Inferelator-Prior Network Generation Tool
Project description
inferelator-prior
This is a set of pipelines to create expression and prior matrices for network inference. They are designed to create data that is compatible with the inferelator package.
Usage
python -m inferelator_prior.network_from_motifs
usage: network_from_motifs.py --motif motif_PWM_file.meme
-f genome_fasta_file.fasta
-g genome_annotation_file.gtf
-o ~/output/path/prefix
--species {yeast,fly,mouse,human}
-b constraning_bed_file.bed
--cpu num_cores
This requires a motif PWM database (-m PATH
),
a genome to search (both sequence as a FASTA -f PATH
and annotations -g PATH
),
and an output prefix for several files (-o PATH
).
In addition, default settings for a specific species can be set with (--species
).
A BED file can be provided (-b PATH
) based on some constraining experiment to restrict searching to specific genomic areas.
This will use multiple cores to search for motifs and process the resulting data.
By default, all available processors will be used, but this can be overridden with --cpu N
.
Requirements
In addition to python dependencies, this package also requires STAR, sra-tools, bedtools, samtools, and fimo.
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