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#!/usr/bin/env python3
import os
import logging
from collections import Counter
import gffutils
from gffutils.create import logger
logger.setLevel(logging.INFO)
usage = """
Converts a GFF file downloaded from FlyBase into a GTF file suitable for
use with Cufflinks. Support for ignoring chromosomes, featuretypes, and
fixing various issues with the original GFF file.
"""
def read_ignore_list(fn):
"""
Converts a file into a list
"""
return [i.strip() for i in open(fn) if not i.startswith("#")]
def clean_gff(
gff, cleaned, add_chr=False, chroms_to_ignore=None, featuretypes_to_ignore=None
):
"""
Cleans a GFF file by removing features on unwanted chromosomes and of
unwanted featuretypes. Optionally adds "chr" to chrom names.
"""
logger.info("Cleaning GFF")
chroms_to_ignore = chroms_to_ignore or []
featuretypes_to_ignore = featuretypes_to_ignore or []
with open(cleaned, "w") as fout:
for i in gffutils.iterators.DataIterator(gff):
if add_chr:
i.chrom = "chr" + i.chrom
if i.chrom in chroms_to_ignore:
continue
if i.featuretype in featuretypes_to_ignore:
continue
fout.write(str(i) + "\n")
return cleaned
if __name__ == "__main__":
import argparse
ap = argparse.ArgumentParser(usage=usage)
ap.add_argument(
"--gff",
help="""GFF file downloaded from FlyBase. Not
required if --db already exists""",
)
ap.add_argument(
"--db",
required=True,
help="""Database that will be
created from FlyBase GFF""",
)
ap.add_argument(
"--gtf",
required=True,
help="""GTF file that will
be created""",
)
ap.add_argument(
"--featuretype-ignore",
help="""File containing the
featuretypes to ignore in the GFF file, one featuretype on
each line. This can speed up processing dramatically""",
)
ap.add_argument(
"--chrom-ignore",
help='''File containing chromosomes to
ignore in the GFF file. If --add-chr, then chromosomes in
this list should also have "chr"''',
)
ap.add_argument(
"--add-chr",
action="store_true",
help="""Prepend a "chr"
to chromosome names""",
)
ap.add_argument(
"--fix-strand",
action="store_true",
help="""When exporting
the GTF file, check to ensure that all exons of a gene have
the same strand. If not, then issue a warning and fix them
so that they all have the most common strand across all the
gene's exons.""",
)
ap.add_argument(
"--fix-extent",
choices=["gene", "exon"],
help="""When
exporting the GTF file, check that all exons fall within
the gene's annotated extent. If not, then issue a warning,
and, if --fix-extent=gene, then assume the gene annotation
is correct; if --fix-extent=exon then assume the exon
annotations are correct and make no changes to the exported
exons""",
)
args = ap.parse_args()
if args.gff:
chroms_to_ignore = []
if args.chrom_ignore:
chroms_to_ignore = read_ignore_list(args.chrom_ignore)
featuretypes_to_ignore = []
if args.featuretype_ignore:
featuretypes_to_ignore = read_ignore_list(args.featuretype_ignore)
cleaned = clean_gff(
args.gff,
args.gff + ".cleaned",
add_chr=args.add_chr,
chroms_to_ignore=chroms_to_ignore,
featuretypes_to_ignore=featuretypes_to_ignore,
)
db = gffutils.create_db(
args.gff + ".cleaned", args.db, verbose=True, id_spec=["ID"], force=True
)
db = gffutils.FeatureDB(args.db)
logger.info("Creating GTF file")
with open(args.gtf, "w") as fout:
for gene in db.features_of_type("gene"):
gene_id = gene.id
transcripts = []
exons = []
for child in db.children(gene, level=1):
transcript_id = child.id
transcripts.append(child)
for grandchild in db.children(child, level=1):
if grandchild.featuretype not in ["exon", "CDS"]:
continue
exons.append(grandchild)
if args.fix_strand:
c = Counter([i.strand for i in exons])
if len(c) > 1:
# Exons have inconsistent strands. So assume the most
# common strand is the "true" strand to use.
most_common = c.most_common()
new_strand = most_common[0][0]
logger.warning(
"Gene %s has inconsistent strands: %s. "
'Changing all exons to "%s" strand'
% (gene_id, most_common, new_strand)
)
new_exons = []
for exon in exons:
exon.strand = new_strand
new_exons.append(exon)
exons = new_exons
if args.fix_extent:
if len(exons) > 0:
exon_extent = [
min(i.start for i in exons),
max(i.stop for i in exons),
]
gene_extent = [gene.start, gene.stop]
if exon_extent != gene_extent:
logger.warning(
"Exons of gene %s do not match gene annotation. "
"Gene extent: %s. Exon extent: %s"
% (gene_id, exon_extent, gene_extent)
)
if args.fix_extent == "gene":
new_exons = sorted(exons, key=lambda x: x.start)
new_exons[0].start = gene.start
new_exons[-1].stop = gene.stop
exons = new_exons
for exon in exons:
fields = str(grandchild).split("\t")[:-1]
attributes = (
'gene_id "{0}"; transcript_id "{1}"; '
'gene_name "{2}" transcript_type="{3}"'
).format(
gene_id,
transcript_id,
gene.attributes["Name"][0],
child.featuretype,
)
fields.append(attributes)
fout.write("\t".join(fields) + "\n")
logger.info("Wrote %s" % args.gtf)
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