X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=misc%2Fsamtools.pl;h=320e8aaeda8ff2fab7fd91ab5e02073d5f3ba8fe;hp=86b285c5fa6c144a1d60ed61cb48a23bde7f134f;hb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351;hpb=4a17fa7e1f91b2fe04ad334a63fc2b0d5e859d8a

diff --git a/misc/samtools.pl b/misc/samtools.pl
index 86b285c..320e8aa 100755
--- a/misc/samtools.pl
+++ b/misc/samtools.pl
@@ -11,7 +11,7 @@ my $version = '0.3.3';
 
 my $command = shift(@ARGV);
 my %func = (showALEN=>\&showALEN, pileup2fq=>\&pileup2fq, varFilter=>\&varFilter,
-			unique=>\&unique, uniqcmp=>\&uniqcmp);
+			unique=>\&unique, uniqcmp=>\&uniqcmp, sra2hdr=>\&sra2hdr);
 
 die("Unknown command \"$command\".\n") if (!defined($func{$command}));
 &{$func{$command}};
@@ -37,6 +37,16 @@ sub showALEN {
 # varFilter
 #
 
+#
+# Filtration code:
+#
+# d low depth
+# D high depth
+# W too many SNPs in a window (SNP only)
+# G close to a high-quality indel (SNP only)
+# Q low RMS mapping quality (SNP only)
+# g close to another indel with higher quality (indel only)
+
 sub varFilter {
   my %opts = (d=>3, D=>100, l=>30, Q=>25, q=>10, G=>25, s=>100, w=>10, W=>10, N=>2, p=>undef);
   getopts('pq:d:D:l:Q:w:W:N:G:', \%opts);
@@ -216,6 +226,59 @@ sub p2q_print_str {
   }
 }
 
+#
+# sra2hdr
+#
+
+# This subroutine does not use an XML parser. It requires that the SRA
+# XML files are properly formated.
+sub sra2hdr {
+  my %opts = ();
+  getopts('', \%opts);
+  die("Usage: samtools.pl sra2hdr <SRA.prefix>\n") if (@ARGV == 0);
+  my $pre = $ARGV[0];
+  my $fh;
+  # read sample
+  my $sample = 'UNKNOWN';
+  open($fh, "$pre.sample.xml") || die;
+  while (<$fh>) {
+	$sample = $1 if (/<SAMPLE.*alias="([^"]+)"/i);
+  }
+  close($fh);
+  # read experiment
+  my (%exp2lib, $exp);
+  open($fh, "$pre.experiment.xml") || die;
+  while (<$fh>) {
+	if (/<EXPERIMENT.*accession="([^\s"]+)"/i) {
+	  $exp = $1;
+	} elsif (/<LIBRARY_NAME>\s*(\S+)\s*<\/LIBRARY_NAME>/i) {
+	  $exp2lib{$exp} = $1;
+	}
+  }
+  close($fh);
+  # read run
+  my ($run, @fn);
+  open($fh, "$pre.run.xml") || die;
+  while (<$fh>) {
+	if (/<RUN.*accession="([^\s"]+)"/i) {
+	  $run = $1; @fn = ();
+	} elsif (/<EXPERIMENT_REF.*accession="([^\s"]+)"/i) {
+	  print "\@RG\tID:$run\tSM:$sample\tLB:$exp2lib{$1}\n";
+	} elsif (/<FILE.*filename="([^\s"]+)"/i) {
+	  push(@fn, $1);
+	} elsif (/<\/RUN>/i) {
+	  if (@fn == 1) {
+		print STDERR "$fn[0]\t$run\n";
+	  } else {
+		for (0 .. $#fn) {
+		  print STDERR "$fn[$_]\t$run", "_", $_+1, "\n";
+		}
+	  }
+	}
+  }
+  close($fh);
+}
+
 #
 # unique
 #