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Perl script to run GeneWise, comparing a file of multiple of HMMs to a fasta file of multiple sequences
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| #!/usr/local/bin/perl | |
| =head1 NAME | |
| run_genewisedb.pl | |
| =head1 SYNOPSIS | |
| run_genewisedb.pl input_fasta input_hmms output outputdir spliceflat parameterfile | |
| where input_fasta is the input fasta file of scaffolds, | |
| input_hmms is the input file of HMMs, | |
| output is the genewise output file, | |
| outputdir is the output directory for writing output files, | |
| spliceflat says whether to use the -splice flat option (yes/no), | |
| parameterfile is the name of the intron parameter file (none if there is none). | |
| =head1 DESCRIPTION | |
| This script takes an input fasta file of scaffolds (<input_fasta>) and an | |
| input file of HMMs (<input_hmms>) and runs genewise on the scaffolds, using | |
| one HMM at a time. The output is then written in the output file <output>. | |
| Before running this perl script you need to run: | |
| setenv WISECONFIGDIR /nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/ | |
| =head1 VERSION | |
| Perl script last edited 31-Oct-2012. | |
| =head1 CONTACT | |
| alc@sanger.ac.uk (Avril Coghlan) | |
| =cut | |
| # | |
| # Perl script run_genewisedb.pl | |
| # Written by Avril Coghlan (alc@sanger.ac.uk) | |
| # 31-Oct-12. | |
| # Last edited 31-Oct-2012. | |
| # SCRIPT SYNOPSIS: run_genewisedb.pl: runs GeneWise using TreeFam HMMs, on an input fasta file of scaffolds. | |
| # | |
| #------------------------------------------------------------------# | |
| # CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS: | |
| use strict; | |
| use warnings; | |
| my $num_args = $#ARGV + 1; | |
| if ($num_args != 6) | |
| { | |
| print "Usage of run_genewisedb.pl\n\n"; | |
| print "perl run_genewisedb.pl <input_fasta> <input_hmms> <output> <outputdir> <spliceflat> <parameterfile>\n"; | |
| print "where <input_fasta> is the input fasta file,\n"; | |
| print " <input_hmms> is the input file of HMMs,\n"; | |
| print " <output> is the genewise output file,\n"; | |
| print " <outputdir> is the output directory for writing output files,\n"; | |
| print " <spliceflat> says whether to use the -splice flat option (yes/no),\n"; | |
| print " <parameterfile> is the name of the intron parameter file (none if there is none)\n"; | |
| print "For example, >perl run_genewisedb.pl /lustre/scratch108/parasites/es9/50HGgenebuild/brpah/genome_small.fa\n"; | |
| print "/lustre/scratch108/parasites/es9/GeneWise/TreeFam8.hmm genewise_output\n"; | |
| print "/nfs/users/nfs_a/alc/Documents/GeneWise50Helminths yes mygenestat.stat\n"; | |
| print "NOTE: Before running this perl script, you need to run:\n"; | |
| print "setenv WISECONFIGDIR /nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/\n"; | |
| exit; | |
| } | |
| # FIND THE PATH TO THE INPUT FASTA FILE: | |
| my $input_fasta = $ARGV[0]; | |
| # FIND THE INPUT FILE OF HMMs: | |
| my $input_hmms = $ARGV[1]; | |
| # FIND THE GENEWISE OUTPUT FILE: | |
| my $output = $ARGV[2]; | |
| # FIND THE DIRECTORY TO USE FOR OUTPUT FILES: | |
| my $outputdir = $ARGV[3]; | |
| # FIND OUT WHETHER WE WANT TO USE THE -splice flat OPTION IN GENEWISE: | |
| my $spliceflat = $ARGV[4]; | |
| # FIND THE NAME OF THE INTRON PARAMETER FILE: | |
| my $parameterfile = $ARGV[5]; | |
| #------------------------------------------------------------------# | |
| # TEST SUBROUTINES: | |
| my $PRINT_TEST_DATA = 0; # SAYS WHETHER TO PRINT DATA USED DURING TESTING. | |
| &test_print_error; | |
| &test_write_fasta_file($outputdir); | |
| #------------------------------------------------------------------# | |
| # RUN THE MAIN PART OF THE CODE: | |
| &run_main_program($outputdir,$input_fasta,$input_hmms,$output,$spliceflat,$parameterfile); | |
| print STDERR "FINISHED.\n"; | |
| #------------------------------------------------------------------# | |
| # RUN THE MAIN PART OF THE CODE: | |
| sub run_main_program | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES IN. | |
| my $input_fasta = $_[1]; # THE INPUT FASTA FILE | |
| my $input_hmms = $_[2]; # THE INPUT FILE OF HMMs | |
| my $output = $_[3]; # THE OUTPUT FILE NAME | |
| my $spliceflat = $_[4]; # SAYS WHETHER WE WANT TO USE THE -splice flat OPTION IN GENEWISE | |
| my $parameterfile = $_[5]; # THE NAME OF THE INTRON PARAMETER FILE | |
| my $errorcode; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg; # RETURNED AS 'none' IF THERE IS NO ERROR. | |
| # CHECK THAT THE WISECONFIGDIR IS SET CORRECTLY: | |
| ($errorcode,$errormsg) = &check_wiseconfigdir; | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # RUN GENEWISE WITH ONE SCAFFOLD/CONTIG AT A TIME, ON ONE HMM AT A TIME: | |
| ($errorcode,$errormsg) = &run_genewise_on_scaffolds($outputdir,$input_fasta,$input_hmms,$output,$spliceflat,$parameterfile); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| } | |
| #------------------------------------------------------------------# | |
| # RUN GENEWISE WITH ONE SCAFFOLD/CONTIG AT A TIME, ON ONE HMM AT A TIME: | |
| sub run_genewise_on_scaffolds | |
| { | |
| my $outputdir = $_[0]; # THE DIRECTORY FOR WRITING OUTPUT FILES | |
| my $input_fasta = $_[1]; # THE INPUT FASTA FILE OF SCAFFOLDS | |
| my $input_hmms = $_[2]; # THE INPUT FILE OF HMMs | |
| my $output = $_[3]; # THE OUTPUT FILE | |
| my $spliceflat = $_[4]; # SAYS WHETHER TO USE THE SPLICE FLAT OPTION | |
| my $parameterfile = $_[5]; # THE INTRON PARAMETER FILE NAME | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| my $line; # | |
| my @temp; # | |
| my $name; # NAME OF A SCAFFOLD | |
| my $seq = ""; # SEQUENCE OF A SCAFFOLD | |
| my $seq_fasta; # FASTA FILE FOR SEQUENCE OF A SCAFFOLD | |
| # OPEN THE OUTPUT FILE: | |
| $output = $outputdir."/".$output; | |
| open(OUTPUT,">$output") || die "ERROR: run_genewise: cannot open $output\n"; | |
| close(OUTPUT); | |
| # READ IN THE INPUT FASTA FILE AND TAKE ONE SCAFFOLD AT A TIME: | |
| open(INPUTFASTA,"$input_fasta") || die "ERROR: run_genewise_on_scaffolds: cannot open $input_fasta\n"; | |
| while(<INPUTFASTA>) | |
| { | |
| $line = $_; | |
| chomp $line; | |
| if (substr($line,0,1) eq '>') | |
| { | |
| # WRITE THE SEQUENCE TO A TEMPORARY FASTA FILE: | |
| if ($seq ne '') | |
| { | |
| ($seq_fasta,$errorcode,$errormsg) = &write_fasta_file($seq,$name,$outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # RUN GENEWISE ON $seq_fasta, ONE HMM AT A TIME: | |
| ($errorcode,$errormsg) = &run_genewise($outputdir,$seq_fasta,$input_hmms,$output,$spliceflat,$parameterfile,$name); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # DELETE TEMPORARY FILE: | |
| system "rm -f $seq_fasta"; | |
| } | |
| @temp = split(/\s+/,$line); | |
| $name = $temp[0]; | |
| $name = substr($name,1,length($name)-1); | |
| } | |
| else | |
| { | |
| $seq = $seq.$line; | |
| } | |
| } | |
| close(INPUTFASTA); | |
| # WRITE THE SEQUENCE TO A TEMPORARY FASTA FILE: | |
| if ($seq ne '') | |
| { | |
| ($seq_fasta,$errorcode,$errormsg) = &write_fasta_file($seq,$name,$outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # RUN GENEWISE ON $seq_fasta: | |
| ($errorcode,$errormsg) = &run_genewise($outputdir,$seq_fasta,$input_hmms,$output,$spliceflat,$parameterfile,$name); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # DELETE TEMPORARY FILE: | |
| system "rm -f $seq_fasta"; | |
| } | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &write_fasta_file | |
| sub test_write_fasta_file | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO WRITE OUTPUT FILES TO | |
| my $errorcode; # RETURNED AS 0 BY A FUNCTION IF THERE IS NO ERROR | |
| my $errormsg; # RETURNED AS 'none' BY A FUNCTION IF THERE IS NO ERROR | |
| my $fasta; # FASTA FILE | |
| my $expected_fasta; # EXPECTED CONTENTS OF FASTA FILE | |
| my $random_number; # RANDOM NUMBER TO USE IN TEMPORARY FILE NAMES | |
| my $differences; # DIFFERENCES BETWEEN $fasta AND $expected_fasta | |
| my $length_differences; # LENGTH OF $differences | |
| my $line; # | |
| ($fasta,$errorcode,$errormsg) = &write_fasta_file("AGCTAGCT","myseq",$outputdir); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_write_fasta_file: failed test1\n"; exit;} | |
| $random_number = rand(); | |
| $expected_fasta = $outputdir."/tmp".$random_number; | |
| open(EXPECTED,">$expected_fasta") || die "ERROR: write_fasta_file: cannot open $expected_fasta\n"; | |
| print EXPECTED ">myseq\n"; | |
| print EXPECTED "AGCTAGCT\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $fasta $expected_fasta |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_write_fasta_file: failed test1 (files $fasta $expected_fasta)\n"; exit;} | |
| system "rm -f $fasta"; | |
| system "rm -f $expected_fasta"; | |
| } | |
| #------------------------------------------------------------------# | |
| # WRITE THE SEQUENCE TO A TEMPORARY FASTA FILE: | |
| sub write_fasta_file | |
| { | |
| my $seq = $_[0]; # SEQUENCE | |
| my $name = $_[1]; # NAME OF THE SEQUENCE | |
| my $outputdir = $_[2]; # DIRECTORY FOR WRITING OUTPUT FILES TO | |
| my $fasta; # FASTA FILE | |
| my $random_number; # RANDOM NUMBER TO USE IN TEMPORARY FILE NAMES | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| $random_number = rand(); | |
| $fasta = $outputdir."/tmp".$random_number; | |
| open(FASTA,">$fasta") || die "ERROR: write_fasta_file: cannot open $fasta\n"; | |
| print FASTA ">$name\n"; | |
| print FASTA "$seq\n"; | |
| close(FASTA); | |
| return($fasta,$errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # CHECK THAT THE WISECONFIGDIR IS SET CORRECTLY: | |
| sub check_wiseconfigdir | |
| { | |
| my $wiseconfigdir = "none";# THE WISECONFIGDIR | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| open(TMP,"echo \$WISECONFIGDIR |"); | |
| while(<TMP>) | |
| { | |
| $wiseconfigdir = $_; | |
| chomp($wiseconfigdir); | |
| } | |
| close(TMP); | |
| if ($wiseconfigdir ne '/nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/') | |
| { | |
| $errormsg = "ERROR: check_wiseconfigdir: wiseconfigdir $wiseconfigdir\nBefore running this perl script, you must run:\nsetenv WISECONFIGDIR /nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/\n"; | |
| $errorcode = 6; # ERRORCODE=6 | |
| return($errorcode,$errormsg); | |
| } | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # RUN GENEWISE ON ONE HMM AT A TIME: | |
| sub run_genewise | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY FOR WRITING OUTPUT FILES TO | |
| my $input_fasta = $_[1]; # THE INPUT FASTA FILE | |
| my $input_hmms = $_[2]; # THE INPUT FILE OF HMMs | |
| my $output = $_[3]; # THE OUTPUT FILE NAME | |
| my $spliceflat = $_[4]; # SAYS WHETHER WE WANT TO USE THE -splice flat OPTION IN GENEWISE | |
| my $parameterfile = $_[5]; # THE NAME OF THE INTRON PARAMETER FILE | |
| my $scaffoldname = $_[6]; # THE NAME OF THE SCAFFOLD | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR. | |
| my $line; # | |
| my $hmm = ""; # A HMM | |
| my $hmmname = "none";# HMM NAME | |
| my @temp; # | |
| # READ IN ONE HMM AT A TIME FROM THE INPUT FILE OF HMMs: | |
| open(HMMS,"$input_hmms") || die "ERROR: run_genewise: cannot open $input_hmms\n"; | |
| while(<HMMS>) | |
| { | |
| $line = $_; | |
| $hmm = $hmm.$line; | |
| if (substr($line,0,2) eq '//') | |
| { | |
| # CHECK WE HAVE A NAME FOR THE HMM: | |
| if ($hmmname eq 'none') | |
| { | |
| $errormsg = "ERROR: run_genewise: do not have name for hmm $hmm\n"; | |
| $errorcode = 3; # ERRORCODE=3 | |
| return($errorcode,$errormsg); | |
| } | |
| # RUN GENEWISE FOR THIS HMM: | |
| ($errorcode,$errormsg) = &run_genewise_on_hmm($hmm,$outputdir,$input_fasta,$output,$hmmname,$spliceflat,$parameterfile,$scaffoldname); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| $hmm = ""; | |
| $hmmname = "none"; | |
| } | |
| if (substr($line,0,4) eq 'NAME') | |
| { | |
| @temp = split(/\s+/,$line); | |
| $hmmname = $temp[1]; | |
| chomp($hmmname); | |
| } | |
| } | |
| close(HMMS); | |
| if ($hmm ne '') | |
| { | |
| $errormsg = "ERROR: run_genewise: at end of file hmm should be empty\n"; | |
| $errorcode = 1; # ERRORCODE=1 | |
| return($errorcode,$errormsg); | |
| } | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # READ IN ONE HMM AT A TIME FROM THE INPUT FILE OF HMMs: | |
| sub run_genewise_on_hmm | |
| { | |
| my $hmm = $_[0]; # THE HMM | |
| my $outputdir = $_[1]; # DIRECTORY TO WRITE OUTPUT FILES TO | |
| my $input_fasta = $_[2]; # INPUT FASTA FILE | |
| my $output = $_[3]; # FILE FOR GENEWISE OUTPUT | |
| my $hmmname = $_[4]; # NAME OF THE HMM | |
| my $spliceflat = $_[5]; # SAYS WHETHER WE WANT TO USE THE -splice flat OPTION IN GENEWISE | |
| my $parameterfile = $_[6]; # THE NAME OF THE INTRON PARAMETER FILE | |
| my $scaffoldname = $_[7]; # NAME OF THE SCAFFOLD | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR. | |
| my $random_number; # RANDOM NUMBER FOR TEMPORARY FILE NAME | |
| my $hmmfile; # FILE CONTAINING THE HMM | |
| my $genewise; # TEMPORARY FILE FOR THE GENEWISE OUTPUT FOR THIS HMM | |
| my $cmd; # THE GENEWISE COMMAND TO RUN | |
| my $genewise_exe = "/nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/src/bin/genewise"; # wise 2.4.1, can use -genestats | |
| # CHECK THE HMM LOOKS OK: | |
| if (substr($hmm,0,8) ne 'HMMER2.0' && substr($hmm,length($hmm)-2,2) ne '//') | |
| { | |
| $errormsg = "ERROR: run_genewise_on_hmm: hmm $hmm\n"; | |
| $errorcode = 2; # ERRORCODE=2 | |
| return($errorcode,$errormsg); | |
| } | |
| # CHECK THE SPLICEFLAT OPTION IS 'yes' OR 'no': | |
| if ($spliceflat ne 'yes' && $spliceflat ne 'no') | |
| { | |
| $errormsg = "ERROR: run_genewise_on_hmm: spliceflat is $spliceflat (should be yes or no)\n"; | |
| $errorcode = 4; # ERRORCODE=4 | |
| return($errorcode,$errormsg); | |
| } | |
| # WRITE THE HMM TO A FILE: | |
| $random_number = rand(); | |
| $hmmfile = $outputdir."/tmp".$random_number; | |
| open(HMMFILE,">$hmmfile") || die "ERROR: run_genewise_on_hmm: cannot open $hmmfile\n"; | |
| print HMMFILE "$hmm"; | |
| close(HMMFILE); | |
| # WRITE THE FAMILY NAME IN THE OUTPUT FILE: | |
| system "echo $hmmname >> $output"; | |
| # RUN GENEWISE: | |
| $random_number = rand(); | |
| $genewise = $outputdir."/tmp".$random_number; | |
| print STDERR "Scaffold $scaffoldname: running genewise for HMM $hmmname ...\n"; | |
| if ($parameterfile ne 'none' && $spliceflat eq 'no') | |
| { | |
| $cmd = "$genewise_exe $hmmfile $input_fasta -gff -hmmer -genestats $parameterfile -nosplice_gtag > $genewise"; | |
| } | |
| elsif ($parameterfile eq 'none' && $spliceflat eq 'yes') | |
| { | |
| $cmd = "$genewise_exe $hmmfile $input_fasta -gff -hmmer -splice_gtag > $genewise"; | |
| } | |
| elsif ($parameterfile eq 'none' && $spliceflat eq 'no') | |
| { | |
| $cmd = "$genewise_exe $hmmfile $input_fasta -gff -hmmer -nosplice_gtag > $genewise"; # USES THE gene.stats FILE THAT COMES WITH GENEWISE, /nfs/users/nfs_a/alc/Documents/GeneWise/wise2.4.1/wisecfg/gene.stat | |
| } | |
| elsif ($parameterfile ne 'none' && $spliceflat eq 'yes') | |
| { | |
| $errormsg = "ERROR: run_genewise_on_hmm: cannot have spliceflat $spliceflat and parameterfile $parameterfile\n"; | |
| $errorcode = 5; # ERRORCODE=5 | |
| return($errorcode,$errormsg); | |
| } | |
| system "$cmd"; | |
| # CONCATENATE THIS GENEWISE OUTPUT ONTO THE MAIN OUTPUT FILE OF GENEWISE OUTPUT: | |
| sleep(1); | |
| system "cat $genewise"; | |
| system "cat $genewise >> $output"; | |
| # DELETE TEMPORARY FILES: | |
| system "rm -f $hmmfile"; | |
| system "rm -f $genewise"; | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &print_error | |
| sub test_print_error | |
| { | |
| my $errormsg; # RETURNED AS 'none' FROM A FUNCTION IF THERE WAS NO ERROR | |
| my $errorcode; # RETURNED AS 0 FROM A FUNCTION IF THERE WAS NO ERROR | |
| ($errormsg,$errorcode) = &print_error(45,45,1); | |
| if ($errorcode != 12) { print STDERR "ERROR: test_print_error: failed test1\n"; exit;} | |
| ($errormsg,$errorcode) = &print_error('My error message','My error message',1); | |
| if ($errorcode != 11) { print STDERR "ERROR: test_print_error: failed test2\n"; exit;} | |
| ($errormsg,$errorcode) = &print_error('none',45,1); | |
| if ($errorcode != 13) { print STDERR "ERROR: test_print_error: failed test3\n"; exit;} | |
| ($errormsg,$errorcode) = &print_error('My error message', 0, 1); | |
| if ($errorcode != 13) { print STDERR "ERROR: test_print_error: failed test4\n"; exit;} | |
| } | |
| #------------------------------------------------------------------# | |
| # PRINT OUT AN ERROR MESSAGE AND EXIT. | |
| sub print_error | |
| { | |
| my $errormsg = $_[0]; # THIS SHOULD BE NOT 'none' IF AN ERROR OCCURRED. | |
| my $errorcode = $_[1]; # THIS SHOULD NOT BE 0 IF AN ERROR OCCURRED. | |
| my $called_from_test = $_[2]; # SAYS WHETHER THIS WAS CALLED FROM test_print_error OR NOT | |
| if ($errorcode =~ /[A-Z]/ || $errorcode =~ /[a-z]/) | |
| { | |
| if ($called_from_test == 1) | |
| { | |
| $errorcode = 11; $errormsg = "ERROR: print_error: the errorcode is $errorcode, should be a number.\n"; # ERRORCODE=11 | |
| return($errormsg,$errorcode); | |
| } | |
| else | |
| { | |
| print STDERR "ERROR: print_error: the errorcode is $errorcode, should be a number.\n"; | |
| exit; | |
| } | |
| } | |
| if (!($errormsg =~ /[A-Z]/ || $errormsg =~ /[a-z]/)) | |
| { | |
| if ($called_from_test == 1) | |
| { | |
| $errorcode = 12; $errormsg = "ERROR: print_error: the errormessage $errormsg does not seem to contain text.\n"; # ERRORCODE=12 | |
| return($errormsg,$errorcode); | |
| } | |
| else | |
| { | |
| print STDERR "ERROR: print_error: the errormessage $errormsg does not seem to contain text.\n"; | |
| exit; | |
| } | |
| } | |
| if ($errormsg eq 'none' || $errorcode == 0) | |
| { | |
| if ($called_from_test == 1) | |
| { | |
| $errorcode = 13; $errormsg = "ERROR: print_error: errormsg $errormsg, errorcode $errorcode.\n"; # ERRORCODE=13 | |
| return($errormsg,$errorcode); | |
| } | |
| else | |
| { | |
| print STDERR "ERROR: print_error: errormsg $errormsg, errorcode $errorcode.\n"; | |
| exit; | |
| } | |
| } | |
| else | |
| { | |
| print STDERR "$errormsg"; | |
| exit; | |
| } | |
| return($errormsg,$errorcode); | |
| } | |
| #------------------------------------------------------------------# | |
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