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avrilcoghlan/embl_to_fasta.pl

Created January 7, 2013 11:56
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Perl script to convert an embl format file to a fasta format file
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embl_to_fasta.pl
#!/usr/local/bin/perl
=head1 NAME
embl_to_fasta.pl
=head1 SYNOPSIS
embl_to_fasta.pl input_embl output_fasta outputdir
where input_embl is the input embl file,
output_fasta is the output fasta file,
outputdir is the output directory for writing output files.
=head1 DESCRIPTION
This script takes an input embl file (<input_embl>), and converts it to
fasta format, and writes the output file (<output_fasta>) in directory
<outputdir>.
=head1 VERSION
Perl script last edited 3-Jan-2013.
=head1 CONTACT
[email protected] (Avril Coghlan)
=cut
#
# Perl script embl_to_fasta.pl
# Written by Avril Coghlan ([email protected])
# 3-Jan-13.
# Last edited 3-Jan-2013.
#
#------------------------------------------------------------------#
# CHECK IF THERE ARE THE CORRECT NUMBER OF COMMAND-LINE ARGUMENTS:
use strict;
use warnings;
my $num_args = $#ARGV + 1;
if ($num_args != 3)
{
print "Usage of embl_to_fasta.pl\n\n";
print "perl embl_to_fasta.pl <input_embl> <output_fasta> <outputdir>\n";
print "where <input_embl> is the input embl file,\n";
print " <output_fasta> is the output fasta file,\n";
print " <outputdir> is the output directory for writing output files\n";
print "For example, >perl embl_to_fasta.pl Pk_strainH_chr01.embl Pk_strainH_chr01.fa\n";
print "/lustre/scratch108/parasites/alc/RNA-SeQC/Pknowlesi\n";
exit;
}
# FIND THE PATH TO THE INPUT EMBL FILE:
my $input_embl = $ARGV[0];
# FIND THE PATH TO THE OUTPUT FASTA FILE:
my $output_fasta = $ARGV[1];
# FIND THE DIRECTORY TO USE FOR OUTPUT FILES:
my $outputdir = $ARGV[2];
#------------------------------------------------------------------#
# TEST SUBROUTINES:
my $PRINT_TEST_DATA = 0; # SAYS WHETHER TO PRINT DATA USED DURING TESTING.
&test_print_to_output($outputdir);
&test_convert_embl_to_fasta($outputdir);
&test_print_error;
#------------------------------------------------------------------#
# RUN THE MAIN PART OF THE CODE:
&run_main_program($outputdir,$input_embl,$output_fasta);
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_fasta = $_[2]; # THE OUTPUT FASTA FILE
my $errorcode; # RETURNED AS 0 IF THERE IS NO ERROR.
my $errormsg; # RETURNED AS 'none' IF THERE IS NO ERROR.
# READ IN THE INPUT EMBL FILE, AND MAKE THE OUTPUT FASTA FILE:
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); }
}
#------------------------------------------------------------------#
# READ IN THE INPUT EMBL FILE, AND MAKE THE OUTPUT FASTA FILE:
sub convert_embl_to_fasta
{
my $outputdir = $_[0]; # DIRECTORY TO PUT OUTPUT FILES IN
my $input_embl = $_[1]; # INPUT EMBL FILE
my $output_fasta = $_[2]; # OUTPUT FASTA FILE
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 $expected_length = "none";# EXPECTED LENGTH OF THE SEQUENCE
my $found_seq_start = 0; # SAYS WHETHER THE SEQUENCE WAS FOUND
my $seq = ""; # SEQUENCE
my $i; #
my $found_file_end = 0; # SAYS WHETHER WE FOUND THE END OF THE FILE
my $length; # LENGTH OF SEQUENCE $seq
# READ IN THE INPUT EMBL FILE:
open(EMBL,"$input_embl") || die "ERROR: convert_embl_to_fasta: cannot open input_embl $input_embl\n";
while(<EMBL>)
{
$line = $_;
chomp $line;
@temp = split(/\s+/,$line);
if (substr($line,0,2) eq 'ID')
{
if ($name ne 'none' || $expected_length ne 'none')
{
$errormsg = "ERROR: convert_embl_to_fasta: name $name expected_length $expected_length\n";
$errorcode = 1; # ERRORCODE=1
return($errorcode,$errormsg);
}
$name = $temp[1];
$expected_length = $temp[$#temp-1];
}
elsif (substr($line,0,2) eq 'SQ')
{
if ($found_seq_start == 1)
{
$errormsg = "ERROR: convert_embl_to_fasta: found_seq_start $found_seq_start\n";
$errorcode = 3; # ERRORCODE=3
return($errorcode,$errormsg);
}
$found_seq_start = 1;
}
elsif ($found_seq_start == 1 && substr($line,0,2) ne '//')
{
for ($i = 1; $i <= $#temp-1; $i++) { $seq = $seq.$temp[$i];}
}
elsif ($found_seq_start == 1 && substr($line,0,2) eq '//')
{
$found_file_end = 1;
}
}
close(EMBL);
if ($name eq 'none' || $expected_length eq 'none')
{
$errormsg = "ERROR: convert_embl_to_fasta: name $name expected_length $expected_length\n";
$errorcode = 2; # ERRORCODE=2
return($errorcode,$errormsg);
}
if ($found_seq_start == 0)
{
$errormsg = "ERROR: convert_embl_to_fasta: found_seq_start $found_seq_start\n";
$errorcode = 4; # ERRORCODE=4
return($errorcode,$errormsg);
}
if ($found_file_end == 0)
{
$errormsg = "ERROR: convert_embl_to_fasta: found_file_end $found_file_end\n";
$errorcode = 5; # ERRORCODE=5
return($errorcode,$errormsg);
}
$length = length($seq);
if ($length != $expected_length)
{
$errormsg = "ERROR: convert_embl_to_fasta: length $length expected_length $expected_length\n";
$errorcode = 7; # ERRORCODE=7
return($errorcode,$errormsg);
}
# WRITE OUT THE SEQUENCE IN THE OUTPUT FASTA FILE:
($errorcode,$errormsg) = &print_to_output($output_fasta,$seq,$name);
if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); }
}
#------------------------------------------------------------------#
# TEST &convert_embl_to_fasta
sub test_convert_embl_to_fasta
{
my $outputdir = $_[0]; # DIRECTORY TO WRITE OUTPUT FILES IN
my $input_embl; # NAME OF EMBL FILE
my $output_fasta; # NAME OF OUTPUT FASTA 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_fasta; # FILE CONTAINING THE EXPECTED CONTENTS OF $output_fasta
my $differences; # DIFFERENES BETWEEN $output_fasta AND $expected_output_fasta
my $length_differences; # LENGTH OF $differences
my $line; #
($output_fasta,$errorcode,$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); }
system "wget --quiet http://www.maths.tcd.ie/~avrillee/tests/embl_to_fasta_1.embl -O $input_embl";
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 0) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test1\n"; exit;}
($expected_output_fasta,$errorcode,$errormsg) = &make_filename($outputdir);
if ($errorcode != 0) { ($errorcode,$errormsg) = &print_error($errormsg,$errorcode,0); }
open(EXPECTED,">$expected_output_fasta") || die "ERROR: test_convert_embl_to_fasta: cannot open $expected_output_fasta\n";
print EXPECTED ">SC10H5\n";
print EXPECTED "gatcagtagacccagcgacagcagggcggggcccagcaggccggccgtggcgtagagcgc\n";
print EXPECTED "gaggacggcgaccggcgtggccaccgacaggatggctgcggcgacgcggacgacaccgga\n";
print EXPECTED "gtgtgccagggcccaccacacgccgatggccgcgagcgcgagtcccgcgctgccgaacag\n";
print EXPECTED "ggcccacagcacactgcgcagaccggcggccacgagtggcgccaggacggtgcccagcag\n";
print EXPECTED "gagcagcagggtgacgtgggcgcgcgctgcactgtggccgccccgtccgcccgacgcgcg\n";
print EXPECTED "cggctcgtcatctcgcggtcccaccaccggtcggccccattactcgtcctcaaccctgtg\n";
print EXPECTED "gcgactgacgttccccggacaggtcgtaccgattgccgccacgccccaccacgcacaggg\n";
print EXPECTED "cccagacgacgaagcctgacatggtgatcatgacgacggaccacaccgggtagtacggca\n";
print EXPECTED "gcgagaggaagttggcgatgatcaccagcccggcgatggcgaccccggtgacacgtgccc\n";
print EXPECTED "acatcgccgttttgagcagcccggcgctgacgaccatggcgagcgcgccgagcgcgagat\n";
print EXPECTED "ggatccacccccacccggtgagatcgaactggaaaacgtagttgggcgtggtgacgaaga\n";
print EXPECTED "cgtcgtcctcggcgatggccatgatgccccggaagaggctgagcagcccggcgaggaaga\n";
print EXPECTED "gcatcaccgccgcgaaggcggtaaggcccgtcgcccattcctgcctcgcggtgtgtgccg\n";
print EXPECTED "ggtggtgggtatgtgacgtggtcatctcggacctcgtttcgtggaatgcggatgcttcag\n";
print EXPECTED "cgagcggaggcgccggtgcccgccgcgcccgtgtgccctgccgggccgtgaccggacagg\n";
print EXPECTED "accaattccttcgccttgcggaactcctcgtccgtgatggcaccccggtctcggatctcg\n";
print EXPECTED "gagagccgggccagctcgtcgacgctgctggacccgccgcccacggtcttcctgatgtag\n";
print EXPECTED "gcgtcgaactcctcctgctgagcccgtgcccgcgttgtctcccggctgcccatgttcttg\n";
print EXPECTED "ccgcgagcgatcacgtagacgaaaacgcccaggaagggcaggaggatgcagaacaccaac\n";
print EXPECTED "cagccggccttcgcccagccactcagtccgtcgtcccggaagatgtcggtgacgacgcgg\n";
print EXPECTED "aagagcaggacgaaccacatgatccacaggaagatcatcagcatcgtccagaaggcaccc\n";
print EXPECTED "agcagtgggtagtcgtacgccaggtaggtctgtgcactcatgtccgtcctccgtcctccg\n";
print EXPECTED "gggcgcggcccggcggccctcgttccgtactgacatcagggtggtcacgggtcccaccgg\n";
print EXPECTED "tcggcatcacccggcacgggtgagtggggcgccgaggccgtcgtggtcaggcccgggaca\n";
print EXPECTED "ccggtgtgaccctggtggaaggacgcgtcccgtggggcacgcaccgccggccgagggcga\n";
print EXPECTED "ccaccgcctcggtcagtccgagcaggcccagccacaggccgagaagtcgggtcagggcac\n";
print EXPECTED "gggccgactcggcgggcagcgcgaggacgacgattccggcgacgtcgacggccagcgggt\n";
print EXPECTED "tgcgcaggcccagcactccggccggggcgcccggcaccagcgtggcgagggccgatgcca\n";
print EXPECTED "tgagccaggtccaggaacccccaagcctggcgaggacgtgcgccggatcgctcaatgctc\n";
print EXPECTED "cggtgaccgccccgcccgacccgtctcccttgtcggcaggttccgccgcatcacgcggaa\n";
print EXPECTED "cggagatggctcccctgtggatcgggcggccgctgcggggccgcccggttggtcggtcgg\n";
print EXPECTED "tgagcgccggactcccccttcagctcttccagggtcggggtcgacaccgaggtcctggat\n";
print EXPECTED "cacccgtcaggggtgatccgggcatgccgtcgtggcggtgaggtgggatacgggaacgat\n";
print EXPECTED "cggcccacgggggaccggacgagacgaagagacgtgagatgagcgatacgaactcgggcg\n";
print EXPECTED "gcgggcgccaggccgcttccggaccggccccacgtggccgactccctttccgccggcgcg\n";
print EXPECTED "tggccctggtcgctgtcgcacgtcccctgatcgtcacggtcggtctcgtcaccgcctact\n";
print EXPECTED "acctgcttcccctggacgagagactcagcgccggcaccctggtgtcgctggtgtgcggac\n";
print EXPECTED "tgctcgcagtccttctggtgttctgctgggaggtgcgggccatcacgcgctccccgcatc\n";
print EXPECTED "cgcgtctgagagcgatcgagggcctggccgccacgctggtgctgttcctggtcctcttcg\n";
print EXPECTED "ccggctcctactacctgctgggtcgctccgcgcccggctccttcagcgagccgctgaaca\n";
print EXPECTED "ggacggacgcgctgtacttcactctgaccacgttcgccaccgtcggcttcggggacatca\n";
print EXPECTED "ccgcacgctccgagaccgggcggatcctcacgatggcgcagatgacgggagggctactgc\n";
print EXPECTED "tcgtcggagtcgccgcccgggtgctggcgagcgcagtgcaggcggggctgcaccgacagg\n";
print EXPECTED "gccggggaccggcggcatcgccacgctccggtgctgcggaggagccggaggccggaccat\n";
print EXPECTED "gaccgtacccggtggcttcaccgcctccctgccgccggccgagcgagccgcgtacggcag\n";
print EXPECTED "gaaggcccgtaaaagggcctcacgttcgtgccacggctggtacgagccggggcagcggcg\n";
print EXPECTED "gcctgaccccgtcgacctgctggagcgccagtccggcgagcgtgtcccggcactcgtgcc\n";
print EXPECTED "catccgctacggtcgcatgctggagtcgccgttccgcttctaccgcggtgcggcagcgat\n";
print EXPECTED "catggcggcggacctggcacccctgcccagcagcggactccaggtgcaattgtgcgggga\n";
print EXPECTED "cgcgcacccgttgaacttccggctcctggcctcaccggagcgccggctggtcttcgacat\n";
print EXPECTED "caacgacttcgacgagacgctgcccggccccttcgagtgggacgtcaaacggctggcggc\n";
print EXPECTED "cggattcgtgatcgcggcccggtcgaacggcttctcgtccaaggaacagaaccgcaccgt\n";
print EXPECTED "tcgggcctgtgtgcgggcctaccgggagcgcatgagggagttcgccgtcatgccgaccct\n";
print EXPECTED "ggacatctggtacgcccaggacgacgccgaccacgtacggcaactgctggctacggaggc\n";
print EXPECTED "cagaggagaagctgagcagcggctcagggacgcggctgcgaaggcccgcacacgcaccca\n";
print EXPECTED "catgagggcgttcgcgaagctcacccgcgtcacggccgagggccggcgcatcacccccga\n";
print EXPECTED "cccgccgctgatcaccccactcggcgatctgctcaccgacccggccgaagccggccggga\n";
print EXPECTED "ggaggaactgcggtccgtcgtgaacggctacgcacggtccctgccgcccgagcgccggca\n";
print EXPECTED "cctgctgcgtcactaccggcttgtggacatggcgcgcaaggtggtcggcgtcggcagtgt\n";
print EXPECTED "cggcacccgctgctgggtactgcttctgctcggcagggacgacgacgatcctctgctgct\n";
print EXPECTED "ccaggccaaggaagcctcggaatcggtgctggcggcccacacgggcggcgaacgctacga\n";
print EXPECTED "ccatcagggccgcagggtcgtggccggccagcgtctgatccagaccaccggtgacatctt\n";
print EXPECTED "tctcggctgggcgcgcgtcaccggcttcgacggaaaggcccgggacttctacgtgcgtca\n";
print EXPECTED "actgtgggactggaagggcgtcgcgcggccggaaaccatggggcccgacctgctctccct\n";
print EXPECTED "cttcgcccggctgtgcggtgcctgcctggcgagggcccacgcccgttccggtgaccccgt\n";
print EXPECTED "cgcgctcgccgcgtacctgggcggcagcgaccgcttcgacggcgcgctcaccgagttcgc\n";
print EXPECTED "ccagtcctacgccgatcagaatgaacgcgaccacgaagctctgctggcggcctgccgctc\n";
print EXPECTED "cggcagggtcacggccgcccgtttgtgaggccgacccgggaacggccggcgggctggcac\n";
print EXPECTED "acaccgccgccggtcggcgtcattccggaagctgccgcatctccaggacgcgcaggccca\n";
print EXPECTED "gcgactggcagcgggtgagcaacccgtacagatgggcctcgtcgatcaccgtgccgaaca\n";
print EXPECTED "gcacggtctggccggacatgacgacgtgctccagctccgggaacgcgttggccagcgtcc\n";
print EXPECTED "gtgacaggtgtccctcgacgcggatctcgtagcgcacgagcggtcctttcaccgtaggag\n";
print EXPECTED "ctcgggacaccgcccggggctccgggtcggacggtgctcttggtgacgagcctgcgcctc\n";
print EXPECTED "gtcgccctccggtgccctcacccagcacaggtgactccaaccgcagtgtcagtgcctttc\n";
print EXPECTED "agtgcgtcactgtgatcttgacgacgacgatcaccaggccgagcagtacgttgaccgtcg\n";
print EXPECTED "cggtgacggccaccagtcgtcgcgaggcgcccgcgcggtgcgccgcggcgacggaccagc\n";
print EXPECTED "ccacctgaccggcgacggcgacggacagcgccagccacagggtgcccgggacgtccagcc\n";
print EXPECTED "ccagtacggggctgacggcgatggccgcggccggaggcacggcggccttgacgatcggcc\n";
print EXPECTED "actcctcgcggcacacacgcagaatcacccgccggtccggagtgtgccgcgcgagacgcg\n";
print EXPECTED "ctccgaacagttcggcgtggacgtgagcgatccagaacaccaagctggtgagcaacagca\n";
print EXPECTED "gaagaaccagttcggcgcgggggaacgagcccagggtgccggcgccgatcacgacggagg\n";
print EXPECTED "ctgcgagcat\n";
close(EXPECTED);
$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_convert_embl_to_fasta: failed test1 (output_fasta $output_fasta expected_output_fasta $expected_output_fasta)\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
system "rm -f $expected_output_fasta";
# TEST FOR ERRORCODE=1 (ID. APPEARS TWICE IN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 1) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test2\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
# TEST FOR ERRORCODE=2 (ID. DOES NOT APPEAR IN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n";
print EMBL " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n";
print EMBL " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n";
print EMBL " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n";
print EMBL " ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag 240\n";
print EMBL " gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg 300\n";
print EMBL " cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg 360\n";
print EMBL "//\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 2) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test3\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
# TEST FOR ERRORCODE=3 (TWO SEQUENCES IN AN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
print EMBL "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n";
print EMBL " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n";
print EMBL " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n";
print EMBL " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n";
print EMBL " ggcccacagc acactgcgca gaccggcggc cacgagtggc gccaggacgg tgcccagcag 240\n";
print EMBL " gagcagcagg gtgacgtggg cgcgcgctgc actgtggccg ccccgtccgc ccgacgcgcg 300\n";
print EMBL " cggctcgtca tctcgcggtc ccaccaccgg tcggccccat tactcgtcct caaccctgtg 360\n";
print EMBL "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n";
print EMBL " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n";
print EMBL " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n";
print EMBL " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n";
print EMBL "//\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 3) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test4\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
# TEST FOR ERRORCODE=4 (NO SEQUENCE IN AN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 4) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test5\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
# TEST FOR ERRORCODE=5 (NO END-OF-FILE SYMBOL IN AN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
print EMBL "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n";
print EMBL " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n";
print EMBL " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n";
print EMBL " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 5) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test6\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
# TEST FOR ERRORCODE=7 (WRONG SEQUENCE LENGTH IN AN EMBL FILE):
($output_fasta,$errorcode,$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_fasta: cannot open input_embl $input_embl\n";
print EMBL "ID SC10H5 standard; DNA; PRO; 4870 BP.\n";
print EMBL "SQ Sequence 4870 BP; 769 A; 1717 C; 1693 G; 691 T; 0 other;\n";
print EMBL " gatcagtaga cccagcgaca gcagggcggg gcccagcagg ccggccgtgg cgtagagcgc 60\n";
print EMBL " gaggacggcg accggcgtgg ccaccgacag gatggctgcg gcgacgcgga cgacaccgga 120\n";
print EMBL " gtgtgccagg gcccaccaca cgccgatggc cgcgagcgcg agtcccgcgc tgccgaacag 180\n";
print EMBL "//\n";
close(EMBL);
($errorcode,$errormsg) = &convert_embl_to_fasta($outputdir,$input_embl,$output_fasta);
if ($errorcode != 7) { print STDERR "ERROR: test_convert_embl_to_fasta: failed test7\n"; exit;}
system "rm -f $input_embl";
system "rm -f $output_fasta";
}
#------------------------------------------------------------------#
# WRITE OUT THE SEQUENCE IN THE OUTPUT FASTA 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($outputdir);
if ($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";
}
#------------------------------------------------------------------#
# 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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