Converts ms and msms peaklist from/to various formats. Formats can be specified or will hopefully be deduced from the files extensions
convertSpectra.pl --in=[format:]file --out=[format:]file
If no files are specified (thus the format must be) I/O are stdin/out.
Defined a default charge for the precursor (msms) of the peak (ms) (it might be overwritten if the input file definesit explicitely. The charge argument can be something like '1+', '1', '2,3', '2+ AND 3+' etc.
Will force the default charge defined into the file to be replaced
Allows for setting a title (one line text)
Allows for using a filter. See 'InSilicoSpectro/t/Spectra/Filter/examples.xml' for more information.
Set sample related info example 'instrument=QTOF;instrumentId=xyz'
turn 2+ and 3+ precursor into (2+ OR 3+)
(or similar) will attribute 1+=>1+, 2+=>2+ or 3+, 3+=>2+,3+ or 4+.
If for example i1=-1 and i2=2, precursor moz will be replicate with -1, +1 and +2 Dalton
Do not read msms or pmf information
Prints all the possible format for input
Prints all the possible format for output
report all possible input/ouput format + relative info (optional/compulsory arguements...)
activates a caching system for large files
./convertSpectra.pl --in=dta:somedir --out=somefile.idj.xml
Copyright (C) 2004-2005 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