RNA-seq scripts and libraries
Project description
RNAseeker
RNA-seq scripts and libraries
Josh Tompkin
https://github.com/jtompkin/rnaseeker
Install with pip
pip3 install rnaseeker
Command line programs
- go_filter: Filter gProfiler output and format for Revigo
rnaseeker go-filter [-h] [-v] [-c TERM_COLUMN] [-d IN_DELIMITER] [-o OUT_FILE] [-p PVAL_COLUMN] [-i ID_COLUMN] [-s OUT_DELIMITER] [--no-format] [--header] [-f FILTER_TERMS] [--filter-file FILTER_PATH] gProfiler_file
- fasta_filter: Filter fasta sequences by length and 'N' content
rnaseeker fasta-filter [-h] [-o OUT_PATH] [-l LINE_LENGTH] fasta_path minimum_basepairs
- fasta_split: Split fasta/fastq files
rnaseeker fasta-split [-h] [-v] [-i INPUT] [-f {fasta,fastq}] [-s] [-p [PREFIX]] [--header-prefix [REGEX]] [-d DIRECTORY] [-e EXTENSION] number
Python libraries
- sequence
- sequence_io: Manipulate sequence files and store sequence information
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