in children)
print ">%s" % feat.id
print feat_seq
def main(gff_file, fasta_file, parents, children):
db_file = gff_file + ".db"
if not op.exists(db_file):
GFFutils.create_gffdb(gff_file, db_file)
f = Fasta(fasta_file)
g = GFFutils.GFFDB(db_file)
parents = set(parents.split(','))
parents_iter = [g.features_of_type(x) for x in parents]
parents_list = itertools.chain(*parents_iter)
children_list = set(children.split(','))
for feat in parents_list:
children = []
for c in g.children(feat.id, 1):
if c.featuretype not in children_list: continue
child = f.sequence(
dict(chr=c.chrom, start=c.start, stop=c.stop, strand=c.strand))
children.append((child, c))
if not children:
print >>sys.stderr, "[warning] %s has no children with type %s" \
% (feat.id, ','.join(children_list))
continue
# sort children in incremental position
children.sort(key=lambda x: x[1].start)
# reverse children if negative strand
if feat.strand == '-': children.reverse()
feat_seq = ''.join(x[0] for x in children)
print ">%s" % feat.id
print feat_seq
#!/usr/bin/python
usage = """
Create a GFF database from a GFF file, e.g., downloaded from FlyBase.
Ryan Dale 2010 ([email protected])
"""
import GFFutils
import optparse
import os
import sys
op = optparse.OptionParser(usage=usage)
op.add_option('--gff',dest='gff',help='Input GFF file')
op.add_option('--gffdb',dest='gffdb',help='Destination GFF database file')
options,args = op.parse_args()
if not options.gff or not options.gffdb:
op.print_help()
print '\nERROR: Please specify an input GFF file and an output GFF database file'
sys.exit()
if not os.path.exists(options.gff):
print 'GFF file %s does not exist!' % options.gff
sys.exit()
GFFutils.create_gffdb(options.gff, options.gffdb)
