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if self.ignore_targets or self.n_tasks == 0:
labels = {}
else:
labels = row.iloc[self.bed_columns:].values.astype(
self.label_dtype)
return interval, labels
def __len__(self):
return len(self.df)
def get_targets(self):
return self.df.iloc[:, self.bed_columns:].values.astype(self.label_dtype)
@kipoi_dataloader(override={"dependencies": deps, 'info.authors': package_authors})
class StringSeqIntervalDl(Dataset):
"""
info:
doc: >
Dataloader for a combination of fasta and tab-delimited input files such as bed files. The dataloader extracts
regions from the fasta file as defined in the tab-delimited `intervals_file`. Returned sequences are of the type
np.array([str]).
args:
intervals_file:
doc: bed3+ file path containing intervals + (optionally) labels
example:
url: https://raw.githubusercontent.com/kipoi/kipoiseq/master/tests/data/intervals_51bp.tsv
md5: a76e47b3df87fd514860cf27fdc10eb4
fasta_file:
doc: Reference genome FASTA file path.
example:
continue
for exon in gtf_db.children(gene, featuretype='exon'):
isLast = False # track whether is last exon
if firstLastNoExtend:
if (gene.strand == "+" and exon.end == gene.end) or (gene.strand == "-" and exon.start == gene.start):
overhang = (overhang[0], 0)
isLast = True
elif (gene.strand == "+" and exon.start == gene.start) or (gene.strand == "-" and exon.end == gene.end):
overhang = (0, overhang[1])
exon = ExonInterval.from_feature(exon, overhang)
exon.isLast = isLast
overhang = default_overhang
yield exon
@kipoi_dataloader(override={"dependencies": deps, 'info.authors': package_authors})
class MMSpliceDl(SampleIterator):
"""
info:
doc: >
Dataloader for splicing models. With inputs as gtf annotation file and fasta file,
each output is an exon sequence with flanking intronic seuqences. Intronic sequnce
lengths specified by the users. Returned sequences are of the type np.array([str])
args:
gtf_file:
doc: file path; Genome annotation GTF file
example:
url: https://raw.githubusercontent.com/kipoi/models/master/MMSplice/tests/data/test.gtf
md5: b20607afe91ec20d6ee79ed95ab0e85b
fasta_file:
doc: Reference Genome sequence in fasta format
example: