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annotate fasta_to_bed.pl @ 0:1b3c339fd390 draft default tip

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planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
author nml
date Wed, 11 Oct 2017 11:46:25 -0400
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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1 #!/usr/bin/env perl
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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2 use strict;
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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3 use warnings;
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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4 use Bio::SeqIO;
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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5 use Bio::Seq;
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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6 use Getopt::Long;
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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8 my ($fasta_file, $out);
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
nml
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10 GetOptions(
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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11 "i|input=s" => \$fasta_file, #contigs fasta file
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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12 "o|output=s" => \$out
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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13 );
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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15 my $seqio_object= Bio::SeqIO->new (-format =>'fasta', -file=>$fasta_file);
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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16 open(my $out_fh, ">", $out) || die "Could write to file '$out'\n";
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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18 while (my $seq_object = $seqio_object->next_seq()) {
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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19 my $seq_id = $seq_object->display_id();
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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20 my $length = $seq_object->length();
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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21 print $out_fh $seq_id . "\t" . "1" . "\t" . $length . "\t" . $seq_id . "\n";
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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23 }
1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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1b3c339fd390 planemo upload for repository https://github.com/phac-nml/galaxy_tools commit a0204b99a722240fe9b03b78a0786b30aa8ecc96
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