Alexandre Masselot > InSilicoSpectro-Databanks > fasta-shuffle-notryptic.pl

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NAME ^

  fasta-shuffle-notryptic.pl - shuffle each sequence, without any original tryptic peptide

DESCRIPTION ^

Reads input fasta file and produce a shuffle databank & avoid known cleaved peptides: shuffle sequence but avoid producing known tryptic peptides

SYNOPSIS ^

#shuffle each sequence fasta-shuffle-notryptic.pl --in=/tmp/uniprot_sprot.fasta

#to limit memory usage, one can use CRC code (--crcsize will ./fasta-shuffle-notryptic.pl --ac-prefix=DECOY_ --in=/home/alex/tmp/a.fasta --out=/tmp/a.fasta --crcsize=33 -v --norandom

ARGUMENTS ^

--in=infile.fasta

An input fasta file (will be uncompressed if ending with gz)

-out=outfile.fasta

A .fasta file [default is stdout]

OPTIONS ^

--ac-prefix=string

Set a key to be prepended before the AC in the randomized bank. By default, it will be dependent on the choosen method.

--peptminlength [default 6]

Set the size of the peptide to be reshuffled if they already exist

--crcsize=int

Building a hash of known cleaved peptide can be quite demanding for memory (uniprot_trembl => ~4GB). Therefore solution is to make an array containing statements if or not a peptide with corresponding crc code was found.

The argument passed here is the number of bits use for the CRC coding: 33 means 2^33 bit of memory => 2^30 bytes => 1GB

--norandomseed

Random generator seed is set to 0, so 2 run on same data will produce the same result

misc

--noprogressbar

do not display terminal progress bar (if possible)

--help

--man

--verbose

Setting an environment variable DO_NOT_DELETE_TEMP=1 will keep the temporay file after the script exit

EXAMPLE ^

COPYRIGHT ^

Copyright (C) 2004-2006 Geneva Bioinformatics www.genebio.com

This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details.

You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

AUTHORS ^

Alexandre Masselot, www.genebio.com

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