Added user-friendly error messages if users forget to compile the source codes

[rsem.git] / rsem_perl_utils.pm

diff --git a/rsem_perl_utils.pm b/rsem_perl_utils.pm
new file mode 100644 (file)
index 0000000..f3edfe4
--- /dev/null
+++ b/rsem_perl_utils.pm
@@ -0,0 +1,97 @@
+#!/usr/bin/perl
+
+package rsem_perl_utils;
+
+use strict;
+
+require Exporter;
+our @ISA = qw(Exporter);
+our @EXPORT = qw(runCommand);
+our @EXPORT_OK = qw(runCommand collectResults showVersionInfo);
+
+# command, {err_msg}
+sub runCommand {
+    print $_[0]."\n";
+    my $status = system($_[0]);
+
+    if ($? == -1) {
+       my @arr = split(/[ \t]+/, $_[0]);
+       print "$arr[0] : $!!\n";
+       print "Please check if you have compiled the associated codes by typing related \"make\" commands and/or made related executables ready to use.\n";
+       exit(-1);
+    }
+
+    if ($status != 0) {
+        my $errmsg = "";
+        if (scalar(@_) > 1) { $errmsg .= $_[1]."\n"; }
+       $errmsg .= "\"$_[0]\" failed! Plase check if you provide correct parameters/options for the pipeline!\n";
+       print $errmsg;
+        exit(-1);
+    }
+    print "\n";
+}
+
+
+my @transcript_title = ("transcript_id", "gene_id", "length", "effective_length", "expected_count", "TPM", "FPKM", "IsoPct", "pme_expected_count", "pme_TPM", "pme_FPKM", "IsoPct_from_pme_TPM", "TPM_ci_lower_bound", "TPM_ci_upper_bound", "FPKM_ci_lower_bound", "FPKM_ci_upper_bound");
+
+my @gene_title = ("gene_id", "transcript_id(s)", "length", "effective_length", "expected_count", "TPM", "FPKM", "pme_expected_count", "pme_TPM", "pme_FPKM", "TPM_ci_lower_bound", "TPM_ci_upper_bound", "FPKM_ci_lower_bound", "FPKM_ci_upper_bound");
+
+# inpF, outF
+sub collectResults {
+    my $local_status;
+    my ($inpF, $outF);
+    my @results = ();
+    my $line;
+
+    $inpF = $_[1];
+    $outF = $_[2];
+
+    $local_status = open(INPUT, $inpF);
+    if ($local_status == 0) { print "Fail to open file $inpF!\n"; exit(-1); }
+    
+    @results = ();
+    
+    while ($line = <INPUT>) {
+       chomp($line);
+       my @local_arr = split(/\t/, $line);
+       push(@results, \@local_arr); 
+    }
+
+    close(INPUT);
+
+    $local_status = open(OUTPUT, ">$outF");
+    if ($local_status == 0) { print "Fail to create file $outF!\n"; exit(-1); }
+
+    my $n = scalar(@results);
+    my $m = scalar(@{$results[0]});
+
+    $" = "\t";
+
+    my @out_arr = ();
+    for (my $i = 0; $i < $n; $i++) {
+       if ($_[0] eq "isoform") { push(@out_arr, $transcript_title[$i]); }
+       elsif ($_[0] eq "gene") { push(@out_arr, $gene_title[$i]); }
+       else { print "A bug on 'collectResults' is detected!\n"; exit(-1); }
+    }
+    print OUTPUT "@out_arr\n";
+
+    for (my $i = 0; $i < $m; $i++) {
+       @out_arr = ();
+       for (my $j = 0; $j < $n; $j++) { push(@out_arr, $results[$j][$i]); }
+       print OUTPUT "@out_arr\n"; 
+    }
+
+    close(OUTPUT);
+}
+
+# dir
+sub showVersionInfo {
+    open(INPUT, "$_[0]\WHAT_IS_NEW");
+    my $line = <INPUT>;
+    chomp($line);
+    close(INPUT);
+    print "$line\n";
+    exit(0);
+}
+
+1;