def nb_transcripts(inputfile=None,
outputfile=None,
text_format=False,
key_name=""):
"""
Compute the number of transcript per gene.
"""
gtf = GTF(inputfile)
message("Computing the number of transcript per gene in input GTF file.")
# Computation of transcript number is performed on exon lines
# Just in case some transcript lines would be lacking (but they should
# not...)
n_tx = gtf.get_gn_to_tx()
if not text_format:
tmp_file = make_tmp_file(prefix="nb_tx", suffix=".txt")
for i in n_tx:
if not text_format:
tmp_file.write(i + "\t" + str(len(n_tx[i])) + "\n")
else:
outputfile.write(i + "\t" + str(len(n_tx[i])) + "\n")
if not text_format:
tmp_file.close()
gtf.add_attr_from_file(feat="gene",
key="gene_id",
new_key=key_name,
inputfile=tmp_file.name).write(outputfile,
gc_off=True)
close_properly(outputfile, inputfile)
def tss_numbering(inputfile=None,
outputfile=None,
compute_dist=False,
key_name='tss_number',
key_name_dist='dist_to_first_tss',
add_nb_tss_to_gene=False,
gene_key='nb_tss'):
"""
Computes the distance between TSS of gene transcripts.
"""
gtf = GTF(inputfile, check_ensembl_format=True)
gn_tss_dist = defaultdict(dict)
message("Getting TSSs.")
tss = gtf.get_tss(name=["transcript_id"], as_dict=True)
tx_to_gn = gtf.get_tx_to_gn()
for k in tss:
gn_id = tx_to_gn[k]
gn_tss_dist[gn_id][k] = int(tss[k])
# if_dict_of_dict is true, get_gn_to_tx() returns a dict of dict
# that maps gene_id to transcript_id and transcript_id to TSS
# numbering (1 for most 5', then 2...). For transcripts having
# the same TSSs, the tss number will be the same.
gn_to_tx_to_tss = gtf.get_gn_to_tx(as_dict_of_dict=True)
message("Numbering TSSs.")
tss_number_file = make_tmp_file(prefix='tx_to_tss_number', suffix='.txt')
gn_how_many_tss = dict()
for gn_id in gn_to_tx_to_tss:
for tx_id in gn_to_tx_to_tss[gn_id]:
tss_num = str(gn_to_tx_to_tss[gn_id][tx_id])
tss_number_file.write(tx_id + "\t" + tss_num + "\n")
if gn_id not in gn_how_many_tss:
gn_how_many_tss[gn_id] = tss_num
else:
if int(tss_num) > int(gn_how_many_tss[gn_id]):
gn_how_many_tss[gn_id] = tss_num
tss_number_file.close()
gtf = gtf.add_attr_from_file(feat='transcript',
key='transcript_id',
new_key=key_name,
inputfile=open(tss_number_file.name),
has_header=False)
if add_nb_tss_to_gene:
gn_how_many_tss_file = make_tmp_file(prefix='gn_how_many_tss',
suffix='.txt')
for a_key, a_val in gn_how_many_tss.items():
gn_how_many_tss_file.write(a_key + "\t" + a_val + "\n")
gn_how_many_tss_file.close()
gtf = gtf.add_attr_from_file(feat='gene',
key='gene_id',
new_key=gene_key,
inputfile=open(gn_how_many_tss_file.name),
has_header=False)
if compute_dist:
gn_to_tx_ordered_by_tss = gtf.get_gn_to_tx(ordered_5p=True)
tss_dist_file = make_tmp_file(prefix='tx_tss_dist_to_first_tss',
suffix='.txt')
for gn_id in gn_to_tx_to_tss:
tx_list = gn_to_tx_ordered_by_tss[gn_id]
tx_first = tx_list.pop(0)
# The first tss as distance 0 to the
# first tss...
tss_dist_file.write(tx_first + "\t0\n")
for tx_id in tx_list:
dist_to_first = abs(int(tss[tx_first]) - int(tss[tx_id]))
tss_dist_file.write(tx_id + "\t" + str(dist_to_first) + "\n")
tss_dist_file.close()
gtf = gtf.add_attr_from_file(feat='transcript',
key='transcript_id',
new_key=key_name_dist,
inputfile=open(tss_dist_file.name),
has_header=False)
gtf.write(outputfile, gc_off=True)
close_properly(outputfile, inputfile)
def join_attr(inputfile=None,
outputfile=None,
join_file=None,
has_header=False,
new_key=None,
target_feature=None,
key_to_join=None,
matrix=None):
"""
Join attributes from a tabulated file.
"""
# -----------------------------------------------------------
# Check argument consistency
# -----------------------------------------------------------
if matrix is True:
if new_key is not None:
message("--new-key and --matrix are mutually exclusive.",
type="ERROR")
else:
if new_key is None:
message("--new-key is required when --matrix is False.",
type="ERROR")
# -----------------------------------------------------------
# load the GTF
# -----------------------------------------------------------
gtf = GTF(inputfile, check_ensembl_format=False)
# -----------------------------------------------------------
# Check target feature
# -----------------------------------------------------------
feat_list = gtf.get_feature_list(nr=True)
if target_feature is not None:
target_feature_list = target_feature.split(",")
for i in target_feature_list:
if i not in feat_list + ["*"]:
message("Feature " + i + " not found.", type="ERROR")
else:
target_feature = ",".join(feat_list)
# -----------------------------------------------------------
# Do it
# -----------------------------------------------------------
if not matrix:
gtf = gtf.add_attr_from_file(feat=target_feature,
key=key_to_join,
new_key=new_key,
inputfile=join_file.name,
has_header=has_header)
gtf.write(outputfile, gc_off=True)
else:
gtf = gtf.add_attr_from_matrix_file(feat=target_feature,
key=key_to_join,
inputfile=join_file.name)
gtf.write(outputfile, gc_off=True)
gc.disable()
close_properly(outputfile, inputfile)
