InSilicoSpectro::Spectra::MSMSSpectra
#set new spectra with source my $sp=InSilicoSpectro::Spectra::MSSpectra->new({source=>$file}); #if the format cannot (or may not) be deduced from the file name, we can set it $sp->format('dta'); $sp->open();
#convert into another format $sp->write('idj', "/tmp/a.idj.xml");
General framework for MS/MS spectra.
This mainly means:
returns the list of data format with available read handlers (known type for input).
returns the list of data format with available write handlers (known type for ouput).
Arguments are through a hash (see $sp->set($name, $val) method.
Set an instance paramter, name can be
the source file (or directory, for .dta)
input data format such as 'mgf', 'pkl', 'dta', 'idj.xml'.
sampling info. $val is either a reference to a hash, or a string such as 'tag1=value1;tag2=value' (ex='intrument=LCQ;instrumentID=xyz'). Setting sampleInfo will erase the former value (consider $sp->addSampleInfoTag($name, $value) instead;
Get an instance parameter.
Returns the number of compounds
header line format is [M+H]+ charge
rem: native dta contains only one ms/ms spectrum. dtas can be concatenated, separated by one blank line
header line format is m/z intensity charge
if true, spectra with same framgementa data and coherent precursor info but diferent charges will be merged into one multiple-charge spectrum. [default=1];
set lib/Phenyx/Spectra/test directory
InSilicoSpectro::Spectra::MSSpectra InSilicoSpectro::Spectra::MSMSCmpd, Phenyx::Config::GlobalParam
Copyright (C) 2004-2007 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, Pierre-Alain Binz, www.genebio.com
To install InSilicoSpectro, copy and paste the appropriate command in to your terminal.
cpanm
cpanm InSilicoSpectro
CPAN shell
perl -MCPAN -e shell install InSilicoSpectro
For more information on module installation, please visit the detailed CPAN module installation guide.