Mercurial > repos > edward-kirton > roche454_toolsuite
annotate roche454/sff_to_fastq_converter.pl @ 1:368a6ebebdde
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | edward-kirton |
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date | Tue, 07 Jun 2011 17:51:04 -0400 |
parents | f036c7107601 |
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rev | line source |
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f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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1 #!/usr/bin/env perl |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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2 |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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3 use warnings; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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4 use strict; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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5 use Getopt::Long; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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6 use File::Basename; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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7 |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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8 # VALIDATE INPUT |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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9 die("Expected 3 args") unless @ARGV == 3; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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10 my ($sff, $extra_files_path, $fastq) = @ARGV; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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11 |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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12 # DEFINE PATHS |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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13 mkdir($extra_files_path) unless -d $extra_files_path; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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14 my $base = basename($sff); |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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15 my $fasta = "$extra_files_path/$base.fasta"; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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16 my $qual = "$extra_files_path/$base.qual"; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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17 |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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18 # GENERATE FASTA, QUAL, FASTQ |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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19 my $outf; |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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20 my $out; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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21 eval { $out=`sffinfo -seq $sff > $fasta` }; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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22 die("ERROR: $out") if $@; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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23 print $out; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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24 eval { $out=`sffinfo -qual $sff > $qual` }; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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25 die("ERROR: $out") if $@; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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26 print $out; |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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27 eval { $out=`fasta_qual_to_fastq $fasta $qual $fastq` }; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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28 die("ERROR: $out") if $@; |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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29 print $out; |
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Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
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30 unlink($fasta, $qual); |
f036c7107601
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
edward-kirton
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31 exit 0; |