[Sashimi-commit] SF.net SVN: sashimi:[9477] trunk/trans_proteomic_ pipeline/perl/bin

[<rea...@us...>]

Revision: 9477
          http://sourceforge.net/p/sashimi/code/9477
Author:   real_procopio
Date:     2026-04-02 00:46:49 +0000 (Thu, 02 Apr 2026)
Log Message:
-----------
[ProteoMapper] v1.7.0: Ignore specified mass tolerance if not doing fuzzy matching; Accept U and O in input sequences; Correctly capture error code from system call to find number of cores; Some cleanup

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/perl/bin/clips.pl
    trunk/trans_proteomic_pipeline/perl/bin/promast.pl

Modified: trunk/trans_proteomic_pipeline/perl/bin/clips.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/bin/clips.pl	2026-02-26 03:01:35 UTC (rev 9476)
+++ trunk/trans_proteomic_pipeline/perl/bin/clips.pl	2026-04-02 00:46:49 UTC (rev 9477)
@@ -8,7 +8,7 @@
 #                                                                           #
 # Generate reverse index of n-AA keys, for use in mapping observed          #
 #  peptide sequences to all proteins                                        #
-# Copyright (C) 2018-2023 Luis Mendoza                                      #
+# Copyright (C) 2018-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -38,7 +38,7 @@
 use FindBin qw($Bin);
 use lib "$Bin/../lib/perl";
 
-my $VersionInfo = "stand-alone 1.5";
+my $VersionInfo = "stand-alone 1.7.0";
 my $rc = eval {
   require tpplib_perl; # exported TPP lib function points
   tpplib_perl->import();
@@ -202,10 +202,7 @@
 	    $protvar[$1] .= $2;
 	}
 
-
 	my $new = 0;
-
-
 	if ($new) {
 	    my @variants = @protvar[1..$pepkeysize];
 	    my %ret = ();
@@ -214,7 +211,6 @@
 	    &assemble_variants_NEW('', $alias, 1, \@variants, \%ret);
 
 	    my $pos = 1;
-
 	    for (my $i = $pepkeysize+1; $i <= length($protseq); $i++) {
 		$pos++;
 
@@ -256,8 +252,6 @@
 }
 
 
-
-
 ####################################################################################
 sub assemble_variants_NEW {    # recurse me...recurse me, my friend...
 ####################################################################################
@@ -272,8 +266,6 @@
 	if (1+length($str) == $pepkeysize) {
 	    $index{"$str$aa"} .= ":$prt,$pos";    # format:  PROT,POS    #### speed this up with arrays??
 
-
-
 	    ###$index{"$str$aa"} .= ":$prt,".($pos+1);    # format:  PROT,POS    #### speed this up with arrays??
 	    ## $index{"$str$aa"} .= ":".($pos+1).".$prt"; # format:  POS.PROT (allows numerical treatment)
 	    ## $ret{"$str$aa"} = 1;
@@ -284,8 +276,6 @@
 
 #	    print "==$str$aa\n";
 
-
-
 	}
 	else {
 	    &assemble_variants_NEW("$str$aa", $prt, $pos, $varaas, $prestr);
@@ -293,12 +283,6 @@
     }
 }
 
-
-
-
-
-
-
 ####################################################################################
 sub assemble_variants {    # recurse me...recurse me, my friend...
 ####################################################################################

Modified: trunk/trans_proteomic_pipeline/perl/bin/promast.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/bin/promast.pl	2026-02-26 03:01:35 UTC (rev 9476)
+++ trunk/trans_proteomic_pipeline/perl/bin/promast.pl	2026-04-02 00:46:49 UTC (rev 9477)
@@ -7,7 +7,7 @@
 # SVN Info      : $Id$
 #                                                                           #
 # Find all instances of input peptide sequence(s) by index lookup           #
-# Copyright (C) 2018-2023 Luis Mendoza                                      #
+# Copyright (C) 2018-2026 Luis Mendoza                                      #
 #                                                                           #
 # This library is free software; you can redistribute it and/or             #
 # modify it under the terms of the GNU Lesser General Public                #
@@ -45,7 +45,7 @@
 my @btimes;
 push @btimes, Benchmark->new; #0 :: exec start time
 
-my $VersionInfo = "stand-alone 1.6.0";
+my $VersionInfo = "stand-alone 1.7.0";
 my $rc = eval {
   require tpplib_perl;  # exported TPP lib function points
   tpplib_perl->import();
@@ -175,6 +175,10 @@
     if ($p =~ /X/) {
       print STDERR "...with wildcards";
       print STDERR " (ignoring fuzzy matching)" if $options{'f'};
+      if ($options{'m'}) {
+	print STDERR " (ignoring mass tolerance)";
+	$options{'m'} = undef;
+      }
       &expand_wildcards('',$p);
     }
     elsif ($options{'f'}) {
@@ -1153,7 +1157,7 @@
 sub dispatchPeps {
 ####################################################################################
   chomp(my $ncores = `getconf _NPROCESSORS_ONLN`);
-  if ($@) {
+  if ($?) {
     $ncores = $ENV{"NUMBER_OF_PROCESSORS"} || 1;
   }
   my $batches = 1 + int (scalar(keys %peps) / 5000);
@@ -1211,7 +1215,7 @@
       delete $peps{$pep};
       next;
     }
-    if ($pep =~ /[JUZBOX]/ ||
+    if ($pep =~ /[JZBX]/ ||  # changed to also accept U, O
 	$pep !~ /^[A-Z]+$/ ) {
       print STDERR "Warning: ignoring peptide containing non-AA characters: $pep\n";
       delete $peps{$pep};

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