rnaseeker 1.0.0

RNA-seq scripts and libraries

RNAseeker

RNA-seq scripts and libraries

Josh Tompkin

[e-mail]

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