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ags_to_gff_conv.py
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ags_to_gff_conv.py
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#!/usr/bin/env python
"""
Program to convert gene structure in mGene AGS format to GFF3.
Usage: python ags_to_gff_conv.py in.mat > out.gff
Requirements:
NumPy:- http://www.numpy.org/
SciPy:- http://www.scipy.org/
"""
import sys
import numpy as NP
import scipy.io as SIO
def ags_to_gff(fname):
"""
read the mGene AGS data format.
@args fname: mat file stores the AGS structure
@type fname: str
"""
mat_info = SIO.loadmat(fname, squeeze_me=True, struct_as_record=False)
gene_details = mat_info['genes'] #TODO automatically detect the struct identifier.
for each_entry in gene_details: #Iterate over the matlab struct
SOURCE = '.'
#SOURCE = str(NP.atleast_1d(each_entry.strain)[0]) if each_entry.strain.size else SOURCE
SOURCE = str(each_entry.gene_info.Source) if each_entry.gene_info.Source else SOURCE
geneLine = [str(each_entry.chr),
SOURCE,
str(each_entry.gene_type),
str(each_entry.start),
str(each_entry.stop),
'.',
str(each_entry.strand),
'.',
'ID=%s;Name=%s' % (each_entry.name, each_entry.name)]
print '\t'.join(geneLine) ## gene line in GFF3
tidx = 0
for transcript in NP.atleast_1d(each_entry.transcripts):
try:
try:
start = int(NP.atleast_1d(each_entry.exons)[tidx][0][0])
stop = int(NP.atleast_1d(each_entry.exons)[tidx][-1][1])
except:
start = int(NP.atleast_1d(each_entry.exons)[tidx][0])
stop = int(NP.atleast_1d(each_entry.exons)[tidx][1])
except:
try:
start = int(NP.atleast_1d(each_entry.exons)[0][0])
stop = int(NP.atleast_1d(each_entry.exons)[-1][1])
except:
start = NP.atleast_1d(each_entry.exons)[0]
stop = NP.atleast_1d(each_entry.exons)[1]
TYPE = '.'
TYPE = str(NP.atleast_1d(each_entry.transcript_type)[tidx]) if each_entry.transcript_type.size else TYPE
tLine = [str(each_entry.chr),
SOURCE,
TYPE,
str(start),
str(stop),
'.',
str(each_entry.strand),
'.',
'ID=%s;Parent=%s' % (transcript, each_entry.name)]
print '\t'.join(tLine) ##
if each_entry.utr5_exons.size:## UTR5
try:
try:
if len(NP.atleast_1d(each_entry.transcripts))==1:
for eidx in range(len(each_entry.utr5_exons)):
u5Line = [str(each_entry.chr),
SOURCE,
'five_prime_UTR',
str(each_entry.utr5_exons[eidx][0]),
str(each_entry.utr5_exons[eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent=%s' % transcript]
print '\t'.join(u5Line)
else:
u5_start = int(each_entry.utr5_exons[tidx][0])
u5_stop = int(each_entry.utr5_exons[tidx][1])
u5Line = [str(each_entry.chr),
SOURCE,
'five_prime_UTR',
str(u5_start),
str(u5_stop),
'.',
str(each_entry.strand),
'.',
'Parent=%s' % transcript]
print '\t'.join(u5Line)
except:
u5_start = int(each_entry.utr5_exons[0])
u5_stop = int(each_entry.utr5_exons[1])
u5Line = [str(each_entry.chr),
SOURCE,
'five_prime_UTR',
str(u5_start),
str(u5_stop),
'.',
str(each_entry.strand),
'.',
'Parent=%s' % transcript]
print '\t'.join(u5Line)
except:
for eidx in range(len(each_entry.utr5_exons[tidx])):
u5Line = [str(each_entry.chr),
SOURCE,
'five_prime_UTR',
str(each_entry.utr5_exons[tidx][eidx][0]),
str(each_entry.utr5_exons[tidx][eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent=%s' % transcript]
print '\t'.join(u5Line)
if each_entry.cds_exons.size:## CDS
try:
try:
if len(NP.atleast_1d(each_entry.transcripts))==1:
for eidx in range(len(each_entry.cds_exons)):
cLine = [str(each_entry.chr),
SOURCE,
'CDS',
str(each_entry.cds_exons[eidx][0]),
str(each_entry.cds_exons[eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(cLine)
else:
c_start = int(each_entry.cds_exons[tidx][0])
c_stop = int(each_entry.cds_exons[tidx][1])
cLine = [str(each_entry.chr),
SOURCE,
'CDS',
str(c_start),
str(c_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(cLine)
except:
c_start = int(each_entry.cds_exons[0])
c_stop = int(each_entry.cds_exons[1])
cLine = [str(each_entry.chr),
SOURCE,
'CDS',
str(c_start),
str(c_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(cLine)
except:
for eidx in range(len(each_entry.cds_exons[tidx])):
cLine = [str(each_entry.chr),
SOURCE,
'CDS',
str(each_entry.cds_exons[tidx][eidx][0]),
str(each_entry.cds_exons[tidx][eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(cLine)
if each_entry.utr3_exons.size: ## UTR3
try:
try:
if len(NP.atleast_1d(each_entry.transcripts))==1:
for eidx in range(len(each_entry.utr3_exons)):
u3Line = [str(each_entry.chr),
SOURCE,
'three_prime_UTR',
str(each_entry.utr3_exons[eidx][0]),
str(each_entry.utr3_exons[eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(u3Line)
else:
u3_start = int(each_entry.utr3_exons[tidx][0])
u3_stop = int(each_entry.utr3_exons[tidx][1])
u3Line = [str(each_entry.chr),
SOURCE,
'three_prime_UTR',
str(u3_start),
str(u3_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(u3Line)
except:
u3_start = int(each_entry.utr3_exons[0])
u3_stop = int(each_entry.utr3_exons[1])
u3Line = [str(each_entry.chr),
SOURCE,
'three_prime_UTR',
str(u3_start),
str(u3_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(u3Line)
except:
for eidx in range(len(each_entry.utr3_exons[tidx])):
u3Line = [str(each_entry.chr),
SOURCE,
'three_prime_UTR',
str(each_entry.utr3_exons[tidx][eidx][0]),
str(each_entry.utr3_exons[tidx][eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(u3Line)
if each_entry.exons.size:## Exons
try:
try:
if len(NP.atleast_1d(each_entry.transcripts))==1:
for eidx in range(len(each_entry.exons)):
eLine = [str(each_entry.chr),
SOURCE,
'exon',
str(each_entry.exons[eidx][0]),
str(each_entry.exons[eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(eLine)
else:
e_start = int(each_entry.exons[tidx][0])
e_stop = int(each_entry.exons[tidx][1])
eLine = [str(each_entry.chr),
SOURCE,
'exon',
str(e_start),
str(e_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(eLine)
except:
e_start = int(each_entry.exons[0])
e_stop = int(each_entry.exons[1])
eLine = [str(each_entry.chr),
SOURCE,
'exon',
str(e_start),
str(e_stop),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(eLine)
except:
for eidx in range(len(each_entry.exons[tidx])):
eLine = [str(each_entry.chr),
SOURCE,
'exon',
str(each_entry.exons[tidx][eidx][0]),
str(each_entry.exons[tidx][eidx][1]),
'.',
str(each_entry.strand),
'.',
'Parent='+str(transcript)]
print '\t'.join(eLine)
tidx += 1
if __name__== "__main__":
try:
mat_fname = sys.argv[1]
except:
print __doc__
sys.exit(-1)
ags_to_gff(mat_fname)