any2fasta 0.4.2-2 source package in Ubuntu
Changelog
any2fasta (0.4.2-2) unstable; urgency=medium * Standards-Version: 4.6.2 (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository-Browse. -- Andreas Tille <email address hidden> Sat, 07 Jan 2023 17:02:41 +0100
Upload details
- Uploaded by:
- Debian Med
- Uploaded to:
- Sid
- Original maintainer:
- Debian Med
- Architectures:
- all
- Section:
- misc
- Urgency:
- Medium Urgency
Downloads
| File | Size | SHA-256 Checksum |
|---|---|---|
| any2fasta_0.4.2-2.dsc | 2.0 KiB | 94f92599a37452d30d51ea50daf1d8894f33f86a619fd23531b11b8512376b1d |
| any2fasta_0.4.2.orig.tar.gz | 6.4 MiB | e4cb2ddccda6298f5b0aee0c10184a75307a08b584d2abbfbf0d59d37b197e73 |
| any2fasta_0.4.2-2.debian.tar.xz | 2.8 KiB | 3d1bb1c01bb1c6ef9013db82a63d67d344b43552aed60ae593466f25d1a9e905 |
Available diffs
- diff from 0.4.2-1 to 0.4.2-2 (878 bytes)
No changes file available.
Binary packages built by this source
- any2fasta: 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
- any2fasta-examples: convert various sequence formats to FASTA (example data)
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
.
This package contains some example data for testing.
