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annotate libs/sratoolkit.2.8.0-centos_linux64/example/perl/dump-reference.pl @ 3:38ad1130d077 draft

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planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
author charles_s_test
date Mon, 27 Nov 2017 11:21:07 -0500
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1 #!/usr/bin/env perl
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2 # ===========================================================================
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3 #
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4 # PUBLIC DOMAIN NOTICE
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5 # National Center for Biotechnology Information
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6 #
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7 # This software/database is a "United States Government Work" under the
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8 # terms of the United States Copyright Act. It was written as part of
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9 # the author's official duties as a United States Government employee and
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10 # thus cannot be copyrighted. This software/database is freely available
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11 # to the public for use. The National Library of Medicine and the U.S.
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12 # Government have not placed any restriction on its use or reproduction.
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13 #
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14 # Although all reasonable efforts have been taken to ensure the accuracy
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15 # and reliability of the software and data, the NLM and the U.S.
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16 # Government do not and cannot warrant the performance or results that
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17 # may be obtained by using this software or data. The NLM and the U.S.
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18 # Government disclaim all warranties, express or implied, including
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19 # warranties of performance, merchantability or fitness for any particular
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20 # purpose.
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21 #
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22 # Please cite the author in any work or product based on this material.
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23 #
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24 # ===========================================================================
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25
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26 use warnings;
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27
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28 my %opts = (
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29 'local-name' => 0,
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30 'line-length' => 70
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31 );
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32
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33 sub usage()
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34 {
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35 print <<"HELP";
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36 extracts the reference sequence as FASTA from an aligned SRA
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37
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38 Usage:
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39 $0 [<options>...] <accession>...
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40 options are
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41 -h | -? | --help this message
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42 --use-local toggle def-line between reference accession and
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43 original (local to run) name of reference
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44 --line-length N sequence line length (use 0 for unlimited)
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45 (default is $opts{'line-length'})
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46
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47 Example:
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48 $0 SRR341548 > ref.fasta
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49
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50 HELP
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51 exit 0;
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52 }
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53
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54 usage if scalar @ARGV == 0;
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55 foreach (@ARGV) {
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56 usage() if (/^-h$/ || /^-\?$/ || /^--help$/);
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57 }
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58
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59 my $VDB_DUMP = `which vdb-dump` or die "Please put path to vdb-dump in PATH";
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60 chomp $VDB_DUMP;
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61
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62 sub process($)
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63 {
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64 my $defline = '';
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65 my $ref = '';
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66
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67 open IN, '-|', "$VDB_DUMP -f tab -T REFERENCE -C \"NAME,SEQ_ID,READ\" \"$_[0]\"" or die "$!";
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68
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69 while (defined($_ = <IN>)) {
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70 chomp;
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71 my ($name, $seqid, $seq) = \split /\t/;
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72 my $new_defline;
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73
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74 if ($opts{'local-name'}) {
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75 $new_defline = ">$$name $$seqid";
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76 }
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77 else {
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78 $new_defline = ">$$seqid $$name";
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79 }
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80 if ($defline ne $new_defline) {
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81 print "$ref\n" if $ref;
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82 print "$new_defline\n";
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83 $defline = $new_defline;
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84 $ref = '';
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85 }
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86 $ref .= $$seq;
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87 if ($opts{'line-length'} != 0) {
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88 while (length($ref) >= $opts{'line-length'}) {
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89 print substr($ref, 0, $opts{'line-length'})."\n";
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90 $ref = substr($ref, $opts{'line-length'});
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91 }
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92 }
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93 }
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94 print "$ref\n" if $ref;
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95 close IN;
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96 }
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97
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98 for (my $i = 0; $i < scalar @ARGV; ++$i) {
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99 $_ = $ARGV[$i];
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100
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101 if (/^-/) {
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102 if (/^--use-local$/) {
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103 $opts{'local-name'} = 1 - $opts{'local-name'};
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104 next;
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105 }
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106 if (/^--line-length$/) {
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107 $_ = $ARGV[++$i];
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108 /^(\d+)$/ or usage();
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109 $opts{'line-length'} = $1;
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110 next;
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111 }
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112 usage();
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113 }
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114 process $_;
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115 }