diff galaxy-tools/tools/rdock/bin/sdsplit @ 2:0faa03a92843 draft default tip

Uploaded

--- a/galaxy-tools/tools/rdock/bin/sdsplit	Fri Aug 26 09:55:15 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,72 +0,0 @@
-#!/usr/bin/perl
-# Splits SD records into multiple files of equal no. of records
-use lib "$ENV{'RBT_ROOT'}/lib";
-
-use FileHandle;
-use SDRecord;
-
-# Record size to split into
-my $recSize = 1000;
-
-#output root
-my $outRoot = "tmp";
-
-#Print help if no command line arguments
-printHelpAndExit() if (scalar(@ARGV) == 0);
-
-#Parse command line arguments
-my @files;
-while (scalar(@ARGV)) {
-  my $arg = shift @ARGV;
-  printHelpAndExit() if ($arg eq '-h');
-  if (index($arg,'-o')==0) {
-    $outRoot = substr($arg,2);
-  }    
-  elsif (index($arg,'-')==0) {
-    $recSize = substr($arg,1);
-  }    
-  else {
-    push @files,$arg;#must be a filename
-  }
-}
-push @ARGV,@files;#put the filenames back in the arg list
-
-my $sdRec = new SDRecord;
-my $nRec=0;
-my $nFile=0;
-my $sdfh;
-
-#read records
-while ($sdRec->readRec('LINES'=>1)) {
-  #check if we need to start a new output file
-  if ($nRec % $recSize == 0) {
-    $nFile++;
-    my $outFile = $outRoot . $nFile . ".sd";
-    if (defined $sdfh) {
-      undef $sdfh;
-    }
-    $sdfh = new FileHandle ">$outFile";
-    if (!defined $sdfh) {
-      die "Can't open $outFile";
-    }
-    else {
-      print STDOUT "Opening $outFile\n";
-    }
-    $sdfh->autoflush(1);
-    select($sdfh);
-  }
-  $nRec++;
-  $sdRec->writeRec();
-}
-undef $sdfh;
-select(STDOUT);#reselect STDOUT as default
-
-#######################################################################
-sub printHelpAndExit {
-  print "\Splits SD records into multiple files of equal size\n";
-  print "\nUsage:\tsdsplit [-<RecSize>] [-o<OutputRoot>] [sdFiles]\n\n";
-  print "\t-<RecSize>\trecord size to split into (default = 1000 records)\n";
-  print "\t-o<OutputRoot>\tRoot name for output files (default = tmp)\n";
-  print "\n\tIf SD file list not given, reads from standard input\n";
-  exit;
-}