fasta-decoy.pl - decoy input databanks following several moethods
Reads input fasta file and produce a decoyed databank with several methods:
#reverse sequences for a local (optionaly compressed) file fasta-decoy.pl --in=/tmp/uniprot_sprot.fasta.gz --method=reverse #download databanks from the web | uncompress it and shuffle the sequence wget -silent -O - ftp://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz | zcat | databatanks-decoy.pl --method=shuffle #use a .dat file (with splice forms) as an input uniprotdat2fasta.pl --in=uniprot_sprot_human.dat | fasta-decoy.pl --method=markovmodel #reversing each sequence fasta-decoy.pl --ac-prefix=DECOY_ --in=mitoch.fasta --method=reverse --out=mitoch-reverse.fasta #drawing amino acid following distribution in original fasta (end of sequence is considered as a learned random event) fasta-decoy.pl --ac-prefix=DECOY_ --in=mitoch.fasta --method=markovmodel --markovmodel-level=0 --out=mitoch-markovmodel_0.fasta #drawing amino acid with a markov model (here of length 3) fasta-decoy.pl --ac-prefix=DECOY_ --in=mitoch.fasta --method=markovmodel --markovmodel-level=3 --out=mitoch-markovmodel_3.fasta #each sequence is randomly shuffled fasta-decoy.pl --ac-prefix=DECOY_ --in=mitoch.fasta --method=shuffle --out=mitoch-shuffle.fasta #idem, but no tryptic peptide (of length>=6) from the original bank must be found in the random one; => see script fasta-shuffle-notryptic.pl
An input fasta file (will be uncompressed if ending with gz)
A .fasta file [default is stdout]
Set the decoying method
Set a key to be prepended before the AC in the randomized bank. By default, it will be dependent on the choosen method.
Set length of the model (0 means only AA distrbution will be respected, 3 means chains of length 3 distribution etc.). Setting a length >3 can deal to memory burnout.
Random generator seed is set to 0, so 2 run on same data will produce the same result
do not display terminal progress bar (if possible)
Setting an environment variable DO_NOT_DELETE_TEMP=1 will keep the temporay file after the script exit
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
Alexandre Masselot, www.genebio.com
To install InSilicoSpectro::Databanks, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro::Databanks
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro::Databanks
For more information on module installation, please visit the detailed CPAN module installation guide.