[Debian-med-packaging] Bug#1023262: ITP: any2fasta -- convert various sequence formats to FASTA

[Andreas Tille]

Package: wnpp
Severity: wishlist

Subject: ITP: any2fasta -- convert various sequence formats to FASTA
Package: wnpp
Owner: Andreas Tille <tille at debian.org>
Severity: wishlist

* Package name    : any2fasta
  Version         : 0.4.2
  Upstream Author : Torsten Seemann
* URL             : https://github.com/tseemann/any2fasta
* License         : GPL-3+
  Programming Lang: (C, C++, C#, Perl, Python, etc.)
  Description     : convert various sequence formats to FASTA
 Established tools like readseq and seqret from EMBOSS, both create mangled
 IDs containing | or . characters, and there is no way to fix this behaviour.
 This resultes in inconsitences between .gbk and .fna versions of files in
 pipelines.
 .
 This script uses only core Perl modules, has no other dependencies like
 Bioperl or Biopython, and runs very quickly.
 .
 It supports the following input formats:
 .
  1. Genbank flat file, typically .gb, .gbk, .gbff (starts with LOCUS)
  2. EMBL flat file, typically .embl, (starts with ID)
  3. GFF with sequence, typically .gff, .gff3 (starts with ##gff)
  4. FASTA DNA, typically .fasta, .fa, .fna, .ffn (starts with >)
  5. FASTQ DNA, typically .fastq, .fq (starts with @)
  6. CLUSTAL alignments, typically .clw, .clu (starts with CLUSTAL or MUSCLE)
  7. STOCKHOLM alignments, typically .sth (starts with # STOCKHOLM)
  8. GFA assembly graph, typically .gfa (starts with ^[A-Z]\t)
 .
 Files may be compressed with:
 .
  1. gzip, typically .gz
  2. bzip2, typically .bz2
  3. zip, typically .zip

Remark: This package is maintained by Debian Med Packaging Team at
   https://salsa.debian.org/med-team/any2fasta