Introduction
The bioinformatics core facility has various scripts
availible which have been written by local users. The
following is a brief listing and details on how to use them.
The scripts are located in a shared directory, so they can
be used directly from the command line (no need to copy them
anywhere) from any of the facilities Debian Linux computers.
Most of these scripts allow their input/output to be either
standard in, standard out and/or a file. They all have a
--help option to view a full listing of all options. Type
the command name followed by --help at the command line.
alignconv
| Description |
This script allows easy conversion from one alignment
file format to another. The formats supported (through
the use of BioPerl) are: bl2seq, clustalw, emboss,
fasta, mase, mega, meme, metafasta, msf, nexus, pfam,
phylip, prodom, psi, selex, and stockholm.
|
| Usage |
alignconv [options] informat outformat |
fafetch
| Description |
This script will fetch a sequence from a fasta index
file (created by faindex).
|
| Usage |
fafetch [options] accession1 ... |
faindex
| Description |
This script will create a fasta index file from any
number of sequence files. This index file can then be
used to quickly retrieve files using the fafetch script.
|
| Usage |
faindex [options] file1 file2 ... fileN |
gbfetch
| Description |
This script will fetch a sequence from a GenBank index
file (created by gbindex).
|
| Usage |
gbfetch [options] accession1 accession2 ... |
gbindex
| Description |
This script will create a GenBank index file from any
number of sequence files. This index file can then be
used to quickly retrieve files using the gbfetch script.
|
| Usage |
gbindex [options] file1 ... |
seqconv
| Description |
seqconv will convert sequences from any BioPerl
supported format to any other. Some formats do not
support writing. The formats supported are: abi, ace,
alf, bsml, chado, chadoitext, chadosxpr, chadoxml, ctf,
embl, exp, fasta, fastq, game, gcg, genbank, largefasta,
lucuslink, metafasta, phd, pir, pln, qual, raw, scf,
swiss, tab, tigr, ztr.
|
| Usage |
seqconv [options] informat outformat |
seqsplit
| Description |
seqplit will split large sequence files into smaller
sequence files. No sequence format conversion is done,
however you might try: seqconv GenBank Fasta <
myseq.gb | seqsplit -f Fasta -l 10 -s 3 myseq- to split
a genbank file named myseq.gb into many smaller fasta
formated files called myseq-000, myseq-001, ...
|
| Usage |
seqsplit [options] prefix |
|