#!/usr/bin/env perl use strict; use Carp; use Pod::Usage; =head1 NAME =head1 DESCRIPTION This program is only useful for InSilicoSpectro used in the Phenyx environment. Returns a given file corresponding to a given user (for example, the file with the user modifications). =head1 SYNOPSIS http://www.phenyx-ms.com/tools/cgi/getUserFile.pl?user=jo&file=modres.xml =head1 ARGUMENTS =over 4 =item user=name =item file=filename =back =head1 OPTIONS =over 4 =item zip=1 Make a zip archive with the file. =item opt=1 Does not CORE::die if a requested file does not exist =item help=1 =back =head1 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 =head1 AUTHORS Alexandre Masselot, www.genebio.com =cut BEGIN{ eval{ require DefEnv; DefEnv::read(); }; if($@){ } } END{ } $|=1; # flush immediately; my $isCGI; use CGI qw(:standard); if($isCGI){ use CGI::Carp qw(fatalsToBrowser warningsToBrowser); warningsToBrowser(1); } use InSilicoSpectro; use InSilicoSpectro::InSilico::CleavEnzyme; use InSilicoSpectro::InSilico::ModRes; BEGIN{ $isCGI=$ENV{GATEWAY_INTERFACE}=~/CGI/; sub carp_error{ my $msg=shift; if ($isCGI){ my $q=new CGI; error($q, $msg); }else{ print STDERR $msg; } } CGI::Carp::set_message(\&carp_error);# if $isCGI; sub error(){ my($q, $msg)=@_; # $q->header; print $q->start_html(-title=>"$0", -author=>'alexandre.masselot@genebio.com', -BGCOLOR=>'white'); print "

$0

\n"; print "$msg\n"; $q->end_html; exit; } } my $query = new CGI; my $frame=$query->param('frame'); my @args; push @args, "file=".$query->param('file') if $query->param('file'); push @args, "user=".$query->param('user') if $query->param('user'); my $edit=$query->param('edit'); my $username=$query->param('user'); my $filename=$query->param('file'); my $args=join '&', @args; unless(defined $frame){ print $query->header; print < $0 EOT exit(0); }elsif($frame eq 'contents'){ print $query->header; print <

cleavage enzymes
residue modif.

EOT } if($query->param('actiontype') eq 'save'){ my $defUser=Phenyx::Manage::User->new(name=>'default'); InSilicoSpectro::InSilico::MassCalculator::init($defUser->getFile('insilicodef.xml')); } my $target=$username?"user [$username]":"file [$filename] (server side)"; if($cat eq 'cleavenzyme'){ print "

Cleavage enzymes setup for $target

\n"; my $key=$query->param('key'); $key=~s/\s/_/g; if($query->param('actiontype') eq 'save'){ my @tmp=$twig->root->get_xpath("//oneCleavEnzyme[\@name='$key']"); my $el; if(@tmp){ $el=$tmp[0]; }else{ $el=XML::Twig::Elt->new()->parse("")->paste(last_child=> $twig->root->first_child('cleavEnzymes')); } query2cleavEnzyme($query, $el); $lockmgr->trylock("$defFile") || croak "can't lock [$defFile]: $!\n"; open (fd, ">$defFile") or CORE::die "cannot open for writeing [$defFile]: $!"; $twig->print(\*fd); close fd; $lockmgr->unlock("$defFile") || croak "can't unlock [$defFile]: $!\n"; } if($query->param('actiontype') eq 'delete'){ my @tmp=$twig->root->get_xpath("//oneCleavEnzyme[\@name='$key']"); my $el; if(@tmp){ $el=$tmp[0]; $el->delete; $lockmgr->trylock("$defFile") || croak "can't lock [$defFile]: $!\n"; open (fd, ">$defFile") or CORE::die "cannot open for writeing [$defFile]: $!"; $twig->print(\*fd); close fd; $lockmgr->unlock("$defFile") || croak "can't unlock [$defFile]: $!\n"; } } print "

EOT if ($edit){ print < EOT } print <

Name

Cleavage site

Site

cleav at
adjacent
terminus	C N

Regular expression

Gain (formula)

N-term
C-term

EOT foreach (@args){ my ($n, $v)=split /=/, $_, 2; print " \n"; } print " \n"; print " \n"; print " \n"; print < EOT print <
EOT foreach (@args){ my ($n, $v)=split /=/, $_, 2; print " \n"; } print " \n"; print " \n"; print " \n"; print " \n" if $edit; print " \n"; print " \n"; print " \n" if defined $key; if($query->param('actiontype') eq 'test'){ my $el=($twig->root->get_xpath("//oneCleavEnzyme[\@name='$key']"))[0]; twig_addEnzyme($twig, $el); my $enzyme=InSilicoSpectro::InSilico::CleavEnzyme::getFromDico($key); print "/".($enzyme->regexp)."/\n"; print "

\n";
    foreach(split $enzyme->regexp, $testSequence){
      print "$_\n";
    }
    print "

\n"; } print < EOT } ############################################################### if($cat eq 'modres'){ print "

Residue modifications setup for $target

\n"; my $key=$query->param('key'); $key=~s/\s/_/g; if($query->param('actiontype') eq 'save'){ my @tmp=$twig->root->get_xpath("//oneModRes[\@name='$key']"); my $el; if(@tmp){ $el=$tmp[0]; }else{ $el=XML::Twig::Elt->new()->parse("")->paste(last_child=> $twig->root->first_child('modRes')); } query2modres($query, $el); $lockmgr->trylock("$defFile") || croak "can't lock [$defFile]: $!\n"; open (fd, ">$defFile") or CORE::die "cannot open for writeing [$defFile]: $!"; $twig->print(\*fd); close fd; $lockmgr->unlock("$defFile") || croak "can't unlock [$defFile]: $!\n"; } if($query->param('actiontype') eq 'delete'){ my @tmp=$twig->root->get_xpath("//oneModRes[\@name='$key']"); my $el; if(@tmp){ $el=$tmp[0]; $el->delete; $lockmgr->trylock("$defFile") || croak "can't lock [$defFile]: $!\n"; open (fd, ">$defFile") or CORE::die "cannot open for writeing [$defFile]: $!"; $twig->print(\*fd); close fd; $lockmgr->unlock("$defFile") || croak "can't unlock [$defFile]: $!\n"; } } print "

EOT if ($edit){ print <

Name

Description

Position

Modif site

Residue
Regular expression

Peptide terminus

nterm cterm

Mass modification

Delta mass

mono isotopic
average

Formula

Uniprot annotations

Uniprot FT mask

EOT } print < EOT foreach (@args){ my ($n, $v)=split /=/, $_, 2; print " \n"; } print " \n"; print " \n"; print " \n"; print < EOT print <
EOT foreach (@args){ my ($n, $v)=split /=/, $_, 2; print " \n"; } print " \n"; print " \n"; print " \n"; print " \n" if $edit; print " \n"; print " \n"; print " \n" if defined $key; if($query->param('actiontype') eq 'test'){ my $el=($twig->root->get_xpath("//oneModRes[\@name='$key']"))[0]; twig_addModRes($twig, $el); my $mr=InSilicoSpectro::InSilico::ModRes::getFromDico($key); my $qr=$mr->regexp; print "

$qr

\n"; $testSequence=~s/($qr)/$1<\/b>/g; print "$testSequence\n"; } print < EOT } sub query2cleavEnzyme{ my ($q, $el)=@_; foreach ($el->children){ $_->delete; } if($q->param('sitetype')eq 'classic'){ my $els=XML::Twig::Elt->new()->parse(" ".(uc $q->param('site_cleav'))." ".((uc $q->param('site_adjacent'))||'.')." ".(uc $q->param('site_terminus'))." ")->paste(first_child=>$el);; }else{ my $els=XML::Twig::Elt->new()->parse("param('siteregexp')."]]>")->paste(first_child=>$el);; } XML::Twig::Elt->new()->parse("".$q->param('CTermGain')."")->paste(last_child=>$el); XML::Twig::Elt->new()->parse("".$q->param('NTermGain')."")->paste(last_child=>$el); } sub query2modres{ my ($q, $el)=@_; foreach ($el->children){ $_->delete; } XML::Twig::Elt->new()->parse("".$q->param('description')."")->paste(last_child=>$el); if($q->param('sitetype')eq 'classic'){ my $contents=""; $contents.="".(uc $q->param('residue')).""; $contents.="" if $q->param('nterm'); $contents.="" if $q->param('cterm'); $contents.=""; my $els=XML::Twig::Elt->new()->parse($contents)->paste(last_child=>$el);; }else{ my $atts; $atts.=" nterm='yes'" if $q->param('nterm'); $atts.=" cterm='yes'" if $q->param('cterm'); my $els=XML::Twig::Elt->new()->parse("param('siteregexp')."]]>")->paste(first_child=>$el); } my $formula=$q->param('formula'); my $dm_mono=$q->param('delta_mono')||-999; my $dm_avg=$q->param('delta_avg')||-999; if ($formula){ ($dm_mono, $dm_avg)=InSilicoSpectro::InSilico::MassCalculator::massFromComposition($formula); } XML::Twig::Elt->new()->parse("")->paste(last_child=>$el); XML::Twig::Elt->new()->parse("$formula")->paste(last_child=>$el) if $q->param('formula'); XML::Twig::Elt->new()->parse("param('sprotFT')."]]>")->paste(last_child=>$el); }