Metabolomics::Banks::PeakForest - Perl extension for PeakForest bank
Version 0.2 - supporting/integrating REST API V2 methods Version 0.3 - Completing object properties + GCMS bank generation Version 0.4 - Integration of deltaType
use Metabolomics::Banks::PeakForest;
Metabolomics::Banks::PeakForest is a full package for Perl allowing to build a generic Perl bank object from PeakForest bank resource.
use Metabolomics::Banks::PeakForest qw( :all ) ;
## Description : new ## Input : $self ## Ouput : bless $self ; ## Usage : new() ;
## Description : PRIVATE method __refpeakforestcompound__ object ## Input : void ## Output : __refpeakforestcompound__ ## Usage : $self->__refpeakforestcompound__ ;
## Description : PRIVATE method __refpeakforestspectra__ object ## Input : void ## Output : __refpeakforestspectra__ ## Usage : $self->__refpeakforestspectra__ ;
## Description : build a spectra bank from PeakForest matching REST API ## Input : ## Output : $oBank ## Usage : $oBank->buildSpectralBankFromPeakForest ( ) ;
## Description : get a peakforest compound by Id, based on REST API V2 ## Input : $cpdId ## Output : $oCpd ## Usage : my ( $oCpd ) = $self->_getCompoundFromId ($cpdId) ;
## Description : match a GC-MS spectra from a list of peaks, based on REST API V2 ## Input : $cpdId ## Output : $oSpectra ## Usage : my ( $oSpectra ) = $self->_getGcmsSpectraFromIds () ;
## Description : match a GC-MS spectra from a list of peaks, based on REST API V2 ## Input : $cpdId ## Output : $oSpectra ## Usage : my ( $oSpectra ) = $self->_getGcmsSpectraByMatchingPeaks () ;
## Description : Deprecated - initiate a peakforest query based on REST API V1 ## Input : $peakforestInstance ## Output : $query ## Usage : my ( $entriesNb ) = $self->initPeakForestQuery () ;
## Description : get the list of spectra entries from a peakforest instance and a mz range (min/max) based on REST API V1 ## Input : $oPeakForestQuery, $minMass, $maxMass ## Output : $Spectra ## Usage : my ( $Spectra ) = $oPeakForestQuery->getCleanRangeSpectraFromSource ( $minMass, $maxMass ) ;
## Description : Deprecated - building from a Metabolomics::Banks::PhytoHub object, a bank integrating each potential entry in a metabolomics format (POSITIVE or NEGATIVE forms) ## Input : $queryMode [POS|NEG] ## Output : int as $entryNb ## Usage : my $nb = $oBank->buildTheoPeakBankFromEntries() ;
## Description : init a new peakforest spectral entry ## Input : void ## Output : refEntry ## Usage : $self->__refPeakForestSpectralEntry__() ;
## Description : PRIVATE method _getEntry_INCHIKEY on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_INCHIKEY () ;
## Description : PRIVATE method _getEntry_SMILES on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_SMILES () ;
## Description : PRIVATE method _getEntry_MOLECULAR_FORMULA on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_MOLECULAR_FORMULA () ;
## Description : PRIVATE method _getEntry_EXACT_MASS on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_THEO_EXACT_MASS () ;
## Description : PRIVATE method _getEntry_EXACT_MASS on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_EXACT_MASS () ;
## Description : PRIVATE method _getEntry_DELTA_PPM on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_DELTA_PPM () ;
## Description : PRIVATE method _getEntry_RELATIVE_INTENSITY on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_RELATIVE_INTENSITY () ;
## Description : PRIVATE method _getEntry_COMPOUND_ID on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $PhytoHub_ID ) = $entry->_getEntry_COMPOUND_ID () ;
## Description : PRIVATE method _getEntry_SPECTRAL_ID on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $PhytoHub_ID ) = $entry->_getEntry_SPECTRAL_ID () ;
## Description : PRIVATE method _getEntry_COMPOUND_NAME on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_COMPOUND_NAME () ;
## Description : PRIVATE method _getEntry_MOLECULAR_COMPOSITION on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_MOLECULAR_COMPOSITION () ;
## Description : PRIVATE method _getEntry_PEAK_ATTRIBUTION on a refPeakForestSpectraEntry object ## Input : void ## Output : $VALUE ## Usage : my ( $VALUE ) = $entry->_getEntry_PEAK_ATTRIBUTION () ;
## Description : PRIVATE method _getSpectra_ID on a __refpeakforestspectra__ object ## Input : void ## Output : $VALUE ## Usage : my ( $ID ) = $spectrum->_getSpectra_ID () ;
## Description : PRIVATE method _getSpectra_PEAKS on a refPeakForestSpectra object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_PEAKS () ;
## Description : PRIVATE method _getSpectra_COMPOUNDS on a refPeakForestSpectra object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_COMPOUNDS () ;
## Description : PRIVATE method _getSpectra_SPECTRUM_NAME on a refPeakForestSpectra object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getSpectra_SPECTRUM_NAME () ;
## Description : PRIVATE method _getCpd_NAME on a refPeakForestCompound object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getCpd_NAME () ;
## Description : PRIVATE method _getCpd_INCHIKEY on a refPeakForestCompound object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getCpd_INCHIKEY () ;
## Description : PRIVATE method _getCpd_CAN_SMILES on a refPeakForestCompound object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getCpd_CAN_SMILES () ;
## Description : PRIVATE method _getCpd_FORMULA on a refPeakForestCompound object ## Input : void ## Output : $VALUES ## Usage : my ( $VALUES ) = $spectrum->_getCpd_FORMULA () ;
## Description : PRIVATE method _launchGenericRestQuery launch Rest queries and return json object ## Input : $QUERY ## Output : $JSON ## Usage : my ( $JSON ) = $self->_launchGenericRestQuery ($QUERY) ;
Franck Giacomoni, <franck.giacomoni at inrae.fr>
<franck.giacomoni at inrae.fr>
All information about Metabolomics::Banks::PeakForest would be find here: https://services.pfem.clermont.inra.fr/gitlab/fgiacomoni/metabolomics-fragnot
Please report any bugs or feature requests to bug-Metabolomics-Fragment-Annotation at rt.cpan.org, or through the web interface at https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
bug-Metabolomics-Fragment-Annotation at rt.cpan.org
You can find documentation for this module with the perldoc command.
perldoc Metabolomics::Fragment::Annotation
RT: CPAN's request tracker (report bugs here)
https://rt.cpan.org/Public/Dist/Display.html?Name=Metabolomics-Fragment-Annotation
AnnoCPAN: Annotated CPAN documentation
http://annocpan.org/dist/Metabolomics-Fragment-Annotation
CPAN Ratings
https://cpanratings.perl.org/d/Metabolomics-Fragment-Annotation
Search CPAN
https://metacpan.org/release/Metabolomics-Fragment-Annotation
Thank you to INRAE and All metabolomics colleagues.
CeCILL Copyright (C) 2019 by Franck Giacomoni
Initiated by Franck Giacomoni
followed by INRA PFEM team
Web Site = INRA PFEM
To install Metabolomics::Fragment::Annotation, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Metabolomics::Fragment::Annotation
CPAN shell
perl -MCPAN -e shell install Metabolomics::Fragment::Annotation
For more information on module installation, please visit the detailed CPAN module installation guide.