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April 4, 2013 14:48
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Perl script that, given an input file of DNA sequences of transcripts, infers their translations.
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| #!/usr/local/bin/perl | |
| =head1 NAME | |
| translate_spliced_dna.pl | |
| =head1 SYNOPSIS | |
| translate_spliced_dna.pl spliced_dna translated_dna outputdir | |
| where spliced_dna is the input fasta file of spliced DNA sequences for transcripts, | |
| translated_dna is the output fasta file of amino acid translations of transcripts, | |
| outputdir is the output directory for writing output files. | |
| =head1 DESCRIPTION | |
| This script reads in a fasta file of transcript DNA sequences (<spliced_dna>) and translates | |
| each transcript. It prints out a fasta file of amino acid sequences for transcripts (<translated_dna>). | |
| Note: this expects different genes to have unique names: two genes on different scaffolds cannot have the | |
| same name. | |
| =head1 VERSION | |
| Perl script last edited 2-Apr-2013. | |
| =head1 CONTACT | |
| alc@sanger.ac.uk (Avril Coghlan) | |
| =cut | |
| # | |
| # Perl script translate_spliced_dna.pl | |
| # Written by Avril Coghlan (alc@sanger.ac.uk) | |
| # 2-Apr-13. | |
| # Last edited 2-Apr-2013. | |
| # SCRIPT SYNOPSIS: translate_spliced_dna.pl: given an input file of DNA sequences of transcripts, infers their translations. | |
| # | |
| #------------------------------------------------------------------# | |
| # CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS: | |
| $num_args = $#ARGV + 1; | |
| if ($num_args != 3) | |
| { | |
| print "Usage of translate_spliced_dna.pl\n\n"; | |
| print "perl translate_spliced_dna_.pl <spliced_dna> <translated_dna> <outputdir>\n"; | |
| print "where <spliced_dna> is the input fasta file of spliced DNA sequences for transcripts,\n"; | |
| print " <translated_dna> is the output fasta file of amino acid translations of transcripts,\n"; | |
| print " <outputdir> is the output directory for writing output files.\n"; | |
| print "For example, >perl -w translate_spliced_dna.pl spliced_dna translated_dna /lustre/scratch108/parasites/alc/50HGI_maker_translations\n"; | |
| exit; | |
| } | |
| # FIND THE NAME OF THE INPUT FASTA FILE: | |
| $spliced_dna = $ARGV[0]; | |
| # FIND THE NAME OF THE OUTPUT FASTA FILE: | |
| $translated_dna = $ARGV[1]; | |
| # FIND THE NAME OF THE OUTPUT DIRECTORY: | |
| $outputdir = $ARGV[2]; | |
| # TEST SUBROUTINES: | |
| my $PRINT_TEST_DATA = 0; # SAYS WHETHER TO PRINT DATA USED DURING TESTING. | |
| &test_print_to_output($outputdir); | |
| &test_print_error; | |
| &test_read_assembly($outputdir); | |
| &test_write_out_translations($outputdir); | |
| &test_translate; | |
| &test_run_main_program($outputdir); | |
| print STDERR "Finished tests: now running main code...\n"; | |
| #------------------------------------------------------------------# | |
| # RUN THE MAIN PART OF THE CODE: | |
| ($errorcode,$errormsg) = &run_main_program($outputdir,$spliced_dna,$translated_dna); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| print STDERR "FINISHED.\n"; | |
| #------------------------------------------------------------------# | |
| # TEST &run_main_program | |
| sub test_run_main_program | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES INTO | |
| my $input; # INPUT FILE OF SPLICED DNA SEQUENCES | |
| my $output; # OUTPUT FILE OF TRANSLATIONS | |
| my $expected_output; # FILE CONTAINING EXPECTED CONTENT OF $output | |
| my $differences; # DIFFERENCES BETWEEN $output AND $expected_output | |
| my $length_differences; # LENGTH OF $differences | |
| my $line; # | |
| my @temp; # | |
| ($input,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(INPUT,">$input") || die "ERROR: test_run_main_program: cannot open $input\n"; | |
| print INPUT ">seq1\n"; | |
| print INPUT "ATGCAGTAA\n"; | |
| print INPUT ">seq2\n"; | |
| print INPUT "ATGGGTGCAACATTGTCTTCAACTTCTTCTTCACCATCTTCTATTGATGGAAGAGAAAATTTGATAAGAAGAAATAACACATCAACATACAATCATTTATTTGTCACACCTGGTAATACAAAAAATAAGAATAATAATTTTCTATTTGATTCAAAAAATCGGCACTCATCTCTTTCTTCATCTTCTTCTATGCTTGGTATTGCATGGAACTTTGCCAAAAAAACAACTACGGGAATTCCTAATAAAGAAAAAAGAAATATAAATAGATTATCATCATCTAGTTCAGTATCATCTGCTTTATCAAAATCTCATGATTCTGCAACTTCATTAACTTTTAATTCAAGTTTTTCTATTAATTCATCAAGTGACCAATTATCAGCATACTCTTCTAGTGCATCAAATTCTTCATCAGGTGATAGTGGTATTGGAATATCTAGAAAAATAACAATATCTAATCAATGTTATCATGAAATTGATGGCAAAAATAACAATAATAATATTGTAAATAATGTACCTACTTTAAATACTAATGAAAAATTTATTTGTATTAGAAAAAAAGAATCAATTTTATCAAGTAAAATAATGTCCGTACCATTAAATAATATAAAAAAAGGAAGTTCTAAAGTTCGTGATCATATATTAGCAATGACAAGATCAAAATCAACAAATATGCGTACAGAAAAAAATGGAAACATAATTATAAATGGTAATAATTATAATATTGAAAATAAATTTAATGATAATTTAAAATTATCATCAACAACTTATGATTATGAAAAAAAATTAAATCAAAATATAGAAAATAATATATCTAAATCATTGAAAAATGTTACTTTAACAAATCGAAATAATAATTCAAATTTATATAATACTGCAATATTTAATTTCGGCATTAAAAATGATAGTAATGTTATAGATAAAACAAGAAAAAAAACAATTATACAAGCATCAACAACTGAATTATTAAAAGGTGTTTCATTATTAATTACAACTAAATGTTCCCATAAAGTACCAGATTTTTTTGCTAATCAATTAACAATGTGGTTAAGAAGTGTTGATAGATCTTTAATTGTTCAGGGTTGGCAAGATATCGCATTTTTAAATCCAGCTAACATGGTATTTTTTTTTATGCTTTTAAGATCAATGCTTAATGATGAAGAAACATTTCCTGTTAATAATTTGGAAGACCTTCAAATGATTGTTTTTACTTGTTTATTTATTAGTTACAGTTACATGGGTAATGAAATTAGTTATCCGTTAAAACCATTTATTTCACAACAGGATCGCTCAAAATTTTGGGATATGTGTGTTCAAATAGTTAATAAATATTCTGGGGATATGTTACAATTAAATACATCAGCTTCATTTTTTACACAAGTTTTTAGTGATCTCAAAAATTTTACAACTATTGCTAACAATTAA\n"; | |
| close(INPUT); | |
| # WRITE OUT THE OUTPUT FILE OF TRANSLATED SEQUENCES: | |
| ($output,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| @temp = split(/\//,$output); | |
| $output = $temp[$#temp]; | |
| ($errorcode,$errormsg) = &run_main_program($outputdir,$input,$output); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_run_main_program: failed test1\n"; exit;} | |
| ($expected_output,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output") || die "ERROR: test_run_main_program: cannot open $expected_output\n"; | |
| print EXPECTED ">seq1\n"; | |
| print EXPECTED "MQ*\n"; | |
| print EXPECTED ">seq2\n"; | |
| print EXPECTED "MGATLSSTSSSPSSIDGRENLIRRNNTSTYNHLFVTPGNTKNKNNNFLFDSKNRHSSLSS\n"; | |
| print EXPECTED "SSSMLGIAWNFAKKTTTGIPNKEKRNINRLSSSSSVSSALSKSHDSATSLTFNSSFSINS\n"; | |
| print EXPECTED "SSDQLSAYSSSASNSSSGDSGIGISRKITISNQCYHEIDGKNNNNNIVNNVPTLNTNEKF\n"; | |
| print EXPECTED "ICIRKKESILSSKIMSVPLNNIKKGSSKVRDHILAMTRSKSTNMRTEKNGNIIINGNNYN\n"; | |
| print EXPECTED "IENKFNDNLKLSSTTYDYEKKLNQNIENNISKSLKNVTLTNRNNNSNLYNTAIFNFGIKN\n"; | |
| print EXPECTED "DSNVIDKTRKKTIIQASTTELLKGVSLLITTKCSHKVPDFFANQLTMWLRSVDRSLIVQG\n"; | |
| print EXPECTED "WQDIAFLNPANMVFFFMLLRSMLNDEETFPVNNLEDLQMIVFTCLFISYSYMGNEISYPL\n"; | |
| print EXPECTED "KPFISQQDRSKFWDMCVQIVNKYSGDMLQLNTSASFFTQVFSDLKNFTTIANN*\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output $expected_output |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_run_main_program: failed test1 (output $output expected_output $expected_output)\n"; exit;} | |
| system "rm -f $output"; | |
| system "rm -f $expected_output"; | |
| system "rm -f $input"; | |
| } | |
| #------------------------------------------------------------------# | |
| # RUN THE MAIN PART OF THE CODE: | |
| sub run_main_program | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES IN. | |
| my $spliced_dna = $_[1]; # FASTA FILE OF SPLICED DNA SEQUENCES | |
| my $translated_dna = $_[2]; # OUTPUT FASTA FILE OF TRANSLATIONS | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg = 'none';# RETURNED AS 'none' IF THERE IS NO ERROR. | |
| my $SEQ; # HASH TABLE OF SPLICED DNA SEQUENCES | |
| # READ IN THE FASTA FILE OF SPLICED DNA SEQUENCES: | |
| ($SEQ,$errorcode,$errormsg) = &read_assembly($spliced_dna); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # WRITE OUT THE OUTPUT FILE OF TRANSLATED SEQUENCES: | |
| ($errorcode,$errormsg) = &write_out_translations($SEQ,$translated_dna,$outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &write_out_translations | |
| sub test_write_out_translations | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES INTO | |
| my %SEQ = (); # HASH TABLE OF SPLICED DNA SEQUENCES | |
| my $output; # OUTPUT FILE OF TRANSLATIONS | |
| my $expected_output; # FILE CONTAINING EXPECTED CONTENT OF $output | |
| my $differences; # DIFFERENCES BETWEEN $output AND $expected_output | |
| my $length_differences; # LENGTH OF $differences | |
| my $line; # | |
| my @temp; # | |
| $SEQ{"seq1"} = "ATGCAGTAA"; | |
| $SEQ{"seq2"} = "ATGGGTGCAACATTGTCTTCAACTTCTTCTTCACCATCTTCTATTGATGGAAGAGAAAATTTGATAAGAAGAAATAACACATCAACATACAATCATTTATTTGTCACACCTGGTAATACAAAAAATAAGAATAATAATTTTCTATTTGATTCAAAAAATCGGCACTCATCTCTTTCTTCATCTTCTTCTATGCTTGGTATTGCATGGAACTTTGCCAAAAAAACAACTACGGGAATTCCTAATAAAGAAAAAAGAAATATAAATAGATTATCATCATCTAGTTCAGTATCATCTGCTTTATCAAAATCTCATGATTCTGCAACTTCATTAACTTTTAATTCAAGTTTTTCTATTAATTCATCAAGTGACCAATTATCAGCATACTCTTCTAGTGCATCAAATTCTTCATCAGGTGATAGTGGTATTGGAATATCTAGAAAAATAACAATATCTAATCAATGTTATCATGAAATTGATGGCAAAAATAACAATAATAATATTGTAAATAATGTACCTACTTTAAATACTAATGAAAAATTTATTTGTATTAGAAAAAAAGAATCAATTTTATCAAGTAAAATAATGTCCGTACCATTAAATAATATAAAAAAAGGAAGTTCTAAAGTTCGTGATCATATATTAGCAATGACAAGATCAAAATCAACAAATATGCGTACAGAAAAAAATGGAAACATAATTATAAATGGTAATAATTATAATATTGAAAATAAATTTAATGATAATTTAAAATTATCATCAACAACTTATGATTATGAAAAAAAATTAAATCAAAATATAGAAAATAATATATCTAAATCATTGAAAAATGTTACTTTAACAAATCGAAATAATAATTCAAATTTATATAATACTGCAATATTTAATTTCGGCATTAAAAATGATAGTAATGTTATAGATAAAACAAGAAAAAAAACAATTATACAAGCATCAACAACTGAATTATTAAAAGGTGTTTCATTATTAATTACAACTAAATGTTCCCATAAAGTACCAGATTTTTTTGCTAATCAATTAACAATGTGGTTAAGAAGTGTTGATAGATCTTTAATTGTTCAGGGTTGGCAAGATATCGCATTTTTAAATCCAGCTAACATGGTATTTTTTTTTATGCTTTTAAGATCAATGCTTAATGATGAAGAAACATTTCCTGTTAATAATTTGGAAGACCTTCAAATGATTGTTTTTACTTGTTTATTTATTAGTTACAGTTACATGGGTAATGAAATTAGTTATCCGTTAAAACCATTTATTTCACAACAGGATCGCTCAAAATTTTGGGATATGTGTGTTCAAATAGTTAATAAATATTCTGGGGATATGTTACAATTAAATACATCAGCTTCATTTTTTACACAAGTTTTTAGTGATCTCAAAAATTTTACAACTATTGCTAACAATTAA"; | |
| # WRITE OUT THE OUTPUT FILE OF TRANSLATED SEQUENCES: | |
| ($output,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| @temp = split(/\//,$output); | |
| $output = $temp[$#temp]; | |
| ($errorcode,$errormsg) = &write_out_translations(\%SEQ,$output,$outputdir); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_write_out_translation: failed test1\n"; exit;} | |
| ($expected_output,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED,">$expected_output") || die "ERROR: test_write_out_translations: cannot open $expected_output\n"; | |
| print EXPECTED ">seq1\n"; | |
| print EXPECTED "MQ*\n"; | |
| print EXPECTED ">seq2\n"; | |
| print EXPECTED "MGATLSSTSSSPSSIDGRENLIRRNNTSTYNHLFVTPGNTKNKNNNFLFDSKNRHSSLSS\n"; | |
| print EXPECTED "SSSMLGIAWNFAKKTTTGIPNKEKRNINRLSSSSSVSSALSKSHDSATSLTFNSSFSINS\n"; | |
| print EXPECTED "SSDQLSAYSSSASNSSSGDSGIGISRKITISNQCYHEIDGKNNNNNIVNNVPTLNTNEKF\n"; | |
| print EXPECTED "ICIRKKESILSSKIMSVPLNNIKKGSSKVRDHILAMTRSKSTNMRTEKNGNIIINGNNYN\n"; | |
| print EXPECTED "IENKFNDNLKLSSTTYDYEKKLNQNIENNISKSLKNVTLTNRNNNSNLYNTAIFNFGIKN\n"; | |
| print EXPECTED "DSNVIDKTRKKTIIQASTTELLKGVSLLITTKCSHKVPDFFANQLTMWLRSVDRSLIVQG\n"; | |
| print EXPECTED "WQDIAFLNPANMVFFFMLLRSMLNDEETFPVNNLEDLQMIVFTCLFISYSYMGNEISYPL\n"; | |
| print EXPECTED "KPFISQQDRSKFWDMCVQIVNKYSGDMLQLNTSASFFTQVFSDLKNFTTIANN*\n"; | |
| close(EXPECTED); | |
| $differences = ""; | |
| open(TEMP,"diff $output $expected_output |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_write_out_translation: failed test1 (output $output expected_output $expected_output)\n"; exit;} | |
| system "rm -f $output"; | |
| system "rm -f $expected_output"; | |
| } | |
| #------------------------------------------------------------------# | |
| # WRITE OUT THE OUTPUT FILE OF TRANSLATED SEQUENCES: | |
| sub write_out_translations | |
| { | |
| my $SEQ = $_[0]; # HASH TABLE WITH SPLICED DNA SEQUENCES FOR TRANSCRIPTS | |
| my $translated_dna = $_[1]; # OUTPUT FILE | |
| my $outputdir = $_[2]; # DIRECTORY TO PUT OUTPUT FILES INTO. | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR. | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR. | |
| my $seqname; # NAME OF A TRANSCRIPT | |
| my $seq; # DNA SEQUENCE OF A TRANSCRIPT | |
| # OPEN THE OUTPUT FILE: | |
| $translated_dna = $outputdir."/".$translated_dna; | |
| open(OUTPUT,">$translated_dna") || die "ERROR: write_out_translations: cannot open $translated_dna\n"; | |
| close(OUTPUT); | |
| # LOOP THROUGH ALL THE DNA SEQUENCES: | |
| foreach $seqname (keys %{$SEQ}) | |
| { | |
| $seq = $SEQ->{$seqname}; | |
| # TRANSLATE THIS SEQUENCE: | |
| ($seq,$errorcode,$errormsg) = &translate($seq); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| # WRITE OUT THE SEQUENCE IN THE OUTPUT FASTA FILE: | |
| ($errorcode,$errormsg) = &print_to_output($translated_dna,$seq,$seqname); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| } | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &translate | |
| sub test_translate | |
| { | |
| my $errorcode; # RETURNED AS 0 FROM A FUNCTION IF THERE IS NO ERROR | |
| my $errormsg; # RETURNED AS 'none' FROM A FUNCTION IF THERE IS NO ERROR | |
| my $seq; # TRANSLATED SEQUENCE | |
| ($seq,$errorcode,$errormsg) = &translate("ATGCAGTAA"); | |
| if ($errorcode != 0 || $seq ne "MQ*") { print STDERR "ERROR: test_translate: failed test1 (seq $seq errorcode $errorcode errormsg $errormsg)\n"; exit;} | |
| ($seq,$errorcode,$errormsg) = &translate("ATGGGTGCAACATTGTCTTCAACTTCTTCTTCACCATCTTCTATTGATGGAAGAGAAAATTTGATAAGAAGAAATAACACATCAACATACAATCATTTATTTGTCACACCTGGTAATACAAAAAATAAGAATAATAATTTTCTATTTGATTCAAAAAATCGGCACTCATCTCTTTCTTCATCTTCTTCTATGCTTGGTATTGCATGGAACTTTGCCAAAAAAACAACTACGGGAATTCCTAATAAAGAAAAAAGAAATATAAATAGATTATCATCATCTAGTTCAGTATCATCTGCTTTATCAAAATCTCATGATTCTGCAACTTCATTAACTTTTAATTCAAGTTTTTCTATTAATTCATCAAGTGACCAATTATCAGCATACTCTTCTAGTGCATCAAATTCTTCATCAGGTGATAGTGGTATTGGAATATCTAGAAAAATAACAATATCTAATCAATGTTATCATGAAATTGATGGCAAAAATAACAATAATAATATTGTAAATAATGTACCTACTTTAAATACTAATGAAAAATTTATTTGTATTAGAAAAAAAGAATCAATTTTATCAAGTAAAATAATGTCCGTACCATTAAATAATATAAAAAAAGGAAGTTCTAAAGTTCGTGATCATATATTAGCAATGACAAGATCAAAATCAACAAATATGCGTACAGAAAAAAATGGAAACATAATTATAAATGGTAATAATTATAATATTGAAAATAAATTTAATGATAATTTAAAATTATCATCAACAACTTATGATTATGAAAAAAAATTAAATCAAAATATAGAAAATAATATATCTAAATCATTGAAAAATGTTACTTTAACAAATCGAAATAATAATTCAAATTTATATAATACTGCAATATTTAATTTCGGCATTAAAAATGATAGTAATGTTATAGATAAAACAAGAAAAAAAACAATTATACAAGCATCAACAACTGAATTATTAAAAGGTGTTTCATTATTAATTACAACTAAATGTTCCCATAAAGTACCAGATTTTTTTGCTAATCAATTAACAATGTGGTTAAGAAGTGTTGATAGATCTTTAATTGTTCAGGGTTGGCAAGATATCGCATTTTTAAATCCAGCTAACATGGTATTTTTTTTTATGCTTTTAAGATCAATGCTTAATGATGAAGAAACATTTCCTGTTAATAATTTGGAAGACCTTCAAATGATTGTTTTTACTTGTTTATTTATTAGTTACAGTTACATGGGTAATGAAATTAGTTATCCGTTAAAACCATTTATTTCACAACAGGATCGCTCAAAATTTTGGGATATGTGTGTTCAAATAGTTAATAAATATTCTGGGGATATGTTACAATTAAATACATCAGCTTCATTTTTTACACAAGTTTTTAGTGATCTCAAAAATTTTACAACTATTGCTAACAATTAA"); | |
| if ($errorcode != 0 || $seq ne "MGATLSSTSSSPSSIDGRENLIRRNNTSTYNHLFVTPGNTKNKNNNFLFDSKNRHSSLSSSSSMLGIAWNFAKKTTTGIPNKEKRNINRLSSSSSVSSALSKSHDSATSLTFNSSFSINSSSDQLSAYSSSASNSSSGDSGIGISRKITISNQCYHEIDGKNNNNNIVNNVPTLNTNEKFICIRKKESILSSKIMSVPLNNIKKGSSKVRDHILAMTRSKSTNMRTEKNGNIIINGNNYNIENKFNDNLKLSSTTYDYEKKLNQNIENNISKSLKNVTLTNRNNNSNLYNTAIFNFGIKNDSNVIDKTRKKTIIQASTTELLKGVSLLITTKCSHKVPDFFANQLTMWLRSVDRSLIVQGWQDIAFLNPANMVFFFMLLRSMLNDEETFPVNNLEDLQMIVFTCLFISYSYMGNEISYPLKPFISQQDRSKFWDMCVQIVNKYSGDMLQLNTSASFFTQVFSDLKNFTTIANN*") { print STDERR "ERROR: test_translate: failed test2\n"; exit;} | |
| # TEST ERRORCODE=1 (NON-ACGTN BASES): | |
| ($seq,$errorcode,$errormsg) = &translate("ATGCAG-TAA"); | |
| if ($errorcode !=1) { print STDERR "ERROR: test_translate: failed test3 (seq $seq errorcode $errorcode errormsg $errormsg)\n"; exit;} | |
| } | |
| #------------------------------------------------------------------# | |
| # SUBROUTINE TO TRANSLATE A DNA SEQUENCE TO A PROTEIN SEQUENCE: | |
| sub translate | |
| { | |
| my $dna = $_[0]; # INPUT DNA SEQUENCE | |
| my $protein = ""; # PROTEIN SEQUENCE | |
| my $triplet; # A TRIPLET OF THE SEQUENCE | |
| my $aa; # AN AMINO ACID | |
| my $length; # LENGTH OF THE SEQUENCE | |
| my $i; # | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| my $first_base; # FIRST BASE OF TRIPLET | |
| my $second_base; # SECOND BASE OF TRIPLET | |
| my $third_base; # THIRD BASE OF TRIPLET | |
| my $protein_length_bp; # LENGTH OF THE PROTEIN SEQUENCE IN BASE-PAIRS | |
| $dna =~ tr/a-z/A-Z/; | |
| $length = length($dna); | |
| $protein = ""; | |
| for ($i = 0; $i <= $length-3; $i = $i+3) | |
| { | |
| $triplet = substr($dna,$i,3); | |
| $first_base = substr($triplet,0,1); | |
| $second_base = substr($triplet,1,1); | |
| $third_base = substr($triplet,2,1); | |
| if (($first_base ne 'A' && $first_base ne 'C' && $first_base ne 'G' && $first_base ne 'T' && $first_base ne 'N') || | |
| ($second_base ne 'A' && $second_base ne 'C' && $second_base ne 'G' && $second_base ne 'T' && $second_base ne 'N') || | |
| ($third_base ne 'A' && $third_base ne 'C' && $third_base ne 'G' && $third_base ne 'T' && $third_base ne 'N')) | |
| { | |
| $errormsg = "ERROR: translate: triplet $triplet contains non-ACGTN bases (first_base $first_base second_base $second_base third_base $third_base)\n"; | |
| $errorcode = 1; # ERRORCODE=1 (TESTED FOR) | |
| return($protein,$errorcode,$errormsg); | |
| } | |
| $aa = "none"; | |
| if ($triplet eq 'TTT') { $aa = 'F';} | |
| if ($triplet eq 'TTC') { $aa = 'F';} | |
| if ($triplet eq 'TTA') { $aa = 'L';} | |
| if ($triplet eq 'TTG') { $aa = 'L';} # 4 | |
| if ($triplet eq 'TCT') { $aa = 'S';} | |
| if ($triplet eq 'TCC') { $aa = 'S';} | |
| if ($triplet eq 'TCA') { $aa = 'S';} | |
| if ($triplet eq 'TCG') { $aa = 'S';} # 8 | |
| if ($triplet eq 'TAT') { $aa = 'Y';} | |
| if ($triplet eq 'TAC') { $aa = 'Y';} | |
| if ($triplet eq 'TAA') { $aa = '*';} | |
| if ($triplet eq 'TAG') { $aa = '*';} # 12 | |
| if ($triplet eq 'TGT') { $aa = 'C';} | |
| if ($triplet eq 'TGC') { $aa = 'C';} | |
| if ($triplet eq 'TGA') { $aa = '*';} | |
| if ($triplet eq 'TGG') { $aa = 'W';} # 16 | |
| if ($triplet eq 'CTT') { $aa = 'L';} | |
| if ($triplet eq 'CTC') { $aa = 'L';} | |
| if ($triplet eq 'CTA') { $aa = 'L';} | |
| if ($triplet eq 'CTG') { $aa = 'L';} # 20 | |
| if ($triplet eq 'CCT') { $aa = 'P';} | |
| if ($triplet eq 'CCC') { $aa = 'P';} | |
| if ($triplet eq 'CCA') { $aa = 'P';} | |
| if ($triplet eq 'CCG') { $aa = 'P';} # 24 | |
| if ($triplet eq 'CAT') { $aa = 'H';} | |
| if ($triplet eq 'CAC') { $aa = 'H';} | |
| if ($triplet eq 'CAA') { $aa = 'Q';} | |
| if ($triplet eq 'CAG') { $aa = 'Q';} # 28 | |
| if ($triplet eq 'CGT') { $aa = 'R';} | |
| if ($triplet eq 'CGC') { $aa = 'R';} | |
| if ($triplet eq 'CGA') { $aa = 'R';} | |
| if ($triplet eq 'CGG') { $aa = 'R';} # 32 | |
| if ($triplet eq 'ATT') { $aa = 'I';} | |
| if ($triplet eq 'ATC') { $aa = 'I';} | |
| if ($triplet eq 'ATA') { $aa = 'I';} | |
| if ($triplet eq 'ATG') { $aa = 'M';} # 36 | |
| if ($triplet eq 'ACT') { $aa = 'T';} | |
| if ($triplet eq 'ACC') { $aa = 'T';} | |
| if ($triplet eq 'ACA') { $aa = 'T';} | |
| if ($triplet eq 'ACG') { $aa = 'T';} # 40 | |
| if ($triplet eq 'AAT') { $aa = 'N';} | |
| if ($triplet eq 'AAC') { $aa = 'N';} | |
| if ($triplet eq 'AAA') { $aa = 'K';} | |
| if ($triplet eq 'AAG') { $aa = 'K';} # 44 | |
| if ($triplet eq 'AGT') { $aa = 'S';} | |
| if ($triplet eq 'AGC') { $aa = 'S';} | |
| if ($triplet eq 'AGA') { $aa = 'R';} | |
| if ($triplet eq 'AGG') { $aa = 'R';} # 48 | |
| if ($triplet eq 'GTT') { $aa = 'V';} | |
| if ($triplet eq 'GTC') { $aa = 'V';} | |
| if ($triplet eq 'GTA') { $aa = 'V';} | |
| if ($triplet eq 'GTG') { $aa = 'V';} # 52 | |
| if ($triplet eq 'GCT') { $aa = 'A';} | |
| if ($triplet eq 'GCC') { $aa = 'A';} | |
| if ($triplet eq 'GCA') { $aa = 'A';} | |
| if ($triplet eq 'GCG') { $aa = 'A';} # 56 | |
| if ($triplet eq 'GAT') { $aa = 'D';} | |
| if ($triplet eq 'GAC') { $aa = 'D';} | |
| if ($triplet eq 'GAA') { $aa = 'E';} | |
| if ($triplet eq 'GAG') { $aa = 'E';} # 60 | |
| if ($triplet eq 'GGT') { $aa = 'G';} | |
| if ($triplet eq 'GGC') { $aa = 'G';} | |
| if ($triplet eq 'GGA') { $aa = 'G';} | |
| if ($triplet eq 'GGG') { $aa = 'G';} # 64 | |
| if ($aa eq "none") { $aa = 'X';} # FOR AN UNKNOWN AMINO ACIDS JUST PUT X. | |
| $protein = $protein.$aa; | |
| } | |
| $protein_length_bp = length($protein) * 3; | |
| # IF THERE WERE 1 OR 2 OVERLHANGING BASES AT THE END OF THE SPLICED GENE DNA: | |
| if ($protein_length_bp < $length) | |
| { | |
| $protein = $protein."X"; | |
| } | |
| return($protein,$errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # WRITE OUT THE SEQUENCE IN THE OUTPUT FASTA FILE (THIS APPENDS TO AN EXISTING OUTPUT FILE): | |
| sub print_to_output | |
| { | |
| my $output_fasta = $_[0]; # OUTPUT FASTA FILE | |
| my $seq = $_[1]; # SEQUENCE | |
| my $name = $_[2]; # NAME OF THE SEQUENCE | |
| my $length; # LENGTH OF THE SEQUENCE | |
| my $offset; # | |
| my $a_line; # A LINE OF THE SEQUENCE | |
| my $errorcode = 0; # RETURNED AS 0 IF THERE IS NO ERROR | |
| my $errormsg = "none";# RETURNED AS 'none' IF THERE IS NO ERROR | |
| # MAKE AN OUTPUT FASTA FILE: | |
| open(OUTPUT,">>$output_fasta") || die "ERROR: print_to_output: cannot open output_fasta $output_fasta\n"; | |
| print OUTPUT ">$name\n"; | |
| $length = length($seq); | |
| $offset = 0; | |
| while ($offset < $length) | |
| { | |
| $a_line = substr($seq,$offset,60); | |
| print OUTPUT "$a_line\n"; | |
| $offset = $offset + 60; | |
| } | |
| # CLOSE THE OUTPUT FILE: | |
| close(OUTPUT); | |
| return($errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &print_to_output | |
| sub test_print_to_output | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY TO WRITE OUTPUT FILES IN | |
| my $output_fasta; # OUTPUT FILE | |
| my $seq; # SEQUENCE | |
| 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 $expected_output_fasta; # FILE CONTAINING EXPECTED CONTENTS OF $output_fasta | |
| my $differences; # DIFFERENCES BETWEEN $output_fasta AND $expected_output_fasta | |
| my $line; # | |
| my $length_differences; # LENGTH OF $differences | |
| ($output_fasta,$errorcode,$errormsg) = &make_filename($outputdir); | |
| open(OUTPUT,">$output_fasta") || die "ERROR: test_print_to_output: cannot open $output_fasta\n"; | |
| close(OUTPUT); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| $seq = "AAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGG"; | |
| ($errorcode,$errormsg) = &print_to_output($output_fasta,$seq,"seq1"); | |
| if ($errorcode != 0) { print STDERR "ERROR: test_print_to_output: failed test1\n"; exit;} | |
| ($expected_output_fasta,$errorcode,$errormsg) = &make_filename($outputdir); | |
| if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); } | |
| open(EXPECTED_OUTPUT,">$expected_output_fasta") || die "ERROR: test_print_to_output: cannot open $expected_output_fasta\n"; | |
| print EXPECTED_OUTPUT ">seq1\n"; | |
| print EXPECTED_OUTPUT "AAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGG\n"; | |
| print EXPECTED_OUTPUT "AAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGGAAAAATTTTTCCCCCGGGGG\n"; | |
| print EXPECTED_OUTPUT "AAAAATTTTTCCCCCGGGGG\n"; | |
| close(EXPECTED_OUTPUT); | |
| $differences = ""; | |
| open(TEMP,"diff $output_fasta $expected_output_fasta |"); | |
| while(<TEMP>) | |
| { | |
| $line = $_; | |
| $differences = $differences.$line; | |
| } | |
| close(TEMP); | |
| $length_differences = length($differences); | |
| if ($length_differences != 0) { print STDERR "ERROR: test_print_to_output: failed test1 (output_fasta $output_fasta expected_output_fasta $expected_output_fasta)\n"; exit;} | |
| system "rm -f $output_fasta"; | |
| system "rm -f $expected_output_fasta"; | |
| } | |
| #------------------------------------------------------------------# | |
| # TEST &read_assembly | |
| sub test_read_assembly | |
| { | |
| my $outputdir = $_[0]; # DIRECTORY WHERE WE CAN WRITE OUTPUT FILES | |
| my $random_number; # RANDOM NUMBER TO USE IN TEMPORARY FILE NAMES | |
| my $assembly; # TEMPORARY ASSEMBLY FILE NAME | |
| my $SEQ; # HASH TABLE WITH SEQUENCES OF SCAFFOLDS | |
| my $errorcode; # RETURNED AS 0 FROM A FUNCTION IF THERE IS NO ERROR | |
| my $errormsg; # RETURNED AS 'none' FROM A FUNCTION IF THERE IS NO ERROR | |
| $random_number = rand(); | |
| $assembly = $outputdir."/tmp".$random_number; | |
| open(ASSEMBLY,">$assembly") || die "ERROR: test_read_assembly: cannot open $assembly\n"; | |
| print ASSEMBLY ">seq1\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| print ASSEMBLY ">seq2\n"; | |
| print ASSEMBLY "AAAAATTTTT\n"; | |
| print ASSEMBLY "\n"; | |
| print ASSEMBLY ">seq3\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| print ASSEMBLY "TTTTT\n"; | |
| print ASSEMBLY ">seq4\n"; | |
| print ASSEMBLY ">seq5\n"; | |
| print ASSEMBLY " AAA AA \n"; | |
| close(ASSEMBLY); | |
| ($SEQ,$errorcode,$errormsg) = &read_assembly($assembly); | |
| if ($SEQ->{'seq1'} ne 'AAAAA' || $SEQ->{'seq2'} ne 'AAAAATTTTT' || $SEQ->{'seq3'} ne 'AAAAATTTTT' || defined($SEQ->{'seq4'}) || | |
| $SEQ->{'seq5'} ne 'AAAAA' || $errorcode != 0) | |
| { | |
| print STDERR "ERROR: test_read_assembly: failed test1\n"; | |
| exit; | |
| } | |
| system "rm -f $assembly"; | |
| $random_number = rand(); | |
| $assembly = $outputdir."/tmp".$random_number; | |
| open(ASSEMBLY,">$assembly") || die "ERROR: test_assembly: cannot open $assembly\n"; | |
| print ASSEMBLY ">seq1\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| print ASSEMBLY ">seq2\n"; | |
| print ASSEMBLY "AAAAATTTTT\n"; | |
| print ASSEMBLY ">seq1\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| close(ASSEMBLY); | |
| ($SEQ,$errorcode,$errormsg) = &read_assembly($assembly); | |
| if ($errorcode != 4) { print STDERR "ERROR: test_assembly: failed test2\n"; exit;} | |
| system "rm -f $assembly"; | |
| $random_number = rand(); | |
| $assembly = $outputdir."/tmp".$random_number; | |
| open(ASSEMBLY,">$assembly") || die "ERROR: test_assembly: cannot open $assembly\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| print ASSEMBLY ">seq2\n"; | |
| print ASSEMBLY "AAAAATTTTT\n"; | |
| print ASSEMBLY ">seq1\n"; | |
| print ASSEMBLY "AAAAA\n"; | |
| close(ASSEMBLY); | |
| ($SEQ,$errorcode,$errormsg) = &read_assembly($assembly); | |
| if ($errorcode != 5) { print STDERR "ERROR: test_assembly: failed test2\n"; exit;} | |
| system "rm -f $assembly"; | |
| } | |
| #------------------------------------------------------------------# | |
| # READ IN THE ASSEMBLY FILE: | |
| # SUBROUTINE SYNOPSIS: read_assembly(): read sequences in a fasta file into a hash | |
| sub read_assembly | |
| { | |
| my $input_assembly = $_[0]; # THE INPUT ASSEMBLY FILE | |
| 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 $scaffold = "none";# NAME OF SCAFFOLD | |
| my @temp; # | |
| my $seq; # SEQUENCE OF SCAFFOLD | |
| my %SEQ = (); # HASH TABLE FOR STORING SCAFFOLD SEQUENCE | |
| $seq = ""; | |
| open(ASSEMBLY,"$input_assembly") || die "ERROR: read_assembly: cannot open $input_assembly\n"; | |
| while(<ASSEMBLY>) | |
| { | |
| $line = $_; | |
| chomp $line; | |
| if (substr($line,0,1) eq '>') | |
| { | |
| if ($seq ne "") | |
| { | |
| if ($scaffold eq 'none') | |
| { | |
| $errormsg = "ERROR: read_assembly: do not know name of scaffold\n"; | |
| $errorcode = 5; # ERRORCODE=5 (TESTED FOR) | |
| return(\%SEQ,$errorcode,$errormsg); | |
| } | |
| if ($SEQ{$scaffold}) | |
| { | |
| $errormsg = "ERROR: read_assembly: already know sequence for scaffold $scaffold\n"; | |
| $errorcode = 4; # ERRORCODE=4 (TESTED FOR) | |
| return(\%SEQ,$errorcode,$errormsg); | |
| } | |
| $SEQ{$scaffold}= $seq; | |
| $seq = ""; | |
| } | |
| @temp = split(/\s+/,$line); | |
| $scaffold = $temp[0]; | |
| $scaffold = substr($scaffold,1,length($scaffold)-1); | |
| } | |
| else | |
| { | |
| $line =~ s/\s+//g; # REMOVE SPACES | |
| $seq = $seq.$line; | |
| } | |
| } | |
| close(ASSEMBLY); | |
| if ($seq ne "") | |
| { | |
| if ($scaffold eq 'none') | |
| { | |
| $errormsg = "ERROR: read_assembly: do not know name of scaffold\n"; | |
| $errorcode = 5; # ERRORCODE=5 (TESTED FOR) | |
| return(\%SEQ,$errorcode,$errormsg); | |
| } | |
| if ($SEQ{$scaffold}) | |
| { | |
| $errormsg = "ERROR: read_assembly: already know sequence for scaffold $scaffold\n"; | |
| $errorcode = 4; # ERRORCODE=4 (TESTED FOR) | |
| return(\%SEQ,$errorcode,$errormsg); | |
| } | |
| $SEQ{$scaffold} = $seq; | |
| $seq = ""; | |
| } | |
| return(\%SEQ,$errorcode,$errormsg); | |
| } | |
| #------------------------------------------------------------------# | |
| # 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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