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101 lines
4.3 KiB
Perl
101 lines
4.3 KiB
Perl
#!/usr/bin/perl -w
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#use lib "/bioseq/Guidance/";
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use strict;
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use Storable;
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use FindBin qw($Bin);
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use lib $Bin;
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use Guidance;
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use Getopt::Long;
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use File::Basename;
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if (scalar @ARGV<2) {die "USAGE: perl $0 --MSA <Base MSA> --Scores <Scores_File> --FilterdMSA <Out_MSA_File> --Cutoff <Cutoff> --RemovedPos <Out_File_With_Removed_Pos>\n";}
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my ($stored_data_file,$Cutoff,$vars_ref,$isServer);
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my %VARS=();
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if ($ARGV[0] =~ m/^-/) { # cmd_line mode
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if (scalar @ARGV<5) {die "USAGE: perl $0 --MSA <Base MSA> --Scores <Scores_File> --FilterdMSA <Out_MSA_File> --Cutoff <Cutoff> --RemovedPos <Out_File_With_Removed_Pos>\n";}
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# Commandline input mode
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my $getoptResult = GetOptions ("MSA=s"=>\$VARS{Alignment_File}, # = means that this parameter is required, s means string
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"Scores=s"=>\$VARS{Col_Scores_File},
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"FilterdMSA=s"=>\$VARS{Alignment_File_without_low_SP_Col},
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"Cutoff=f"=>\$Cutoff,
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"RemovedPos=s"=>\$VARS{removed_low_SP_SITE},
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);
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$isServer="NO";
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}
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else # server mode
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{
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$stored_data_file=shift;
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$Cutoff=shift;
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$vars_ref = retrieve($stored_data_file);
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%VARS = %$vars_ref;
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$VARS{Alignment_File_without_low_SP_Col}=$VARS{WorkingDir}."/".$VARS{Alignment_File_without_low_SP_Col}.".$Cutoff";
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$VARS{Col_Scores_File}="$VARS{WorkingDir}$VARS{Output_Prefix}_res_pair_col.scr";
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$VARS{Alignment_File}="$VARS{WorkingDir}$VARS{Alignment_File}"; # add path
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$VARS{removed_low_SP_SITE}="$VARS{WorkingDir}$VARS{removed_low_SP_SITE}.$Cutoff"; # add path
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$isServer="YES";
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}
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open (LOG,">>$VARS{OutLogFile}") || exit_on_error('sys_error', "Can't open Log File: $VARS{OutLogFile} $!") if ($isServer eq "YES");
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#remove sites with SP-score < Col sp_cutoff
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############################################
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print LOG "Guidance::removeLowSPsites_NoBioPerl (\"$VARS{Alignment_File}\",\"$VARS{Col_Scores_File}\",\"$VARS{Alignment_File_without_low_SP_Col}\",$Cutoff,\"$VARS{removed_low_SP_SITE}\");\n" if ($isServer eq "YES");
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my @ans=Guidance::removeLowSPsites_NoBioPerl ($VARS{Alignment_File},$VARS{Col_Scores_File},$VARS{Alignment_File_without_low_SP_Col},$Cutoff,$VARS{removed_low_SP_SITE});
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if ($ans[0]eq "OK")
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{
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$VARS{REMOVED_SITES}=$ans[1];
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$VARS{MSA_LENGTH}=$ans[2];
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}
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if ($isServer eq "NO")
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{
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print "REMOVED_SITES:$VARS{REMOVED_SITES}\n";
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print "MSA_LENGTH:$VARS{MSA_LENGTH}\n";
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}
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else # server
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{
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print LOG "REMOVED_SITES:$VARS{REMOVED_SITES}\n";
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print LOG "MSA_LENGTH:$VARS{MSA_LENGTH}\n";
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$VARS{Alignment_File_without_low_SP_Col_with_Names}=$VARS{Alignment_File_without_low_SP_Col}.".With_Names";
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my $Alignment_File_without_low_SP_Col_with_Names_NO_PATH=basename($VARS{Alignment_File_without_low_SP_Col_with_Names});
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my $removed_low_SP_SITE_NO_PATH=basename($VARS{removed_low_SP_SITE});
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if (-s $VARS{Alignment_File_without_low_SP_Col} > 0) # Not EMPTY
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{
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my @ans=Guidance::codes2nameFastaFrom1($VARS{Alignment_File_without_low_SP_Col},"$VARS{WorkingDir}$VARS{code_fileName}",$VARS{Alignment_File_without_low_SP_Col_with_Names});
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if ($ans[0] ne "OK") {exit_on_error("sys_error","Guidance::codes2nameFastaFrom1: Guidance::codes2nameFastaFrom1(\"$VARS{Alignment_File_without_low_SP_Col}\",\"$VARS{WorkingDir}$VARS{code_fileName}\",\"$VARS{Alignment_File_without_low_SP_Col_with_Names}\") failed:",join("",@ans),"\n");}
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}
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# Update the output page
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#######################################
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open (OUTPUT,"$VARS{WorkingDir}$VARS{output_page}");
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my @out=<OUTPUT>;
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close (OUTPUT);
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open (OUTPUT,">$VARS{WorkingDir}$VARS{output_page}");
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my $Remove_Pos_Section=0;
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foreach my $line (@out)
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{
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if ($line=~/Remove unreliable columns below confidence score/)
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{
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$Remove_Pos_Section=1;
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print OUTPUT $line;
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}
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elsif (($line=~/form/) and $Remove_Pos_Section==1)
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{
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print OUTPUT $line;
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print_message_to_output("<A HREF='$Alignment_File_without_low_SP_Col_with_Names_NO_PATH' TARGET=_blank>The MSA after the removal of unreliable columns (below $Cutoff)</A><font size=-1> (see list of removed columns <A HREF='$removed_low_SP_SITE_NO_PATH' TARGET=_blank>here</A>)</font><br>");
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$Remove_Pos_Section=0;
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}
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else
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{
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print OUTPUT $line;
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}
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}
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close (OUTPUT);
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}
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#---------------------------------------------
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sub print_message_to_output{
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#---------------------------------------------
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my $msg = shift;
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print OUTPUT "\n<ul><li>$msg</li></ul>\n";
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}
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