lin += '\t'+"ID="+mRNA_ID+';Parent='+chr_name[token[0]]+str(count).zfill(7)+";Name="+mRNA_ID+';Type='+gene_type+';'
print lin
else:
### print rest
match = re.search(r'ID=.+',line)
match = match.group().split(';')[0].replace('ID=','')
variant_no = match.split('.')[-1].replace('exon','') ### Get the mRNA variant number
lin = '\t'.join(line.split('\t')[0:len(line.split('\t'))-1]) ### all information except ID
lin += '\t'+"ID="+mRNA_ID+'.'+token[2]+'.'+variant_no+';Parent='+mRNA_ID+';Type='+gene_type+';'
print lin
if __name__ == "__main__":
gff3,Ns = options(sys.argv[1:])
### hash the N counts from the file
hash = A_hash_file.hash_file(Ns)
### run it by chromosome
size = E_get_chr_size_gff3.get_size(gff3)
for chr in sorted(size):
### modify gene names
modifyGeneNames(gff3,hash,chr)
### close the logfile
o.close()
print lin
else:
### print rest
match = re.search(r'ID=.+', line)
match = match.group().split(';')[0].replace('ID=', '')
variant_no = match.split('.')[-1].replace(
'exon', '') ### Get the mRNA variant number
lin = '\t'.join(
line.split('\t')[0:len(line.split('\t')) -
1]) ### all information except ID
lin += '\t' + "ID=" + mRNA_ID + '.' + token[
2] + '.' + variant_no + ';Parent=' + mRNA_ID + ';'
print lin
if __name__ == "__main__":
gff3, N_counts, specie = options(sys.argv[1:])
### hash the N counts from the file
hash = hash_Ns(N_counts)
### run it by chromosome
size = E_get_chr_size_gff3.get_size(gff3)
for chr in sorted(size):
### modify gene names
modifyGeneNames(gff3, chr, hash, specie)
### close the logfile
o.close()
if i in hash_call:
cds_call_len += 1
print id + '\t' + str(exon_len) + '\t' + str(
exon_call_len) + '\t' + str(cds_len) + '\t' + str(
cds_call_len)
first_transcript = False
hash_exon = {}
hash_cds = {}
id = str(obj)
elif obj.types() == "exon":
for i in range(int(obj.starts()), int(obj.ends())):
hash_exon[i] = ''
elif obj.types() == "CDS":
for i in range(int(obj.starts()), int(obj.ends())):
hash_cds[i] = ''
print id + '\t' + str(exon_len) + '\t' + str(exon_call_len) + '\t' + str(
cds_len) + '\t' + str(cds_call_len)
if __name__ == "__main__":
options(sys.argv[1:])
size = E_get_chr_size_gff3.get_size(ifile)
for chrom in size:
hash_call = parseCall(chrom)
get_exon_fraction(chrom, hash_call)
### close the logfile
o.close()
if i in hash_call:
cds_call_len += 1
print id + "\t" + str(exon_len) + "\t" + str(exon_call_len) + "\t" + str(cds_len) + "\t" + str(
cds_call_len
)
first_transcript = False
hash_exon = {}
hash_cds = {}
id = str(obj)
elif obj.types() == "exon":
for i in range(int(obj.starts()), int(obj.ends())):
hash_exon[i] = ""
elif obj.types() == "CDS":
for i in range(int(obj.starts()), int(obj.ends())):
hash_cds[i] = ""
print id + "\t" + str(exon_len) + "\t" + str(exon_call_len) + "\t" + str(cds_len) + "\t" + str(cds_call_len)
if __name__ == "__main__":
options(sys.argv[1:])
size = E_get_chr_size_gff3.get_size(ifile)
for chrom in size:
hash_call = parseCall(chrom)
get_exon_fraction(chrom, hash_call)
### close the logfile
o.close()
