20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,48 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use FindBin;
+use lib ("$FindBin::Bin/../../PerlLib");
+use Process_cmd;
+
+my $usage = "\n\n\tusage: $0 Trinity.fasta reads.fa [threads=1]\n\n";
+
+my $trin_fa = $ARGV[0] or die $usage;
+my $reads_fa = $ARGV[1] or die $usage;
+my $CPU = $ARGV[2] || 1;
+
+
+
+
+main: {
+
+    my $salmon_index = "$trin_fa.salmon.idx";
+    my $salmon_stderr = "_salmon.$$.stderr";
+    my $cmd = "salmon --no-version-check index -t $trin_fa -i $salmon_index -k 25 -p $CPU  > $salmon_stderr 2>&1";
+    &run_cmd_capture_stderr($cmd, $salmon_stderr);
+
+    
+    $cmd = "salmon --no-version-check quant -i $salmon_index -l U -r $reads_fa -o salmon_outdir -p $CPU --minAssignedFrags 1 --validateMappings > $salmon_stderr 2>&1";
+    &run_cmd_capture_stderr($cmd, $salmon_stderr);
+
+    unlink($salmon_stderr);
+    
+    exit(0);
+
+}
+
+
+####
+sub run_cmd_capture_stderr {
+    my ($cmd, $stderr_file) = @_; 
+    eval {
+        &process_cmd($cmd);
+    };
+    if ($@) {
+        my $errmsg = `cat $stderr_file`;
+        die "Error, cmd: $cmd failed with msg: $errmsg $@";
+    }
+    return;
+}