any2fasta
convert various sequence formats to FASTA
Command lineScience
Not tested on a device yet. What that means
Commands in the package
any2fasta
About any2fasta
From Debian's package description
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
From Debian's description of the any2fasta package, under that package's license.
Dependencies
Depends on
Related apps
- conda-package-handlingcreate and extract conda packages of various formatsCommand line
- seqtkFast and lightweight tool for processing sequences in the FASTA or FASTQ formatCommand line
- gffreadGFF/GTF format conversions, region filtering, FASTA sequence extractionCommand line
- last-aligngenome-scale comparison of biological sequencesCommand line
- readseqConversion between sequence formatsCommand line
- pyfastxfast random access to sequences from FASTA/Q file - commandCommand line
Sources and licenses
- Name: the Debian package name.
- Summary: Debian's short description of the any2fasta package, under that package's license.
- Description: Debian's description of the any2fasta package, under that package's license.
- Versions and sizes: Debian's archive for ARM64, as on packages.debian.org.
- Popularity: Debian Popularity Contest counts.
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