Alexandre Masselot
and 1 contributors

NAME

convertSpectra.pl

DESCRIPTION

Converts ms and msms peaklist from/to various formats. Formats can be specified or will hopefully be deduced from the files extensions

SYNOPSIS

convertSpectra.pl --in=[format:]file --out=[format:]file

ARGUMENTS

-in=[format:]file

If the format is not idj, this parameter can be repeated

-out=[format:]file

If no files are specified (thus the format must be) I/O are stdin/out.

OPTIONS

--defaultcharge=charge

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.

--forcedefaultcharge

Will force the default charge defined into the file to be replaced

--title=string

Allows for setting a title (one line text)

--filter=file

Allows for using a filter. See 'InSilicoSpectro/t/Spectra/Filter/examples.xml' for more information.

--sampleinfo='name1=val1[;name2=val2[...]]'

Set sample related info example 'instrument=QTOF;instrumentId=xyz'

--trustprecursorcharge=medium

turn 2+ and 3+ precursor into (2+ OR 3+)

--trustprecursorcharge=1:1/2:2,3/3:2,3,4

(or similar) will attribute 1+=>1+, 2+=>2+ or 3+, 3+=>2+,3+ or 4+.

--duplicateprecursormoz=i1:i2

If for example i1=-1 and i2=2, precursor moz will be replicate with -1, +1 and +2 Dalton

--skip=[msms|pmf]

Do not read msms or pmf information

--showinputformats

Prints all the possible format for input

--showoutputformats

Prints all the possible format for output

--showformats=(xml|json)
--showdef=[xml|json]

report all possible input/ouput format + relative info (optional/compulsory arguements...)

--propertiessave=file
--propertiesprefix=string
--usefilecaching

activates a caching system for large files

--version
--help
--man
--verbose

EXAMPLE

./convertSpectra.pl --in=dta:somedir --out=somefile.idj.xml

COPYRIGHT

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

AUTHORS

Alexandre Masselot, www.genebio.com