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()
def gff3_writer(blast_records, gff3_file):
gff3 = open(gff3_file, 'a')
gff3.write("##gff-version 3\n")
seq_regions = dict()
for blast_record in blast_records:
query_name = blast_record.query.split(" ")[0]
source = blast_record.application
method = blast_record.matrix
for alignment in blast_record.alignments:
group = {
"parent_field": OrderedDict(),
"parent_attribute": OrderedDict(),
"alignments": []
}
title = alignment.title.split(" ")
contig_name = title[len(title) - 1]
length = alignment.length
group['parent_field']['seqid'] = contig_name
group['parent_field']['source'] = source
group['parent_field']['type'] = 'match'
group['parent_attribute']['ID'] = contig_name + '_' + query_name
group['parent_attribute']['Name'] = query_name
group['parent_attribute']['method'] = method
group['parent_attribute']['length'] = length
if contig_name not in seq_regions:
gff3.write("##sequence-region " + contig_name + ' 1 ' +
str(length) + '\n')
seq_regions[contig_name] = length
match_num = 0
coords = [length, 0]
for hsp in alignment.hsps:
hsp_align = {}
field = OrderedDict()
attribute = OrderedDict()
ref = hsp.sbjct
query = hsp.query
field['seqid'] = contig_name
field['source'] = source
field['type'] = 'match_part'
field['start'] = hsp.sbjct_start
if field['start'] < coords[0]:
coords[0] = field['start']
ref_length = len(ref.replace('-', ''))
# if run tblastn, the actual length of reference should be multiplied by 3
if source.lower() == "tblastn":
ref_length *= 3
field['end'] = field['start'] + ref_length - 1
if field['end'] > coords[1]:
coords[1] = field['end']
field['score'] = hsp.score
#decide if the alignment in the same strand or reverse strand
#reading frame
# (+, +), (0, 0), (-, -) => +
# (+, -), (-, +) => -
if hsp.frame[1] * hsp.frame[0] > 0:
field['strand'] = '+'
elif hsp.frame[1] * hsp.frame[0] < 0:
field['strand'] = '-'
else:
if hsp.frame[0] + hsp.frame[1] >= 0:
field['strand'] = '+'
else:
field['strand'] = '-'
field['phase'] = '.'
target_start = hsp.query_start
target_len = len(query.replace('-', ''))
# if run blastx, the actual length of query should be multiplied by 3
if source.lower() == "blastx":
target_len *= 3
target_end = target_start + target_len - 1
attribute['ID'] = group['parent_attribute'][
'ID'] + '_match_' + str(match_num)
attribute['Parent'] = group['parent_attribute']['ID']
attribute['Target'] = query_name + " " + str(
target_start) + " " + str(target_end)
attribute['Gap'] = align2cigar(query, ref)
#store the query sequence and match string in the file in order to display alignment with BlastAlignment plugin
attribute['subject'] = hsp.sbjct
attribute['query'] = hsp.query
attribute['match'] = hsp.match
attribute['gaps'] = attribute['match'].count(' ')
similar = attribute['match'].count('+')
attribute['identities'] = len(
attribute['match']) - similar - attribute['gaps']
attribute['positives'] = attribute['identities'] + similar
attribute['expect'] = hsp.expect
# show reading frame attribute only if the frame is not (0, 0)
attribute['frame'] = hsp.frame[1]
match_num += 1
hsp_align['field'] = field
hsp_align['attribute'] = attribute
group['alignments'].append(hsp_align)
group['parent_field']['start'] = coords[0]
group['parent_field']['end'] = coords[1]
group['parent_field']['score'] = group['parent_field'][
'strand'] = group['parent_field']['phase'] = '.'
group['parent_attribute']['match_num'] = match_num
group['alignments'].sort(
key=lambda x: (x['field']['start'], x['field']['end']))
subtools.write_features(group['parent_field'],
group['parent_attribute'], gff3)
prev_end = -1
for align in group['alignments']:
overlap = ''
if align['field']['start'] <= prev_end:
overlap += str(
align['field']['start']) + ',' + str(prev_end)
prev_end = align['field']['end']
align['attribute']['overlap'] = overlap
subtools.write_features(align['field'], align['attribute'],
gff3)
gff3.close()