rnaseeker

Name	rnaseeker JSON
Version	1.0.0 JSON
	download
home_page	https://github.com/jtompkin/rnaseeker
Summary	RNA-seq scripts and libraries
upload_time	2024-01-29 04:13:12
maintainer
docs_url	None
author	Josh Tompkin
requires_python	>=3.7
license	MIT
keywords	rna rnaseq dna fasta fastq bio gene
VCS
bugtrack_url
requirements	No requirements were recorded.
Travis-CI	No Travis.
coveralls test coverage	No coveralls.

            # RNAseeker

## RNA-seq scripts and libraries

Josh Tompkin

<jtompkin-dev@proton.me>

<https://github.com/jtompkin/rnaseeker>

### Install with pip

```bash
pip3 install rnaseeker
```

### Command line programs

- go_filter: Filter gProfiler output and format for Revigo

```bash
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

```bash
rnaseeker fasta-filter [-h] [-o OUT_PATH] [-l LINE_LENGTH] fasta_path minimum_basepairs
```

- fasta_split: Split fasta/fastq files

```bash
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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