def splicejunctions_to_gff3(inputBedFile, chrom_sizes, output):
gff3 = open(output, 'w')
gff3.write("##gff-version 3\n")
sizes_dict = subtools.sequence_region(chrom_sizes)
seq_regions = dict()
with open(inputBedFile, 'r') as bed:
for line in bed:
field = OrderedDict()
attribute = OrderedDict()
li = line.rstrip().split("\t")
field['seqid'] = li[0]
if field['seqid'] not in seq_regions:
end_region = sizes_dict[field['seqid']]
gff3.write("##sequence-region " + field['seqid'] + ' 1 ' +
str(end_region) + '\n')
seq_regions[field['seqid']] = end_region
field['source'] = li[3]
field['type'] = 'junction'
# The first base in a chromosome is numbered 0 in BED format
field['start'] = int(li[1]) + 1
field['end'] = li[2]
field['score'] = li[12]
field['strand'] = li[5]
field['phase'] = '.'
attribute['ID'] = li[0] + '_' + li[3]
attribute['Name'] = li[3]
attribute['blockcount'] = li[9]
attribute['blocksizes'] = li[10]
attribute['chromstarts'] = li[11]
subtools.write_features(field, attribute, gff3)
subtools.child_blocks(field, attribute, gff3, 'exon_junction')
gff3.close()
def gtfToGff3(gtf_file, gff3_file, chrom_sizes):
"""
Covert gtf file output from StringTie to gff3 format
"""
gff3 = open(gff3_file, 'w')
gff3.write("##gff-version 3\n")
sizes_dict = subtools.sequence_region(chrom_sizes)
seq_regions = dict()
parents = dict()
with open(gtf_file, 'r') as gtf:
for line in gtf:
if line.startswith('#') or not line.strip():
continue
field = OrderedDict()
attribute = OrderedDict()
li = line.rstrip().split("\t")
#print li
field['seqid'] = li[0]
#print field['seqid']
if field['seqid'] not in seq_regions:
end_region = sizes_dict[field['seqid']]
gff3.write("##sequence-region " + field['seqid'] + ' 1 ' +
str(end_region) + '\n')
seq_regions[field['seqid']] = end_region
field['source'] = li[1]
field['type'] = li[2]
# The first base in a chromosome is numbered 0 in BED format
field['start'] = li[3]
field['end'] = li[4]
field['score'] = li[5]
field['strand'] = li[6]
field['phase'] = li[7]
attr_li = li[8].split(';')
gene_id = attr_li[0].split()[1].strip('"')
attribute['ID'] = gene_id + '_' + field['type'] + '_' + str(
field['start']) + '_' + str(field['end'])
if field['type'] == 'transcript':
parents[gene_id] = attribute['ID']
attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
attribute['coverage'] = attr_li[2].split()[1].strip('"')
attribute['fpkm'] = attr_li[3].split()[1].strip('"')
attribute['tpm'] = attr_li[4].split()[1].strip('"')
elif field['type'] == 'exon':
attribute['Parent'] = parents[gene_id]
attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
attribute['coverage'] = attr_li[3].split()[1].strip('"')
subtools.write_features(field, attribute, gff3)
gff3.close()
def bigpsl_to_gff3(self):
gff3 = open(self.gff3_file.name, 'w')
gff3.write("##gff-version 3\n")
sizes_dict = subtools.sequence_region(self.chromSizesFile)
seq_regions = dict()
with open(self.inputFile, 'r') as bed:
for line in bed:
field = OrderedDict()
attribute = OrderedDict()
li = line.rstrip().split("\t")
field['seqid'] = li[0]
if field['seqid'] not in seq_regions:
end_region = sizes_dict[field['seqid']]
gff3.write("##sequence-region " + field['seqid'] + ' 1 ' +
str(end_region) + '\n')
seq_regions[field['seqid']] = end_region
field['source'] = 'UCSC BLAT alignment tool'
field['type'] = 'match'
# The first base in a chromosome is numbered 0 in BED format
field['start'] = str(int(li[1]) + 1)
field['end'] = li[2]
field['score'] = li[4]
field['strand'] = li[5]
field['phase'] = '.'
attribute['ID'] = li[0] + '_' + li[3]
attribute['Name'] = li[3]
attribute['blockcount'] = li[9]
attribute['blocksizes'] = li[10]
attribute['chromstarts'] = li[11]
attribute['ochrom_start'] = li[12]
attribute['ochrom_end'] = li[13]
attribute['ochrom_strand'] = li[14]
attribute['ochrom_size'] = li[15]
attribute['ochrom_starts'] = li[16]
attribute['sequence on other chromosome'] = li[17]
attribute['cds in ncbi format'] = li[18]
attribute['size of target chromosome'] = li[19]
attribute['number of bases matched'] = li[20]
attribute['number of bases that don\'t match'] = li[21]
attribute[
'number of bases that match but are part of repeats'] = li[
22]
attribute['number of \'N\' bases'] = li[23]
subtools.write_features(field, attribute, gff3)
subtools.child_blocks(field, attribute, gff3, 'match_part')
gff3.close()
def trfbig_to_gff3(inputBedFile, chrom_sizes, output):
gff3 = open(output, 'w')
gff3.write("##gff-version 3\n")
sizes_dict = subtools.sequence_region(chrom_sizes)
seq_regions = dict()
with open(inputBedFile, 'r') as bed:
for line in bed:
field = OrderedDict()
attribute = OrderedDict()
li = line.rstrip().split("\t")
field['seqid'] = li[0]
if field['seqid'] not in seq_regions:
end_region = sizes_dict[field['seqid']]
gff3.write("##sequence-region " + field['seqid'] + ' 1 ' +
str(end_region) + '\n')
seq_regions[field['seqid']] = end_region
field['source'] = li[3]
field['type'] = 'tandem_repeat'
# The first base in a chromosome is numbered 0 in BED format
field['start'] = str(int(li[1]) + 1)
field['end'] = li[2]
field['score'] = li[9]
field['strand'] = '+'
field['phase'] = '.'
attribute['length of repeat unit'] = li[4]
attribute['mean number of copies of repeat'] = li[5]
attribute['length of consensus sequence'] = li[6]
attribute['percentage match'] = li[7]
attribute['percentage indel'] = li[8]
attribute['percent of a\'s in repeat unit'] = li[10]
attribute['percent of c\'s in repeat unit'] = li[11]
attribute['percent of g\'s in repeat unit'] = li[12]
attribute['percent of t\'s in repeat unit'] = li[13]
attribute['entropy'] = li[14]
attribute['sequence of repeat unit element'] = li[15]
subtools.write_features(field, attribute, gff3)
gff3.close()