def select_by_key(inputfile=None,
outputfile=None,
key=None,
value=None,
invert_match=False,
file_with_values=None,
col=0,
select_transcripts=False,
select_genes=False,
select_exons=False,
select_cds=False,
select_start_codon=False,
bed_format=False,
log=False,
separator="|",
names="transcript_id"):
"""Select lines from a GTF file based on attributes and
associated values.
"""
# ----------------------------------------------------------------------
# Check mode
# ----------------------------------------------------------------------
if select_transcripts:
key = "feature"
value = "transcript"
elif select_cds:
key = "feature"
value = "CDS"
elif select_start_codon:
key = "feature"
value = "start_codon"
elif select_genes:
key = "feature"
value = "gene"
elif select_exons:
key = "feature"
value = "exon"
elif file_with_values is None:
if key is None or value is None:
message(
"Key and value are mandatory. Alternatively use -e/t/g/f or -f with -k.",
type="ERROR")
elif file_with_values is not None:
if key is None:
message("Please set -k.", type="ERROR")
if value is not None:
message("The -f and -v arguments are mutually exclusive.",
type="ERROR")
# ----------------------------------------------------------------------
# Load file with value
# ----------------------------------------------------------------------
gtf = GTF(inputfile, check_ensembl_format=False)
all_values = gtf.extract_data(key, as_list=True, no_na=True, nr=True)
if log:
feat_before = len(gtf)
if not file_with_values:
value_list = value.split(",")
gtf = gtf.select_by_key(key, value, invert_match)
else:
value_list = []
for line in file_with_values:
cols = line.split("\t")
value_list += [cols[col - 1]]
file_with_values.close()
file_with_values = open(file_with_values.name)
gtf = gtf.select_by_key(key=key,
invert_match=invert_match,
file_with_values=file_with_values,
col=col)
if log:
not_found = list(set(value_list) - set(all_values))
feat_after = len(gtf)
pct = feat_after / feat_before * 100
message("Number of features before selection: %d" % feat_before)
message("Fraction of feature selected: %.2f%%" % pct)
if len(not_found):
nfj = ",".join(not_found)
max_letter = min(len(nfj), 50)
if len(nfj) > 50:
etc = "..."
else:
etc = ""
message("Values not found: [" + ",".join(not_found)[:max_letter] +
etc + "].")
else:
message("Values not found: [].")
# ----------------------------------------------------------------------
# Write GTF file
# ----------------------------------------------------------------------
if not bed_format:
gtf.write(outputfile, gc_off=True)
else:
nb_tokens = len(names.split(","))
keys = "seqid,start,end," + names + ",score,strand"
nb_fields = len(keys.split(","))
for i in gtf.extract_data_iter_list(keys, zero_based=True):
outputfile.write("\t".join([
i[0],
i[1],
i[2],
separator.join(i[3:(3 + nb_tokens)]),
i[nb_fields - 2],
i[nb_fields - 1],
]) + "\n")
close_properly(outputfile, inputfile)
def splicing_site(inputfile=None,
outputfile=None,
exon_numbering_key=False,
names="exon_id,transcript_id,gene_id",
separator="\t"):
"""
Compute the locations of splice donor are acceptor sites. You may extend them in 3' and 5' depending on your needs.
"""
gtf = GTF(inputfile)
nb_exons = gtf.nb_exons()
info = "feature,seqid,start,end,transcript_id," + exon_numbering_key
info += ",strand," + names
exon_info = gtf.extract_data_iter_list(info)
for i in exon_info:
if i[0] == "exon":
if i[5] == ".":
message(
"Some exon lines do not contain any numbering. "
"Use add_exon_nb or set --exon-numbering-key to the proper key.",
type="ERROR")
if i[6] == "+":
if int(i[5]) < nb_exons[i[4]]:
out = [
i[1], i[3],
str(int(i[3]) + 1),
separator.join(["donor"] + i[7:]), i[5], i[6]
]
outputfile.write("\t".join(out) + "\n")
if int(i[5]) > 1:
out = [
i[1],
str(int(i[2]) - 2),
str(int(i[2]) - 1),
separator.join(["acceptor"] + i[7:]), i[5], i[6]
]
outputfile.write("\t".join(out) + "\n")
elif i[6] == "-":
if int(i[5]) > 1:
out = [
i[1], i[3],
str(int(i[3]) + 1),
separator.join(["acceptor"] + i[7:]), i[5], i[6]
]
outputfile.write("\t".join(out) + "\n")
if int(i[5]) < nb_exons[i[4]]:
out = [
i[1],
str(int(i[2]) - 2),
str(int(i[2]) - 1),
separator.join(["donor"] + i[7:]), i[5], i[6]
]
outputfile.write("\t".join(out) + "\n")
gc.disable()
close_properly(outputfile, inputfile)
