20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,103 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use File::Basename;
+use Cwd;
+use Carp;
+use Getopt::Long qw(:config no_ignore_case bundling);
+
+
+my $usage = <<_EOUSAGE_;
+
+##################################################################
+#
+# Required:
+#
+#     --target <string>    : transcript sequences (eg. 'Trinity.fasta')
+#
+#  If paired reads:
+#
+#     --left  <string>    :left reads
+#     --right <string>    :right reads
+# 
+#  Or, if unpaired reads:
+#
+#      --single <string>   :single reads
+#
+#  
+#  --paired_fragment_length <int>  :size of a read pair insert (def=300)
+#
+#
+#############################################################################################################
+
+
+
+_EOUSAGE_
+
+	;
+
+
+
+my ($target_fasta, $left_file, $right_file, $single_file, $SS_lib_type, $paired_fragment_length);
+
+# defaults:
+$paired_fragment_length = 300;
+
+
+&GetOptions( 
+			 
+			 ## general opts
+			 "target_fasta=s" => \$target_fasta,
+			 "left=s" => \$left_file,
+			 "right=s" => \$right_file,
+			 "single=s" => \$single_file,
+			 
+			 "SS_lib_type=s" => \$SS_lib_type,
+			 
+			 "paired_fragment_length=i" => \$paired_fragment_length,
+			 );
+
+
+## Check options set:
+
+unless  ( ($left_file && $right_file) || $single_file) {
+	die $usage;
+}
+
+
+main: {
+
+	my $cmd = "ln -s $target_fasta TARGET.fa";
+	&process_cmd($cmd) unless (-e "TARGET.fa");
+	
+	$cmd = "bowtie-build TARGET.fa TARGET";
+	&process_cmd($cmd) unless (-s "TARGET.1.ebwt");
+	
+	if ($left_file && $right_file) {
+		$cmd = "tophat --bowtie1 -i 5 -r $paired_fragment_length TARGET $left_file $right_file";
+		&process_cmd($cmd);
+	}
+	else {
+		$cmd = "tophat --bowtie1 -i 5 TARGET $single_file";
+		&process_cmd($cmd);
+	}
+
+
+	exit(0);
+}
+
+####
+sub process_cmd {
+	my ($cmd) = @_;
+
+	print "CMD: $cmd\n";
+	my $ret = system($cmd);
+	if ($ret) {
+		die "Error, cmd: $cmd died with ret $ret";
+	}
+
+	return;
+}