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9274888 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 | defined_as: dataloader.SeqDataset
args:
intervals_file:
doc: bed3 file with `chrom start end id score strand`
example: example_files/intervals.tsv
fasta_file:
doc: Reference genome sequence
example: example_files/hg38_chr22.fa
target_file:
doc: path to the targets (.tsv) file
optional: True
use_linecache:
doc: if True, use linecache https://docs.python.org/3/library/linecache.html to access bed file rows
optional: True
info:
authors:
- name: Lara Urban
github: LaraUrban
- name: Ziga Avsec
github: avsecz
doc: Dataloader for the DeepSEA model.
dependencies:
conda:
- python
- numpy
- pandas
- cython
pip:
- cython
- pybedtools
output_schema:
inputs:
name: input
shape: (1000, 4)
special_type: DNASeq
doc: DNA sequence
associated_metadata: ranges
targets:
name: epigen_mod
shape: (1, )
doc: Specific epigentic feature class (multi-task binary classification)
metadata:
ranges:
type: GenomicRanges
doc: Ranges describing inputs.seq
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