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Perl script to convert an embl file to gff format
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| #!/usr/local/bin/perl | |
| =head1 NAME | |
| embl_to_gff.pl | |
| =head1 SYNOPSIS | |
| embl_to_gff.pl input_embl output_gff outputdir ratt | |
| where input_embl is the input embl file, | |
| output_gff is the output gff file, | |
| outputdir is the output directory for writing output files, | |
| ratt says whether the embl files are from ratt (yes/no). | |
| =head1 DESCRIPTION | |
| This script takes an input embl file (<input_embl>), and converts it to | |
| gff format, and writes the output file (<output_gff>) in directory | |
| <outputdir>. | |
| =head1 VERSION | |
| Perl script last edited 27-Feb-2013. | |
| =head1 CONTACT | |
| [email protected] (Avril Coghlan) | |
| =cut | |
| # | |
| # Perl script embl_to_gff.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 27-Jan-13. | |
| # Last edited 27-Jan-2013. | |
| # SCRIPT SYNOPSIS: embl_to_gff.pl: convert an embl file to a gff file. | |
| # | |
| #------------------------------------------------------------------# | |
| # CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS: | |
| use strict; | |
| use warnings; | |
| my $num_args = $#ARGV + 1; | |
| if ($num_args != 4) | |
| { | |
| print "Usage of embl_to_gff.pl\n\n"; | |
| print "perl embl_to_gff.pl <input_embl> <output_gff> <outputdir> <ratt>\n"; | |
| print "where <input_embl> is the input embl file,\n"; | |
| print " <output_gff> is the output gff file,\n"; | |
| print " <outputdir> is the output directory for writing output files,\n"; | |
| print " <ratt> says whether the embl files are from ratt (yes/no)\n"; | |
| print "For example, >perl embl_to_gff.pl my.embl my.gff\n"; | |
| print "/lustre/scratch108/parasites/alc/StrongyloidesTophat/PTRK/SrattiCurated yes\n"; | |
| exit; | |
| } | |
| # FIND THE PATH TO THE INPUT EMBL FILE: | |
| my $input_embl = $ARGV[0]; | |
| # FIND THE PATH TO THE OUTPUT GFF FILE: | |
| my $output_gff = $ARGV[1]; | |
| # FIND THE DIRECTORY TO USE FOR OUTPUT FILES: | |
| my $outputdir = $ARGV[2]; | |
| # FIND OUT WHETHER THE EMBL FILES ARE FROM RATT: | |
| my $ratt = $ARGV[3]; | |
| #------------------------------------------------------------------# | |
| # TEST SUBROUTINES: | |
| my $PRINT_TEST_DATA = 0; # SAYS WHETHER TO PRINT DATA USED DURING TESTING. | |
| &test_convert_embl_to_gff($outputdir); | |
| &test_print_error; | |
| print STDERR "Finished tests, now running main code...\n"; | |
| #------------------------------------------------------------------# | |
| # RUN THE MAIN PART OF THE CODE: | |
| &run_main_program($outputdir,$input_embl,$output_gff,$ratt); | |
| 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_embl = $_[1]; # THE INPUT EMBL FILE | |
| my $output_gff = $_[2]; # THE OUTPUT GFF FILE | |
| my $ratt = $_[3]; # SAYS WHETHER THE EMBL FILES ARE FROM RATT | |
| my $errorcode; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg; # RETURNED AS 'none' IF THERE IS NO ERROR. | |
| # READ IN THE INPUT EMBL FILE, AND MAKE THE OUTPUT GFF FILE: | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,$ratt); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| } | |
| #------------------------------------------------------------------# | |
| # READ IN THE INPUT EMBL FILE, AND MAKE THE OUTPUT GFF FILE: | |
| sub convert_embl_to_gff | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES IN | |
| my $input_embl = $_[1]; # INPUT EMBL FILE | |
| my $output_gff = $_[2]; # OUTPUT GFF FILE | |
| my $ratt = $_[3]; # SAYS WHETHER THE EMBL FILES ARE FROM RATT | |
| my $line; # | |
| my @temp; # | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| my $name = "none";# NAME OF THE SEQUENCE | |
| my $exons; # EXONS IN A GENE | |
| my $strand; # STRAND OF THE GENE | |
| my @exons; # EXONS IN A GENE | |
| my $i; # | |
| my $exon; # AN EXON IN A GENE | |
| my $start; # START OF AN EXON | |
| my $end; # END OF AN EXON | |
| my $gene; # NAME OF THE GENE | |
| my %CNT = (); # NUMBER OF TIMES THAT WE HAVE SEEN A PARTICULAR GENE NAME | |
| my $cnt; # NUMBER OF TIMES THAT WE HAVE SEEN A PARTICULAR GENE NAME | |
| my $first_exon; # FIRST EXON IN A GENE | |
| my $last_exon; # LAST EXON IN A GENE | |
| my $first_exon_start; # START POINT OF THE FIRST EXON IN A GENE | |
| my $last_exon_end; # END OF THE LAST EXON IN A ENE | |
| my $exon_name; # NAME OF AN EXON | |
| my $transcript_name; # NAME OF A TRANSCRIPT | |
| my $found_seq_start = 0; # SAYS WE HAVE FOUND THE START OF THE SEQUENCE IN THE EMBL FILE | |
| my $prev_line = ""; # PREVIOUS LINE IN THE EMBL FILE | |
| my $prev_prev_line = ""; # LINE BEFORE $prev_line IN THE EMBL FILE | |
| my @temp2; # | |
| # CHECK $ratt IS 'yes' OR 'no': | |
| if ($ratt ne 'yes' && $ratt ne 'no') | |
| { | |
| $errormsg = "ERROR: convert_embl_to_gff: ratt should be yes/no (is $ratt)\n"; | |
| $errorcode = 4; # ERRORCODE=4 | |
| return($errorcode,$errormsg); | |
| } | |
| # OPEN THE OUTPUT GFF FILE: | |
| $output_gff = $outputdir."/".$output_gff; | |
| open(OUTPUT,">$output_gff") || die "ERROR: convert_embl_to_gff: cannot open $output_gff\n"; | |
| # READ IN THE INPUT EMBL FILE: | |
| open(EMBL,"$input_embl") || die "ERROR: convert_embl_to_gff: cannot open input_embl $input_embl\n"; | |
| while(<EMBL>) | |
| { | |
| $line = $_; | |
| if ($found_seq_start == 0) | |
| { | |
| chomp $line; | |
| @temp = split(/\s+/,$line); | |
| if (substr($line,0,2) eq 'ID') | |
| { | |
| $name = $temp[1]; # eg. Transfer1.PTRK.contig.00177.164151.final | |
| if ($ratt eq 'yes') | |
| { | |
| @temp = split(/\./,$name); | |
| $name = ""; | |
| for ($i = 1; $i <= $#temp-1; $i++) { $name = $name.".".$temp[$i];} | |
| $name = substr($name,1,length($name)-1); | |
| } | |
| # IF THERE IS A SEMI-COLON AT THE END OF THE NAME, REMOVE IT: | |
| if (substr($name,length($name)-1,1) eq ';') { chop($name);} | |
| } | |
| elsif (substr($line,0,2) eq 'FT' && $temp[1] eq 'CDS') | |
| { | |
| # eg. FT CDS complement(join(309654..309719,309724..310158)) | |
| $exons = $temp[2]; # eg. complement(join(309654..309719,309724..310158)) | |
| if ($exons =~ /complement/) { $strand = "-";} | |
| else { $strand = "+";} | |
| } | |
| elsif (substr($line,0,2) eq 'FT' && $line =~ /gene_orientation/) | |
| { | |
| # eg. FT /systematic_id="gene_id 0 ; sequence ratti_train136 ; gene_orientation +" | |
| # or | |
| # FT /systematic_id="gene_id 0 ; sequence | |
| # FT T1.PTRK.scaffold.00008.1453643 ; gene_orientation +" | |
| if (!($line =~ /systematic_id/)) # THE INFORMATION ON THE GENE IS SPREAD OVER TWO LINES | |
| { | |
| if ($prev_line =~ /systematic_id/) # THE INFORMATION ON THE GENE IS SPREAD OVER TWO LINES | |
| { | |
| # eg. prev_line IS: FT /systematic_id="gene_id 0 ; sequence | |
| # line is: FT T1.PTRK.scaffold.00008.1453643 ; gene_orientation +" | |
| @temp2 = split(/FT\s+/,$line); | |
| $line = $temp2[1]; # eg. T1.PTRK.scaffold.00008.1453643 ; gene_orientation +" | |
| $line = $prev_line." ".$line; | |
| # eg. FT /systematic_id="gene_id 0 ; sequence T1.PTRK.scaffold.00008.1453643 ; gene_orientation +" | |
| } | |
| elsif ($prev_prev_line =~ /systematic_id/) # THE INFORMATION ON THE GENE IS SPREAD OVER THREE LINES | |
| { | |
| # IF THE INFORMATION ON THE GENE IS SPREAD OVER THREE LINES | |
| # eg. prev_prev_line IS: FT /systematic_id="gene_id 0 ; | |
| # prev_line IS: FT T1.PTRK.scaffold.00010.1389350.embl sequence | |
| # line IS: FT T1.PTRK.scaffold.00010.1389350 ; gene_orientation +" | |
| @temp2 = split(/FT\s+/,$line); | |
| $line = $temp2[1]; | |
| @temp2 = split(/FT\s+/,$prev_line); | |
| $prev_line = $temp2[1]; | |
| $line = $prev_prev_line." ".$prev_line." ".$line; | |
| } | |
| else | |
| { | |
| $errormsg= "ERROR: convert_embl_to_gff: line $line prev_line $prev_line prev_prev_line $prev_prev_line\n"; | |
| $errorcode= 1; # ERRORCODE=1 (TESTED FOR) | |
| return($errorcode,$errormsg); | |
| } | |
| } | |
| @temp = split(/sequence\s+/,$line); | |
| $gene = $temp[1]; # eg. T1.PTRK.scaffold.00010.1389350 ; gene_orientation +" | |
| @temp = split(/\s+/,$gene); | |
| $gene = $temp[0]; # eg. T1.PTRK.scaffold.00010.1389350 | |
| # IF THERE IS A SEMI-COLON AT THE END OF THE GENE NAME, IGNORE IT: | |
| if (substr($gene,length($gene)-1,1) eq ';') { chop($gene);} | |
| if (!($CNT{$gene})) { $CNT{$gene} = 1; } | |
| else { $CNT{$gene}++; } | |
| $cnt = $CNT{$gene}; | |
| $gene = $gene."_".$cnt; | |
| # PRINT OUT THE EXONS: | |
| if ($exons =~ /\(/) | |
| { | |
| @temp = split(/\(/,$exons); | |
| if ($temp[1] =~ /join/) { $exons = $temp[2];} # eg. 309654..309719,309724..310158) | |
| else { $exons = $temp[1];} # eg. 308719..308826 | |
| if (substr($exons,length($exons)-1,1) eq ')') { chop($exons);} | |
| if (substr($exons,length($exons)-1,1) eq ')') { chop($exons);} | |
| } | |
| @exons = split(/\,/,$exons); | |
| for ($i = 0; $i <= $#exons; $i++) | |
| { | |
| $exon = $exons[$i]; | |
| @temp = split(/\.\./,$exon); | |
| $start = $temp[0]; | |
| $end = $temp[1]; | |
| $exon_name = $gene."_".$i; | |
| $transcript_name = $gene."_mRNA"; | |
| # PRINT OUT GFF LINE: | |
| print OUTPUT "$name\tsource\tCDS\t$start\t$end\t.\t$strand\t.\t$exon_name\;Parent=$transcript_name\n"; | |
| } | |
| # PRINT OUT GFF LINE FOR 'mRNA' AND 'gene' FEATURES: | |
| $first_exon = $exons[0]; | |
| @temp = split(/\.\./,$first_exon); | |
| $first_exon_start = $temp[0]; | |
| $last_exon = $exons[$#exons]; | |
| @temp = split(/\.\./,$last_exon); | |
| $last_exon_end = $temp[1]; | |
| print OUTPUT "$name\tsource\tgene\t$first_exon_start\t$last_exon_end\t.\t$strand\t.\t$gene\n"; | |
| print OUTPUT "$name\tsource\tmRNA\t$first_exon_start\t$last_exon_end\t.\t$strand\t.\t$transcript_name\;Parent=$gene\n"; | |
| } | |
| elsif (substr($line,0,2) eq 'SQ') | |
| { | |
| $found_seq_start = 1; | |
| } | |
| } | |
| $prev_prev_line = $prev_line; | |
| $prev_line = $line; | |
| chomp ($prev_line); | |
| } | |
| close(EMBL); | |
| close(OUTPUT); | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &convert_embl_to_gff | |
| sub test_convert_embl_to_gff | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO WRITE OUTPUT FILES IN | |
| my $input_embl; # NAME OF EMBL FILE | |
| my $output_gff; # NAME OF OUTPUT GFF FILE | |
| my $errorcode = 0; # RETURNED AS 0 BY A FUNCTION IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' BY A FUNCTION IF THERE IS NO ERROR | |
| my $expected_output_gff; # FILE CONTAINING THE EXPECTED CONTENTS OF $output_gff | |
| my $differences; # DIFFERENES BETWEEN $output_gff AND $expected_output_gff | |
| my $length_differences; # LENGTH OF $differences | |
| my $line; # | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID Transfer1.PTRK.scaffold.00024.740435.final ; ; ; ; ; 740435 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS complement(join(309654..309719,309724..310158))\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "FT CDS complement(308719..308826)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "SQ Sequence 740435 BP; 276856 A; 85528 C; 86034 G; 273093 T; 18924 other;\n"; | |
| print EMBL "ttagtttttc cagaagcttt agcttttcct ccttttctac gtcctgacat attaataata 60\n"; | |
| print EMBL "aagttataaa atgagtaagt tatttaaaaa ataaaatgtt taaattattt tgttatatag 120\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'no'); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test1 (errorcode $errorcode errormsg $errormsg)\n"; exit;} | |
| ($expected_output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output_gff") || die "ERROR: test_convert_embl_to_gff: cannot open $expected_output_gff\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tCDS\t309654\t309719\t.\t-\t.\tratti_train136_1_0\;Parent=ratti_train136_1_mRNA\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tCDS\t309724\t310158\t.\t-\t.\tratti_train136_1_1\;Parent=ratti_train136_1_mRNA\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tgene\t309654\t310158\t.\t-\t.\tratti_train136_1\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tmRNA\t309654\t310158\t.\t-\t.\tratti_train136_1_mRNA\;Parent=ratti_train136_1\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tCDS\t308719\t308826\t.\t-\t.\tratti_train136_2_0\;Parent=ratti_train136_2_mRNA\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tgene\t308719\t308826\t.\t-\t.\tratti_train136_2\n"; | |
| print EXPECTED "Transfer1.PTRK.scaffold.00024.740435.final\tsource\tmRNA\t308719\t308826\t.\t-\t.\tratti_train136_2_mRNA\;Parent=ratti_train136_2\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output_gff $expected_output_gff |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test1 (output_gff $output_gff expected_output_gff $expected_output_gff)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| system "rm -f $expected_output_gff"; | |
| # TEST ERRORCODE=4 ($ratt IS NOT yes/no): | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID Transfer1.PTRK.scaffold.00024.740435.final ; ; ; ; ; 740435 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS complement(join(309654..309719,309724..310158))\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "FT CDS complement(308719..308826)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "SQ Sequence 740435 BP; 276856 A; 85528 C; 86034 G; 273093 T; 18924 other;\n"; | |
| print EMBL "ttagtttttc cagaagcttt agcttttcct ccttttctac gtcctgacat attaataata 60\n"; | |
| print EMBL "aagttataaa atgagtaagt tatttaaaaa ataaaatgtt taaattattt tgttatatag 120\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'hello'); | |
| if ($errorcode != 4) { print STDERR "ERROR: test_convert_embl_to_gff: failed test2\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| # TEST $ratt='yes': | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID Transfer1.PTRK.scaffold.00024.740435.final ; ; ; ; ; 740435 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS complement(join(309654..309719,309724..310158))\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "FT CDS complement(308719..308826)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence ratti_train136 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=7\n"; | |
| print EMBL "SQ Sequence 740435 BP; 276856 A; 85528 C; 86034 G; 273093 T; 18924 other;\n"; | |
| print EMBL "ttagtttttc cagaagcttt agcttttcct ccttttctac gtcctgacat attaataata 60\n"; | |
| print EMBL "aagttataaa atgagtaagt tatttaaaaa ataaaatgtt taaattattt tgttatatag 120\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'yes'); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test3\n"; exit;} | |
| ($expected_output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output_gff") || die "ERROR: test_convert_embl_to_gff: cannot open $expected_output_gff\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tCDS\t309654\t309719\t.\t-\t.\tratti_train136_1_0\;Parent=ratti_train136_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tCDS\t309724\t310158\t.\t-\t.\tratti_train136_1_1\;Parent=ratti_train136_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tgene\t309654\t310158\t.\t-\t.\tratti_train136_1\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tmRNA\t309654\t310158\t.\t-\t.\tratti_train136_1_mRNA\;Parent=ratti_train136_1\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tCDS\t308719\t308826\t.\t-\t.\tratti_train136_2_0\;Parent=ratti_train136_2_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tgene\t308719\t308826\t.\t-\t.\tratti_train136_2\n"; | |
| print EXPECTED "PTRK.scaffold.00024.740435\tsource\tmRNA\t308719\t308826\t.\t-\t.\tratti_train136_2_mRNA\;Parent=ratti_train136_2\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output_gff $expected_output_gff |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test3 (output_gff $output_gff expected_output_gff $expected_output_gff)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| system "rm -f $expected_output_gff"; | |
| # EXAMPLE LIKE THE EMBL FILES MADE BY THE SGAs: | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID PTRK.scaffold.00008.1453643; SV 1; linear; genomic DNA; HTG; INV; 1453643 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS join(115993..116307,116360..116413)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00008.1453643 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "FT CDS join(535391..535554,535599..537591,537642..537971)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence\n"; | |
| print EMBL "FT T2.PTRK.scaffold.00008.1453643.embl ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "SQ Sequence 1453643 BP; 541339 A; 172091 C; 169611 G; 546324 T; 24278 other;\n"; | |
| print EMBL "atctaaaagc ttcaaaaccg gctttaaagt cattgtgcag caaatagaaa ctaaaaaata 60\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'no'); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test4\n"; exit;} | |
| ($expected_output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output_gff") || die "ERROR: test_convert_embl_to_gff: cannot open $expected_output_gff\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tCDS\t115993\t116307\t.\t+\t.\tT1.PTRK.scaffold.00008.1453643_1_0;Parent=T1.PTRK.scaffold.00008.1453643_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tCDS\t116360\t116413\t.\t+\t.\tT1.PTRK.scaffold.00008.1453643_1_1;Parent=T1.PTRK.scaffold.00008.1453643_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tgene\t115993\t116413\t.\t+\t.\tT1.PTRK.scaffold.00008.1453643_1\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tmRNA\t115993\t116413\t.\t+\t.\tT1.PTRK.scaffold.00008.1453643_1_mRNA;Parent=T1.PTRK.scaffold.00008.1453643_1\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tCDS\t535391\t535554\t.\t+\t.\tT2.PTRK.scaffold.00008.1453643.embl_1_0;Parent=T2.PTRK.scaffold.00008.1453643.embl_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tCDS\t535599\t537591\t.\t+\t.\tT2.PTRK.scaffold.00008.1453643.embl_1_1;Parent=T2.PTRK.scaffold.00008.1453643.embl_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tCDS\t537642\t537971\t.\t+\t.\tT2.PTRK.scaffold.00008.1453643.embl_1_2;Parent=T2.PTRK.scaffold.00008.1453643.embl_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tgene\t535391\t537971\t.\t+\t.\tT2.PTRK.scaffold.00008.1453643.embl_1\n"; | |
| print EXPECTED "PTRK.scaffold.00008.1453643\tsource\tmRNA\t535391\t537971\t.\t+\t.\tT2.PTRK.scaffold.00008.1453643.embl_1_mRNA;Parent=T2.PTRK.scaffold.00008.1453643.embl_1\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output_gff $expected_output_gff |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test4 (output_gff $output_gff expected_output_gff $expected_output_gff)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| system "rm -f $expected_output_gff"; | |
| # ANOTHER EXAMPLE LIKE THE EMBL FILES MADE BY THE SGAs: | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID PTRK.scaffold.00010.1389350; SV 1; linear; genomic DNA; HTG; INV; 1389350 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS join(33177..33365,33583..34248,34731..35867)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ;\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350.embl sequence\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "FT CDS join(33177..33365,33583..34248,34731..35867)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ;\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350.embl sequence\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "SQ Sequence 1389350 BP; 500536 A; 170252 C; 170653 G; 506499 T; 41410 other;\n"; | |
| print EMBL "aaaatatgga cttgaaagat tcatttatat ttggcagtgc aattaccgtt gctttgtttt 60\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'no'); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test4\n"; exit;} | |
| ($expected_output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output_gff") || die "ERROR: test_convert_embl_to_gff: cannot open $expected_output_gff\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t33177\t33365\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_1_0;Parent=T1.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t33583\t34248\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_1_1;Parent=T1.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t34731\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_1_2;Parent=T1.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tgene\t33177\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_1\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tmRNA\t33177\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_1_mRNA;Parent=T1.PTRK.scaffold.00010.1389350_1\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t33177\t33365\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_2_0;Parent=T1.PTRK.scaffold.00010.1389350_2_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t33583\t34248\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_2_1;Parent=T1.PTRK.scaffold.00010.1389350_2_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t34731\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_2_2;Parent=T1.PTRK.scaffold.00010.1389350_2_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tgene\t33177\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_2\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tmRNA\t33177\t35867\t.\t+\t.\tT1.PTRK.scaffold.00010.1389350_2_mRNA;Parent=T1.PTRK.scaffold.00010.1389350_2\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output_gff $expected_output_gff |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test4 (output_gff $output_gff expected_output_gff $expected_output_gff)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| system "rm -f $expected_output_gff"; | |
| # CHECK FOR ERRORCODE=1 (GENE INFORMATION OVER MORE THAN 3 LINES): | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID PTRK.scaffold.00010.1389350; SV 1; linear; genomic DNA; HTG; INV; 1389350 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS join(33177..33365,33583..34248,34731..35867)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ;\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350.embl\n"; | |
| print EMBL "FT sequence\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350 ;\n"; | |
| print EMBL "FT gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "FT CDS join(33177..33365,33583..34248,34731..35867)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ;\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350.embl sequence\n"; | |
| print EMBL "FT T1.PTRK.scaffold.00010.1389350 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "SQ Sequence 1389350 BP; 500536 A; 170252 C; 170653 G; 506499 T; 41410 other;\n"; | |
| print EMBL "aaaatatgga cttgaaagat tcatttatat ttggcagtgc aattaccgtt gctttgtttt 60\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'no'); | |
| if ($errorcode != 1) { print STDERR "ERROR: test_convert_embl_to_gff: failed test4 (errorcode $errorcode errormsg $errormsg)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| # ANOTHER EXAMPLE LIKE THE EMBL FILES MADE BY THE SGAs: | |
| ($output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| ($input_embl,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EMBL,">$input_embl") || die "ERROR: test_convert_embl_to_gff: cannot open $input_embl\n"; | |
| print EMBL "ID PTRK.scaffold.00010.1389350; SV 1; linear; genomic DNA; HTG; INV; 1389350 BP.\n"; | |
| print EMBL "FH Key Location/Qualifiers\n"; | |
| print EMBL "FH\n"; | |
| print EMBL "FT CDS join(1186266..1186427,1186482..1186763)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence\n"; | |
| print EMBL "FT T30.PTRK.scaffold.00010.1389350 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "FT CDS join(1193863..1195911,1195975..1196085)\n"; | |
| print EMBL "FT /systematic_id=\"gene_id 0 ; sequence\n"; | |
| print EMBL "FT T31.PTRK.scaffold.00010.1389350 ; gene_orientation +\"\n"; | |
| print EMBL "FT /colour=1\n"; | |
| print EMBL "SQ Sequence 1389350 BP; 500536 A; 170252 C; 170653 G; 506499 T; 41410 other;\n"; | |
| print EMBL "aaaatatgga cttgaaagat tcatttatat ttggcagtgc aattaccgtt gctttgtttt 60\n"; | |
| close(EMBL); | |
| ($errorcode,$errormsg) = &convert_embl_to_gff($outputdir,$input_embl,$output_gff,'no'); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test5\n"; exit;} | |
| ($expected_output_gff,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output_gff") || die "ERROR: test_convert_embl_to_gff: cannot open $expected_output_gff\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t1186266\t1186427\t.\t+\t.\tT30.PTRK.scaffold.00010.1389350_1_0;Parent=T30.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t1186482\t1186763\t.\t+\t.\tT30.PTRK.scaffold.00010.1389350_1_1;Parent=T30.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tgene\t1186266\t1186763\t.\t+\t.\tT30.PTRK.scaffold.00010.1389350_1\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tmRNA\t1186266\t1186763\t.\t+\t.\tT30.PTRK.scaffold.00010.1389350_1_mRNA;Parent=T30.PTRK.scaffold.00010.1389350_1\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t1193863\t1195911\t.\t+\t.\tT31.PTRK.scaffold.00010.1389350_1_0;Parent=T31.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tCDS\t1195975\t1196085\t.\t+\t.\tT31.PTRK.scaffold.00010.1389350_1_1;Parent=T31.PTRK.scaffold.00010.1389350_1_mRNA\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tgene\t1193863\t1196085\t.\t+\t.\tT31.PTRK.scaffold.00010.1389350_1\n"; | |
| print EXPECTED "PTRK.scaffold.00010.1389350\tsource\tmRNA\t1193863\t1196085\t.\t+\t.\tT31.PTRK.scaffold.00010.1389350_1_mRNA;Parent=T31.PTRK.scaffold.00010.1389350_1\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output_gff $expected_output_gff |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_convert_embl_to_gff: failed test5 (output_gff $output_gff expected_output_gff $expected_output_gff)\n"; exit;} | |
| system "rm -f $input_embl"; | |
| system "rm -f $output_gff"; | |
| system "rm -f $expected_output_gff"; | |
| } | |
| #------------------------------------------------------------------# | |
| # SUBROUTINE TO MAKE A FILE NAME FOR A TEMPORARY FILE: | |
| sub make_filename | |
| { | |
| my $outputdir = $_[0]; # OUTPUT DIRECTORY TO WRITE TEMPORARY FILE NAME TO | |
| my $found_name = 0; # SAYS WHETHER WE HAVE FOUND A FILE NAME YET | |
| my $filename = "none";# NEW FILE NAME TO USE | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| my $poss_filename; # POSSIBLE FILE NAME TO USE | |
| my $random_number; # RANDOM NUMBER TO USE IN TEMPORARY FILE NAME | |
| while($found_name == 0) | |
| { | |
| $random_number = rand(); | |
| $poss_filename = $outputdir."/tmp".$random_number; | |
| if (!(-e $poss_filename)) | |
| { | |
| $filename = $poss_filename; | |
| $found_name = 1; | |
| } | |
| } | |
| if ($found_name == 0 || $filename eq 'none') | |
| { | |
| $errormsg = "ERROR: make_filename: found_name $found_name filename $filename\n"; | |
| $errorcode = 6; # ERRORCODE=6 | |
| return($filename,$errorcode,$errormsg); | |
| } | |
| return($filename,$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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