def main(args):
gfhash = gff3.get_gff_hash(args['gffile'])
gid, Diagstart, Diagstop = get_coordinates_for_diagram(
gfhash, args['genes'])
print gid, Diagstart, Diagstop
gd_diagram = GenomeDiagram.Diagram(gid)
gd_track_for_features = gd_diagram.new_track(1, name="Annotated Genes")
gd_feature_set = gd_track_for_features.new_set()
for gf in sorted(gfhash[gid], key=lambda x: x.start):
if gf.ftype != 'mRNA': continue
if gf.start > gf.stop: gf.start, gf.stop = gf.stop, gf.start
if gf.stop < Diagstart or gf.start > Diagstop: continue
f = SeqFeature(FeatureLocation(max([gf.start, Diagstart]),
min([gf.stop, Diagstop])),
strand=int(gf.strand + '1'),
type=gf.get_attributes()['ID'])
gd_feature_set.add_feature(f,
label=True,
label_size=10,
label_angle=0,
sigil="ARROW")
print gf.get_attributes()['ID'], gf.start, gf.stop
gd_diagram.draw(start=Diagstart,
end=Diagstop,
format='linear',
fragments=1,
pagesize=(100 * cm, 4 * cm))
outfile = os.path.split(args['gffile'])[1] + "_" + string.join(
args['genes'], "_") + '.pdf'
gd_diagram.write(outfile, "PDF")
print outfile
def main( args ):
gfhash = gff3.get_gff_hash(args['gffile'])
sys.stderr.write("gff loaded ")
gid, startpos, endpos = get_coordinates(gfhash, args['genes'])
sys.stderr.write("| coordinates identified ")
if not args['rv']: print ">%s_%s:%s" %(gid, startpos, endpos)
else: print ">%s_%s:%s" %(gid, endpos, startpos)
seqhash = fasta.get_sequence_hash(args['fastafile'])
sys.stderr.write("| fasta loaded ")
seq = seqhash[gid][startpos-1:endpos]
if args['rv']: seq = Seq(seq).reverse_complement().tostring()
sys.stderr.write("| subsequence extracted ")
print seq
sys.stderr.write("\n")
def main(args):
gfhash = gff3.get_gff_hash(args['gffile'])
sys.stderr.write("gff loaded ")
gid, startpos, endpos = get_coordinates(gfhash, args['genes'])
sys.stderr.write("| coordinates identified ")
if not args['rv']: print ">%s_%s:%s" % (gid, startpos, endpos)
else: print ">%s_%s:%s" % (gid, endpos, startpos)
seqhash = fasta.get_sequence_hash(args['fastafile'])
sys.stderr.write("| fasta loaded ")
seq = seqhash[gid][startpos - 1:endpos]
if args['rv']: seq = Seq(seq).reverse_complement().tostring()
sys.stderr.write("| subsequence extracted ")
print seq
sys.stderr.write("\n")
def main( args ):
gfhash = gff3.get_gff_hash(args['gffile'])
gid, Diagstart, Diagstop = get_coordinates_for_diagram(gfhash, args['genes'])
print gid, Diagstart, Diagstop
gd_diagram = GenomeDiagram.Diagram(gid)
gd_track_for_features = gd_diagram.new_track(1, name="Annotated Genes")
gd_feature_set = gd_track_for_features.new_set()
for gf in sorted(gfhash[gid], key=lambda x: x.start):
if gf.ftype != 'mRNA': continue
if gf.start > gf.stop: gf.start, gf.stop = gf.stop, gf.start
if gf.stop < Diagstart or gf.start > Diagstop: continue
f = SeqFeature(FeatureLocation(max([gf.start, Diagstart]), min([gf.stop, Diagstop])), strand=int(gf.strand+'1'), type=gf.get_attributes()['ID'])
gd_feature_set.add_feature(f, label=True, label_size=10, label_angle=0, sigil="ARROW")
print gf.get_attributes()['ID'], gf.start, gf.stop
gd_diagram.draw(start=Diagstart, end=Diagstop, format='linear', fragments=1, pagesize=(100*cm, 4*cm))
outfile = os.path.split(args['gffile'])[1] + "_"+ string.join(args['genes'], "_") + '.pdf'
gd_diagram.write(outfile, "PDF")
print outfile