Package: wnpp Severity: wishlist Subject: ITP: any2fasta -- convert various sequence formats to FASTA Package: wnpp Owner: Andreas Tille <ti...@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
