Example program for retrieving general search information.
#!/usr/local/bin/perl ############################################################################## # file: resfile_info.pl # # 'msparser' toolkit # # Test harness / example code # ############################################################################## # COPYRIGHT NOTICE # # Copyright 1998-2010 Matrix Science Limited All Rights Reserved. # # # ############################################################################## # $Source: parser/examples/test_perl/resfile_info.pl $ # # $Author: villek@matrixscience.com $ # # $Date: 2018-07-30 16:23:53 +0100 $ # # $Revision: 1b450440f9c97e1e41d0fc6016a27d68951d4532 | MSPARSER_REL_2_8_1-0-gea32989045 $ # # $NoKeywords:: $ # ############################################################################## use strict; ############################################################################## use msparser; if (!defined($ARGV[0])) { die "Must specify results filename as parameter"; } my $file = new msparser::ms_mascotresfile($ARGV[0]); if ($file->isValid) { searchInformation($file); } ############################################################################## # searchInformation # # - parameter 0 ms_mascotresfile # # Display parameters from the ms_mascotresfile object. The functions # # anyPMF, anyMSMS, anySQ should normally be used in preference to isPMF etc # # because some people submit MSMS though the sequence query window etc. # ############################################################################## sub searchInformation { my ($resfile) = @_; my $fmt = "%-20s: %s\n"; print "Search information from ms_mascotresfile", "\n"; print "========================================", "\n"; printf $fmt, "Number of queries" , $resfile->getNumQueries(); printf $fmt, "Number of hits" , $resfile->getNumHits(); printf $fmt, "Number of sequences" , $resfile->getNumSeqs(); printf $fmt, "Sequences after tax" , $resfile->getNumSeqsAfterTax(); printf $fmt, "Number of residues" , $resfile->getNumResidues(); printf $fmt, "Execution time" , $resfile->getExecTime(); printf $fmt, "Date (seconds)" , $resfile->getDate(); # Let's jump through a few hoops to get the equivalent of a 'C' asctime call my ($sec, $min, $hour, $mday, $mon, $year, $wday, $yday, $isdst) = localtime($resfile->getDate); printf $fmt, "Date", sprintf("%s %s %d %02d:%02d:%02d %d", (qw(Sun Mon Tue Wed Thu Fri Sat))[$wday], (qw(Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec))[$mon], $mday, $hour, $min, $sec, $year+1900 ); printf $fmt, "Mascot version" , $resfile->getMascotVer(); printf $fmt, "Fasta version" , $resfile->getFastaVer(); printf $fmt, "Is PMF?" , $resfile->isPMF(); printf $fmt, "Is MSMS?" , $resfile->isMSMS(); printf $fmt, "Is SQ?" , $resfile->isSQ(); printf $fmt, "Is Error tolerant" , $resfile->isErrorTolerant(); printf $fmt, "Any PMF?" , $resfile->anyPMF(); printf $fmt, "Any MSMS?" , $resfile->anyMSMS(); printf $fmt, "Any SQ?" , $resfile->anySQ(); printf $fmt, "Any peptides section" , $resfile->doesSectionExist($msparser::ms_mascotresfile::SEC_PEPTIDES); printf $fmt, "Any peptide matches" , $resfile->anyPeptideSummaryMatches(); print "\n"; } =pod Running the program as perl -I../bin resfile_info.pl ../data/F981123.dat will give the following output under Mascot Server 2.3 Search information from ms_mascotresfile ======================================== Number of queries : 67 Number of hits : 50 Number of sequences : 257964 Sequences after tax : 257964 Number of residues : 93947433 Execution time : 6 Date (seconds) : 1171894187 Date : Mon Feb 19 14:09:47 2007 Mascot version : 2.1.119 Fasta version : SwissProt_51.6.fasta Is PMF? : Is MSMS? : 1 Is SQ? : Is Error tolerant : Any PMF? : Any MSMS? : 1 Any SQ? : Any peptides section: 1 Any peptide matches : 1 =cut
Copyright © 2022 Matrix Science Ltd. All Rights Reserved. Generated on Thu Mar 31 2022 01:12:29 |