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

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/libs/sratoolkit.2.8.0-centos_linux64/example/perl/dump-reference.pl	Mon Nov 27 11:21:07 2017 -0500
@@ -0,0 +1,115 @@
+#!/usr/bin/env perl
+# ===========================================================================
+#
+#                            PUBLIC DOMAIN NOTICE
+#               National Center for Biotechnology Information
+#
+#  This software/database is a "United States Government Work" under the
+#  terms of the United States Copyright Act.  It was written as part of
+#  the author's official duties as a United States Government employee and
+#  thus cannot be copyrighted.  This software/database is freely available
+#  to the public for use. The National Library of Medicine and the U.S.
+#  Government have not placed any restriction on its use or reproduction.
+#
+#  Although all reasonable efforts have been taken to ensure the accuracy
+#  and reliability of the software and data, the NLM and the U.S.
+#  Government do not and cannot warrant the performance or results that
+#  may be obtained by using this software or data. The NLM and the U.S.
+#  Government disclaim all warranties, express or implied, including
+#  warranties of performance, merchantability or fitness for any particular
+#  purpose.
+#
+#  Please cite the author in any work or product based on this material.
+#
+# ===========================================================================
+
+use warnings;
+
+my %opts = (
+    'local-name' => 0,
+    'line-length' => 70
+);
+
+sub usage()
+{
+    print <<"HELP";
+extracts the reference sequence as FASTA from an aligned SRA
+
+Usage:
+$0 [<options>...] <accession>...
+options are
+    -h | -? | --help    this message
+    --use-local         toggle def-line between reference accession and
+                        original (local to run) name of reference
+    --line-length N     sequence line length (use 0 for unlimited)
+                        (default is $opts{'line-length'})
+
+Example:
+    $0 SRR341548 > ref.fasta
+
+HELP
+    exit 0;
+}
+
+usage if scalar @ARGV == 0;
+foreach (@ARGV) {
+    usage() if (/^-h$/ || /^-\?$/ || /^--help$/);
+}
+
+my $VDB_DUMP = `which vdb-dump` or die "Please put path to vdb-dump in PATH";
+chomp $VDB_DUMP;
+
+sub process($)
+{
+    my $defline = '';
+    my $ref = '';
+    
+    open IN, '-|', "$VDB_DUMP -f tab -T REFERENCE -C \"NAME,SEQ_ID,READ\" \"$_[0]\"" or die "$!";
+    
+    while (defined($_ = <IN>)) {
+        chomp;
+        my ($name, $seqid, $seq) = \split /\t/;
+        my $new_defline;
+        
+        if ($opts{'local-name'}) {
+            $new_defline = ">$$name $$seqid";
+        }
+        else {
+            $new_defline = ">$$seqid $$name";
+        }
+        if ($defline ne $new_defline) {
+            print "$ref\n" if $ref;
+            print "$new_defline\n";
+            $defline = $new_defline;
+            $ref = '';
+        }
+        $ref .= $$seq;
+        if ($opts{'line-length'} != 0) {
+            while (length($ref) >= $opts{'line-length'}) {
+                print substr($ref, 0, $opts{'line-length'})."\n";
+                $ref = substr($ref, $opts{'line-length'});
+            }
+        }
+    }
+    print "$ref\n" if $ref;
+    close IN;
+}
+
+for (my $i = 0; $i < scalar @ARGV; ++$i) {
+    $_ = $ARGV[$i];
+    
+    if (/^-/) {
+        if (/^--use-local$/) {
+            $opts{'local-name'} = 1 - $opts{'local-name'};
+            next;
+        }
+        if (/^--line-length$/) {
+            $_ = $ARGV[++$i];
+            /^(\d+)$/ or usage();
+            $opts{'line-length'} = $1;
+            next;
+        }
+        usage();
+    }
+    process $_;
+}