add release version to bioseq and bioaln

README.md

@@ -1,5 +1,5 @@
 # Descritpion
-bp-utils are command-line utilities that are wrappers of popular BioPerl classes (e.g., Bio::SeqIO, Bio::Seq; Bio::SimpleAlign). The motivation is to relieve BioPerl users from writing full-blown scripts for routine manipulations of sequences, alignments, trees, and others. For common operations of sequences and alignments, bp-utils make it easy to create workflows with a single BASH script containing a combination of bp-utils calls (and no Perl or BioPerl coding is necessary).
+bp-utils are command-line utilities that are wrappers of popular BioPerl classes (Bio::SeqIO, Bio::Seq, Bio::AlignIO, Bio::SimpleAlign, etc). The motivation is to relieve BioPerl users from writing full-blown scripts for routine manipulations of sequences, alignments, trees, and others. For common operations of sequences and alignments, bp-utils make it easy to create workflows with a single BASH script containing a combination of bp-utils calls (and no Perl or BioPerl coding is necessary).
 
 Internally, bp-utils follow a "Wrap, don't Write" design principle. That is, we have full faith in the robustness of the BioPerl development framework. As such, bp-utils methods should ALL be wrappers to BioPerl methdos so that exceptions can be handled properly by BioPerl. 
 

bioaln

@@ -47,6 +47,7 @@ GetOptions(
     "shuffle-sites|S",
     "third-sites|T",
     "uppercase|U", # make upper case (for DNAStatistics)
+    "version|V",
   #  "dnadist|D=s", # Needs fixing
   #  "inform|Z",    Retired for now
 ) or pod2usage(2);

bioseq

@@ -9,6 +9,7 @@ use 5.010;
 use Getopt::Long qw(:config gnu_getopt);
 use Pod::Usage;
 
+my $RELEASE = '1.0';
 #########################################################################
 # Option parsing
 #########################################################################
@@ -38,6 +39,7 @@ GetOptions(
     "hydroB|H",
     "linearize|L",
     "reloop|R=i", # recircularize a genome at "loop_at"
+    "version|V",
     "removestop|X", # for PAML/codeml    
  #   "longest-orf|C", Retired for now
  #   "extract|e", Retired for now

lib/AlnManipulations.pm

@@ -24,6 +24,7 @@ if ($ENV{'DEBUG'}) {
 
 # Package global variables
 my ($in, $out, $aln, %opts, $file, $in_format, $out_format, @alns);
+my $RELEASE = '1.0';
 
 ## For new options, just add an entry into this table with the same key as in
 ## the GetOpts function in the main program. Make the key be a reference to
@@ -54,8 +55,9 @@ my %opt_dispatch = (
     "pep2dna" => \&protein_to_dna,
     "resample" => \&sample_seqs,
     "shuffle-sites" => \&shuffle_sites,
-	"third-sites" => \&third_sites,
-	"uppercase" => \&upper_case,
+    "third-sites" => \&third_sites,
+    "uppercase" => \&upper_case,
+    "version" => \&print_version,
    );
 
 ##################### initializer & option handlers ###################
@@ -73,6 +75,8 @@ sub initialize {
 
     $in_format = $opts{"input"} || $default_format;
 
+    if ($opts{"version"}) { &print_version(); exit }
+
     if ($opts{"concat"}) { 
 	while ( $file = shift @ARGV ) {
 	    $in = Bio::AlignIO->new(-file => $file, -format => $in_format);
@@ -541,6 +545,11 @@ sub upper_case {
     $aln->uppercase();
 }
 
+sub print_version {
+    say "bp-utils release version: ", $RELEASE;
+}
+
+
 ########################## internal subroutine #######################
 
 # For use in draw_codon_view

lib/SeqManipulations.pm

@@ -23,6 +23,7 @@ if ($ENV{'DEBUG'}) { use Data::Dumper }
 
 # Package global variables
 my ($in, $out, $seq, %opts, $filename, $in_format, $out_format);
+my $RELEASE = '1.0';
 
 ## For new options, just add an entry into this table with the same key as in
 ## the GetOpts function in the main program. Make the key be a reference to the handler subroutine (defined below), and test that it works.  
@@ -46,6 +47,7 @@ my %opt_dispatch = (
     'hydroB' => \&hydroB,
     'linearize' => \&linearize,
     'reloop' => \&reloop_at,
+    'version' => \&print_version,
     'removestop' => \&remove_stop,
 #   'dotplot' => \&draw_dotplot,
 #    'extract' => \&reading_frame_ops,
@@ -325,6 +327,10 @@ sub reloop_at {
     $out->write_seq($new_seq)
 }
 
+sub print_version {
+    say "bp-utils release version: ", $RELEASE;
+}
+
 sub remove_stop {
     my $myCodonTable = Bio::Tools::CodonTable->new();
     while ($seq = $in->next_seq()) {