order_fastx

order_fastx

order_fastx.pl is a script to order sequences in FASTA or FASTQ files.

• Synopsis
• Description
• Usage
• Options
  • Mandatory options
  • Optional options
• Output
• Run environment
• Author - contact
• Citation, installation, and license
• Changelog

Synopsis

perl order_fastx.pl -i infile.fasta -l order_id_list.txt > ordered.fasta

Description

Order sequence entries in FASTA or FASTQ sequence files according to an ID list with a given order. Beware, the IDs in the order list have to be identical to the entire IDs in the sequence file.

However, the ">" or "@" ID identifiers of FASTA or FASTQ files, respectively, can be omitted in the ID list.

The file type is detected automatically. But, you can set the file type manually with option -f. FASTQ format assumes four lines per read, if this is not the case run the FASTQ file through fastx_fix.pl or use Heng Li's seqtk seq:

seqtk seq -l 0 infile.fq > outfile.fq

The script can also be used to pull a subset of sequences in the ID list from the sequence file. Probably best to set option flag -s in this case, see Optional options below. But, rather use filter_fastx.pl.

Usage

perl order_fastx.pl -i infile.fq -l order_id_list.txt -s -f fastq > ordered.fq

perl order_fastx.pl -i infile.fasta -l order_id_list.txt -e > ordered.fasta

Options

Mandatory options

• -i, -input

  Input FASTA or FASTQ file

• -l, -list

  List with sequence IDs in specified order

Optional options

• -h, -help

  Help (perldoc POD)

• -f, -file_type

  Set the file type manually [fasta|fastq]

• -e, -error_files

  Write missing IDs in the seq file or the order ID list without an equivalent in the other to error files instead of STDERR (see Output below)

• -s, -skip_errors

  Skip missing ID error statements, excludes option -e

• -v, -version

  Print version number to STDERR

Output

• STDOUT

  The newly ordered sequences are printed to STDOUT. Redirect or pipe into another tool as needed.

• (order_ids_missing.txt)

  If IDs in the order list are missing in the sequence file with option -e

• (seq_ids_missing.txt)

  If IDs in the sequence file are missing in the order ID list with option -e

Run environment

The Perl script runs under Windows and UNIX flavors.

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Citation, installation, and license

For citation, installation, and license information please see the repository main README.md.

Changelog

• v0.1 (20.11.2014)