#fasta #fastq #list #regex #header #parses #records

app seqsplitter

Parses fasta records based on list of either header names or regexes

5 releases

0.1.4 Oct 3, 2022
0.1.3 Oct 3, 2022
0.1.2 Oct 3, 2022
0.1.1 Sep 20, 2022
0.1.0 Sep 20, 2022

#208 in Biology

Download history 2/week @ 2024-02-25 74/week @ 2024-03-10

76 downloads per month

MIT license

34KB
138 lines

Parses fasta records based on list of either header names or regexes

Installation

Source

Download the source code and run

cargo install

Usage

seqsplitter -f path/to/sequence.fastq -l path/to/list.txt

Arguments:

Parameter Default Description
-f --fasta - The path to the FASTQ file to use
-l --list - List of ids to parse out
-r --regex false Interpret list as regex
-u --assume_unique false Assume list is unique and exit when all seqs in list are found
-v --version - Print version information

Dependencies

~39MB
~783K SLoC