Description

Index a FASTx file using pyfastx to enable random access to a slice of reads in the file. Also returns the raw count of reads in the file.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

fastx (file)

FASTx file of reads to index

*.{fasta,fa,fasta.gz,fa.gz,fq,fq.gz}

Output

Name
Description
Pattern

index

meta (map)

Groovy Map containing sample information e.g. [ id:'sample1' ]

fastx (file)

FASTx file of reads to index

*.{fasta,fa,fasta.gz,fa.gz,fq,fq.gz}

*.fxi (file)

pyfastx-format FASTA index file

*.fxi

versions_slice_fasta

${task.process} (string)

The name of the process

slice_fasta.py (string)

The name of the tool

slice_fasta.py --version (eval)

The expression to obtain the version of the tool

Topics

Name
Description
Pattern

versions

${task.process} (string)

The name of the process

slice_fasta.py (string)

The name of the tool

slice_fasta.py --version (eval)

The expression to obtain the version of the tool

Tools

pyfastx Documentation

The pyfastx is a lightweight Python C extension that enables users to randomly access to sequences from plain and gzipped FASTA/Q files. This module aims to provide simple APIs for users to extract seqeunce from FASTA and reads from FASTQ by identifier and index number.

License: MIT
Pipelines with this module
asccgenomeassemblymetagenomeassembly
Authors