def get_tx_seq(inputfile=None,
outputfile=None,
genome=None,
with_introns=False,
delete_version=False,
del_chr=False,
separator="",
no_rev_comp=False,
label="",
sleuth_format=True,
explicit=True,
assembly="bla"):
"""
Description: Get transcripts sequences in fasta format from a GTF file.
"""
# -----------------------------------------------------------
# Check chromosomes in fasta file
# -----------------------------------------------------------
genome_chr_list = []
message("%d fasta files found." % len(genome))
as_gz_ext = [True for x in genome if x.name.endswith(".gz")]
if any(as_gz_ext):
message("Genome in gz format is not currently supported.",
type="ERROR")
if len(genome) == 1:
message("Checking fasta file chromosome list")
genome = genome[0]
with genome as genome_file:
for i in genome_file:
if i.startswith(">"):
i = i.rstrip("\n")
genome_chr_list += [i[1:]]
else:
message("Merging fasta files")
tmp_genome = make_tmp_file(prefix="genome", suffix=".fa")
with tmp_genome as tg:
for curr_file in genome:
message("Merging %s" % curr_file.name)
with curr_file as cf:
shutil.copyfileobj(cf, tg, 1024 * 1024 * 100)
message("Checking fasta file chromosome list")
genome = open(tmp_genome.name, "r")
with genome as genome_file:
for i in genome_file:
if i.startswith(">"):
i = i.rstrip("\n")
genome_chr_list += [i[1:]]
rev_comp = not no_rev_comp
message("Chromosomes in fasta file: " + ",".join(genome_chr_list))
# -----------------------------------------------------------
# Read gtf
# -----------------------------------------------------------
gtf = GTF(inputfile)
nb_tx_before = gtf.extract_data("transcript_id",
as_list=True,
no_na=True,
nr=True)
# -----------------------------------------------------------
# Select genes falling in chrom defined in the fasta file
# -----------------------------------------------------------
message("Chromosomes in gtf file: " + ",".join(gtf.get_chroms(nr=True)))
message("Selecting chromosome defined in the fasta file")
gtf = gtf.select_by_key(key="seqid", value=",".join(genome_chr_list))
message("Chromosomes in gtf file: " + ",".join(gtf.get_chroms(nr=True)))
if len(gtf) == 0:
message("No genes were found on chromosomes defined in fasta file.",
type="ERROR")
nb_tx_after = gtf.extract_data("transcript_id",
as_list=True,
no_na=True,
nr=True)
if len(nb_tx_after) != len(nb_tx_before):
diff = list(set(nb_tx_before) - set(nb_tx_after))
message("Some transcripts had"
" no corresponding chromosome"
" in the fasta file: " + ",".join(diff)[0:100] + "...")
message("Using genome file: " + genome.name)
message("Retrieving fasta sequences from " + genome.name)
fasta_seq = gtf.get_sequences(genome=genome.name,
intron=with_introns,
rev_comp=rev_comp)
tx_gtf = gtf.select_by_key("feature", "transcript")
if sleuth_format:
tx_biotype = tx_gtf.extract_data("transcript_id,transcript_biotype",
as_dict_of_lists=True,
hide_undef=False)
gn_biotype = tx_gtf.extract_data("gene_id,gene_biotype",
as_dict_of_lists=True,
hide_undef=False)
for i in fasta_seq:
gene_id = i.gene_id
transcript_id = i.transcript_id
chrom = i.chrom
gn_bio = gn_biotype[i.gene_id][0]
tx_bio = tx_biotype[i.transcript_id][0]
if delete_version:
transcript_id = re.sub('\.[0-9]+$', '', transcript_id)
gene_id = re.sub('\.[0-9]+$', '', gene_id)
if del_chr:
chrom = chrom.replace('chr', '')
header = " ".join([
transcript_id, ":".join([
"chromosome", assembly, chrom,
str(i.start),
str(i.end), "1"
]), "gene:" + gene_id, "gene_biotype:" + gn_bio,
"transcript_biotype:" + tx_bio
])
outputfile.write(">" + header + "\n")
outputfile.write(i.sequence + "\n")
else:
tx_info = tx_gtf.extract_data("transcript_id," + label,
as_dict_of_lists=True,
hide_undef=False)
for i in fasta_seq:
if not explicit:
header = separator.join(tx_info[i.transcript_id])
else:
header = [
str(x[0]) + "=" + x[1]
for x in zip(label.split(","), tx_info[i.transcript_id])
]
header = separator.join(header)
outputfile.write(">" + header + "\n")
outputfile.write(i.sequence + "\n")
gc.disable()
close_properly(outputfile, inputfile)
def get_feat_seq(inputfile=None,
outputfile=None,
genome=None,
feature_type="exon",
separator="",
no_rev_comp=False,
label="",
rev_comp_to_header=False,
unique=False):
"""
Description: Get transcripts sequences in fasta format from a GTF file.
"""
# -------------------------------------------------------------------------
# Should sequences be reverse-complemented
# -------------------------------------------------------------------------
force_strandedness = not no_rev_comp
# -------------------------------------------------------------------------
# Check chrom to avoid segfault
# https://github.com/dputhier/libgtftk/issues/27
# -------------------------------------------------------------------------
if genome.name.endswith(".gz"):
message("Genome in gz format is not currently supported.",
type="ERROR")
genome_chr_list = []
message("Fasta files found: %s" % genome.name)
message("Checking fasta file chromosome list")
with genome as geno:
for i in geno:
if i.startswith(">"):
i = i.rstrip("\n")
genome_chr_list += [i[1:]]
gtf = GTF(inputfile, check_ensembl_format=False)
gtf_chr_list = gtf.get_chroms(nr=True)
# Check chrom to avoid segfault
# https://github.com/dputhier/libgtftk/issues/27
message("Comparing chromosomes from GTF and Fasta files.")
gtf_chr_list_found = [x for x in gtf_chr_list if x in genome_chr_list]
if len(gtf_chr_list_found) == 0:
message("Chromosome from GTF were not found in fasta file",
type="ERROR")
if len(gtf_chr_list_found) != len(gtf_chr_list):
not_found = [x for x in gtf_chr_list if x not in gtf_chr_list_found]
message("Some chromosomes were not found in the fasta file: %s" %
",".join(not_found),
type="ERROR")
# -------------------------------------------------------------------------
# Retrieving fasta sequences
#
# -------------------------------------------------------------------------
message("Retrieving fasta sequences.")
try:
# The nameOnly argument is not supported
# through all Bedtools versions
feat_seq = gtf.select_by_key("feature", feature_type).to_bed(
name=label.split(","),
sep=separator).sequence(fi=genome.name,
nameOnly=True,
s=force_strandedness)
except BEDToolsError:
feat_seq = gtf.select_by_key("feature", feature_type).to_bed(
name=label.split(","),
sep=separator).sequence(fi=genome.name,
name=True,
s=force_strandedness)
id_printed = set()
to_print = True
for _, line in enumerate(open(feat_seq.seqfn)):
if line.startswith(">"):
# This (+/-) may be added by pybedtool
# but can be accessed though --label
line = re.sub("\(\+\)$", "", line)
line = re.sub("\(\-\)$", "", line)
if rev_comp_to_header:
if force_strandedness:
line = line + separator + "rev_comp"
else:
line = line + separator + "no_rev_comp"
if unique:
if line in id_printed:
to_print = False
if to_print:
outputfile.write(line)
id_printed.add(line)
else:
if not to_print:
to_print = True
else:
outputfile.write(line)
gc.disable()
close_properly(outputfile, inputfile)
def shift(inputfile=None,
outputfile=None,
shift_value=None,
chrom_info=None,
stranded=False,
allow_outside=False):
"""Shift coordinates in 3' or 5' direction.
"""
gtf = GTF(inputfile, check_ensembl_format=False)
chrom_list_gtf = gtf.get_chroms(nr=True)
chrom_info = chrom_info_as_dict(chrom_info)
for chr in chrom_list_gtf:
if chr not in chrom_info:
raise GTFtkError("Chromosome " + chr +
" was not found in chrom-info file.")
for i in gtf:
size = i.end - i.start + 1
if not stranded:
new_start = i.start + shift_value
new_end = i.end + shift_value
else:
if i.strand == "-":
new_start = i.start - shift_value
new_end = i.end - shift_value
else:
new_start = i.start + shift_value
new_end = i.end + shift_value
# Feature is going outside genome in left direction
if not allow_outside:
if new_start < 1:
new_start = 1
new_end = size
# Feature is going outside genome in right direction
if new_end > int(chrom_info[i.chrom]):
new_end = int(chrom_info[i.chrom])
new_start = new_end - size + 1
else:
if new_start < 1:
new_start = 1
if new_end < 1:
new_end = None
# Feature is going outside genome in right direction
if new_end > int(chrom_info[i.chrom]):
new_end = int(chrom_info[i.chrom])
if new_start > int(chrom_info[i.chrom]):
new_start = None
if new_start is not None and new_end is not None:
i.start = new_start
i.end = new_end
i.write(outputfile)
gc.disable()
close_properly(outputfile, inputfile)