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#!/usr/bin/python3
# encoding: utf-8
from __future__ import (absolute_import, division, print_function, unicode_literals)
import argparse
import math
import string
import os
class fasta_input(object):
def __init__(self, seq):
super(fasta_input, self).__init__()
self.buffer_size = os.stat(seq).st_blksize
self.file = open(seq, "r")
self.contigs_start_positions = {}
self.line_length = -1
self.initialize_fasta_reader()
def initialize_fasta_reader(self):
contig_id = None
buffer_offset = 0
for line in self.file:
buffer_offset += len(line)
if line[0] == ">":
contig_id = line.rstrip().split(" ")[0][1:]
self.contigs_start_positions[contig_id] = buffer_offset # no offset based on contig start index because there are that many N at the begining of the contig to compensate
elif len(line) > self.line_length + 1:
self.line_length = len(line.rstrip())
def finalize(self):
self.file.close()
def make_supertranscript(seq, contig, translation_table, blocks_out, fasta_out, transcripts_out, current_gene_id, starts, ends, transcript_ids, orientations):
current_gene_id = current_gene_id.replace("\"", "")
sstarts = sorted(starts.keys())
sends = sorted(ends.keys())
i = j = 0
current_transcripts = set()
blocks = [] # (start_position, end_position, [transcript_ids])
last_position = -1
while i < len(sstarts) and j < len(sends):
if sstarts[i] == sends[j]:
if last_position != sstarts[i]:
blocks.append((last_position, sstarts[i] - 1, set(current_transcripts)))
for k in starts[sstarts[i]]:
current_transcripts.add(transcript_ids[k])
blocks.append((sstarts[i], sstarts[i], set(current_transcripts)))
for k in ends[sends[j]]:
current_transcripts.remove(transcript_ids[k])
last_position = sstarts[i] + 1
i += 1
j += 1
elif sstarts[i] < sends[j]:
if last_position > 0 and last_position != sstarts[i]:
blocks.append((last_position, sstarts[i] - 1, set(current_transcripts)))
for k in starts[sstarts[i]]:
current_transcripts.add(transcript_ids[k])
last_position = sstarts[i]
i += 1
elif sstarts[i] > sends[j]:
blocks.append((last_position, sends[j], set(current_transcripts)))
for k in ends[sends[j]]:
current_transcripts.remove(transcript_ids[k])
last_position = sends[j] + 1
j += 1
while j < len(sends): # closing blocks
blocks.append((last_position, sends[j], set(current_transcripts)))
for k in ends[sends[j]]:
current_transcripts.remove(transcript_ids[k])
last_position = sends[j] + 1
j += 1
ori = set(orientations)
if len(ori) > 1:
exit("error, one gene contains exons in both orientations")
current_position = 1
ori = ori.pop()
blocks_buffer = ""
fasta_buffer = ""
last_transcripts = None
transcripts_to_output = {}
next_opening = 1
transcript_buffer = ""
if ori == "+":
offset = sstarts[0]
fasta_header_exons = ">" + current_gene_id + " loc:" + contig + "|" + str(blocks[0][0]) + "-" + str(blocks[-1][1]) + "|+ "
fasta_header_exons += "exons:" + str(blocks[0][0])
fasta_header_segs = " segs:1"
for block in blocks: # (start_position, end_position, [transcript_ids])
if len(block[2]) > 0:
end_position = current_position + block[1] - block[0]
if last_transcripts and block[2] != last_transcripts:
blocks_buffer += current_gene_id + "\trtracklayer\texon\t" + str(next_opening) + "\t" + str(current_position - 1) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + current_gene_id + "\"; ID \"" + current_gene_id + "\"\n"
for transcript in last_transcripts - block[2]:
transcripts_to_output[transcript].append(current_position - 1)
for transcript in block[2] - last_transcripts:
if transcript not in transcripts_to_output:
transcripts_to_output[transcript] = [current_position]
else:
transcripts_to_output[transcript].append(current_position)
last_transcripts = block[2]
next_opening = current_position
elif not last_transcripts:
last_transcripts = block[2]
for transcript in last_transcripts:
transcripts_to_output[transcript] = [1]
tmp_fasta = get_fasta(seq, contig, block[0], block[1])
if not tmp_fasta:
print("contig " + contig + " from annotation does not exist in the fasta file.")
return
fasta_buffer += tmp_fasta
current_position = end_position + 1
else: # gap
offset += block[1] - block[0] + 1
fasta_header_exons += "-" + str(block[0] - 1) + "," + str(block[1] + 1) # -1 and +1 because the exons end and start at positions around the gap
fasta_header_segs += "-" + str(current_position - 1) + "," + str(current_position)
for transcript in last_transcripts:
transcripts_to_output[transcript].append(current_position - 1)
for transcript in sorted(transcripts_to_output):
for i in xrange(0, len(transcripts_to_output[transcript]), 2):
transcript_buffer += current_gene_id + "\tsuperTranscript\texon\t" + str(transcripts_to_output[transcript][i]) + "\t" + str(transcripts_to_output[transcript][i + 1]) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + transcript + "\"\n"
transcripts_out.write(transcript_buffer)
blocks_buffer += current_gene_id + "\trtracklayer\texon\t" + str(next_opening) + "\t" + str(end_position) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + current_gene_id + "\"; ID \"" + current_gene_id + "\"\n"
blocks_out.write(blocks_buffer)
fasta_header_segs += "-" + str(current_position - 1)
write_fasta(fasta_out, fasta_header_exons + "-" + str(blocks[-1][1]), fasta_header_segs, fasta_buffer, seq.line_length)
elif ori == "-":
offset = sends[-1]
fasta_header = ">" + current_gene_id + " loc:" + contig + "|" + str(blocks[0][0]) + "-" + str(blocks[-1][1]) + "|- "
fasta_header_exons = ""
fasta_header_segs = " segs:1"
for i in xrange(len(blocks) - 1, -1, -1):
block = blocks[i] # (start_position, end_position, [transcript_ids])
if len(block[2]) > 0:
end_position = current_position + block[1] - block[0]
if last_transcripts and block[2] != last_transcripts:
blocks_buffer += current_gene_id + "\trtracklayer\texon\t" + str(next_opening) + "\t" + str(current_position - 1) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + current_gene_id + "\"; ID \"" + current_gene_id + "\"\n"
for transcript in last_transcripts - block[2]:
transcripts_to_output[transcript].append(current_position - 1)
for transcript in block[2] - last_transcripts:
if transcript not in transcripts_to_output:
transcripts_to_output[transcript] = [current_position]
else:
transcripts_to_output[transcript].append(current_position)
last_transcripts = block[2]
next_opening = current_position
elif not last_transcripts:
last_transcripts = block[2]
for transcript in last_transcripts:
transcripts_to_output[transcript] = [1]
tmp_fasta = get_fasta(seq, contig, block[0], block[1])
if not tmp_fasta:
print("contig " + contig + " from annotation does not exist in the fasta file.")
return
fasta_buffer = tmp_fasta + fasta_buffer
current_position = end_position + 1
else: # gap
offset += block[1] - block[0] + 1
fasta_header_exons = "-" + str(block[0] - 1) + "," + str(block[1] + 1) + fasta_header_exons
fasta_header_segs += "-" + str(current_position - 1) + "," + str(current_position)
for transcript in last_transcripts:
transcripts_to_output[transcript].append(current_position - 1)
for transcript in sorted(transcripts_to_output):
for i in xrange(0, len(transcripts_to_output[transcript]), 2):
transcript_buffer += current_gene_id + "\tsuperTranscript\texon\t" + str(transcripts_to_output[transcript][i]) + "\t" + str(transcripts_to_output[transcript][i + 1]) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + transcript + "\"\n"
transcripts_out.write(transcript_buffer)
blocks_buffer += current_gene_id + "\trtracklayer\texon\t" + str(next_opening) + "\t" + str(end_position) + "\t.\t+\t.\tgene_id \"" + current_gene_id + "\"; transcript_id \"" + current_gene_id + "\"; ID \"" + current_gene_id + "\"\n"
blocks_out.write(blocks_buffer)
fasta_header_exons = fasta_header + "exons:" + str(blocks[0][0]) + fasta_header_exons + "-" + str(blocks[-1][1]) # [:fasta_header_exons.rfind(",")]
fasta_header_segs += "-" + str(current_position - 1)
write_fasta(fasta_out, fasta_header_exons, fasta_header_segs, string.translate(str(fasta_buffer[::-1]), translation_table), seq.line_length)
# write_fasta(fasta_out, fasta_header_exons, fasta_header_segs, fasta_buffer[::-1].translate(translation_table), seq.line_length)
else:
exit("error, invalid orientation " + ori)
def get_fasta(seq, contig, start, end):
offset = None
if contig not in seq.contigs_start_positions:
if len(seq.contigs_start_positions) > 1:
print("\"" + contig + "\"")
# exit("Error, contig IDs do not match between annotation and fasta file.")
return None
else:
offset = seq.contigs_start_positions.values()[0]
else:
offset = seq.contigs_start_positions[contig]
offset += start - 1 + int(math.floor((start - 1) / seq.line_length)) # number of characters + new lines
seq.file.seek(offset, 0)
line_offset = (start - 1) % seq.line_length
newlines_offset = int(math.floor((end - start + 1 + line_offset) / seq.line_length))
sequence = seq.file.read(end - start + 1 + newlines_offset)
sequence = sequence.replace("\n", "")
return sequence
def write_fasta(fasta_out, exons, segs, sequence, line_length):
line_length = 70
fasta_out.write(exons + segs + "\n")
for i in xrange(0, len(sequence), line_length):
fasta_out.write(sequence[i:i + line_length] + "\n")
def main():
usage = "usage: "
parser = argparse.ArgumentParser(usage)
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument('--gtf', dest="gtf", default=None, type=str, help="Path to gtf annotation file.")
group.add_argument('--gff3', dest="gff3", default=None, type=str, help="Path to gff3 annotation file.")
parser.add_argument('--seq', dest="fasta", required=True, type=str, help="Path to fasta file.")
parser.add_argument('-o', dest="output", required=True, type=str, help="Name base and path for output")
args = parser.parse_args()
blocks_out = open(args.output + ".supertranscripts.blocks.gtf", "w")
fasta_out = open(args.output + ".supertranscripts.fasta", "w")
transcripts_out = open(args.output + ".supertranscripts.transcripts.gtf", "w")
translation_table = string.maketrans("ATCGatcg", "TAGCtagc")
seq = fasta_input(args.fasta)
i = 0
starts = {}
ends = {}
previous_contig = ""
transcript_ids = []
orientations = []
current_transcript = ""
current_gene_id = ""
if args.gtf:
with open(args.gtf, "r") as annot:
for l in annot:
if l[0] == "#":
continue
line = l.rstrip().split("\t")
if line[2] == "exon":
fields = line[8].lstrip().split("; ")
current_transcript = ""
for f in fields:
if "gene_id" in f:
if f.split(" ")[1] != current_gene_id:
if current_gene_id:
make_supertranscript(seq, previous_contig, translation_table, blocks_out, fasta_out, transcripts_out, current_gene_id, starts, ends, transcript_ids, orientations)
current_gene_id = f.split(" ")[1]
i = 0
starts = {}
ends = {}
previous_contig = line[0]
transcript_ids = []
orientations = []
if "transcript_id" in f:
current_transcript = f.split(" ")[1]
if int(line[3]) not in starts:
starts[int(line[3])] = []
starts[int(line[3])].append(i)
if int(line[4]) not in ends:
ends[int(line[4])] = []
ends[int(line[4])].append(i)
i += 1
transcript_ids.append(current_transcript.replace("\"", ""))
orientations.append(line[6])
make_supertranscript(seq, previous_contig, translation_table, blocks_out, fasta_out, transcripts_out, current_gene_id, starts, ends, transcript_ids, orientations)
elif args.gff3:
to_parents = {}
with open(args.gff3, "r") as annot:
for l in annot:
if l[0] == "#":
continue
line = l.rstrip().split("\t")
if "Parent" in line[8]:
fields = line[8].lstrip().split(";")
for f in fields:
if "ID=" in f:
current_id = f.split("=")[1]
elif "Parent=" in f:
parents = f.split("=")[1].split(",")
current_n_parents = len(parents)
if current_id not in to_parents:
to_parents[current_id] = parents
if line[2] == "exon":
for f in fields:
# if "gene_id" in f:
# if f.split(" ")[1] != current_gene_id:
if to_parents[parents[0]][0] != current_gene_id:
if current_gene_id:
make_supertranscript(seq, previous_contig, translation_table, blocks_out, fasta_out, transcripts_out, current_gene_id, starts, ends, transcript_ids, orientations)
current_gene_id = to_parents[parents[0]][0]
i = 0
starts = {}
ends = {}
previous_contig = line[0]
transcript_ids = []
orientations = []
if int(line[3]) not in starts:
starts[int(line[3])] = []
if int(line[4]) not in ends:
ends[int(line[4])] = []
for j in xrange(current_n_parents):
starts[int(line[3])].append(i)
ends[int(line[4])].append(i)
i += 1
orientations.append(line[6])
transcript_ids.extend(to_parents[current_id])
make_supertranscript(seq, previous_contig, translation_table, blocks_out, fasta_out, transcripts_out, current_gene_id, starts, ends, transcript_ids, orientations)
seq.finalize()
if __name__ == "__main__":
main()
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