From cd1093b6c1fa9f153bdfe1f8baea756532cdb19e Mon Sep 17 00:00:00 2001
From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Wed, 9 Jul 2008 07:34:56 +0000
Subject: [PATCH] fixed print_usage

git-svn-id: http://biopieces.googlecode.com/svn/trunk@135 74ccb610-7750-0410-82ae-013aeee3265d
---
 code_perl/Maasha/Biopieces.pm | 65 +++++++++++++++++++----------------
 1 file changed, 35 insertions(+), 30 deletions(-)

diff --git a/code_perl/Maasha/Biopieces.pm b/code_perl/Maasha/Biopieces.pm
index a797eba..a0d480f 100644
--- a/code_perl/Maasha/Biopieces.pm
+++ b/code_perl/Maasha/Biopieces.pm
@@ -155,20 +155,15 @@ sub run_script
 
     my ( $options, $in, $out );
 
-#    script_list_biopieces( $ENV{ 'INST_DIR'} . "/biopieces/usage/" ) if $script eq "list_biopieces";
-
     $options = get_options( $script );
 
-    if ( -t STDIN and not @ARGV )
-    {
-        $options->{ "path" } = "$ENV{ 'BP_DIR' }/bp_usage/$script";
-        $script = "print_usage";
-    }
+    $script  = "print_usage" if ( -t STDIN and not @ARGV and $script ne "list_biopieces" );
 
-    $in  = read_stream( $options->{ "stream_in" } );
-    $out = write_stream( $options->{ "stream_out" } );
+    $in      = read_stream( $options->{ "stream_in" } );
+    $out     = write_stream( $options->{ "stream_out" } );
 
     if    ( $script eq "print_usage" )              { script_print_usage( $in, $out, $options ) }
+    elsif ( $script eq "list_biopieces" )           { script_list_biopieces( $in, $out, $options ) }
     elsif ( $script eq "read_fasta" )               { script_read_fasta( $in, $out, $options ) }
     elsif ( $script eq "read_tab" )                 { script_read_tab( $in, $out, $options ) }
     elsif ( $script eq "read_psl" )                 { script_read_psl( $in, $out, $options ) }
@@ -274,7 +269,13 @@ sub get_options
 
     my ( %options, @options, $opt, @genomes );
 
-    if ( $script eq "read_fasta" )
+    if ( $script eq "print_usage" )
+    {
+        @options = qw(
+            data_in|i=s
+        );
+    }
+    elsif ( $script eq "read_fasta" )
     {
         @options = qw(
             data_in|i=s
@@ -894,6 +895,8 @@ sub get_options
 
 #    print STDERR Dumper( \%options ) and exit;
 
+    $options{ "script" }    = $script;
+
     $options{ "cols" }      = [ split ",", $options{ "cols" } ]      if defined $options{ "cols" };
     $options{ "keys" }      = [ split ",", $options{ "keys" } ]      if defined $options{ "keys" };
     $options{ "no_keys" }   = [ split ",", $options{ "no_keys" } ]   if defined $options{ "no_keys" };
@@ -996,9 +999,15 @@ sub script_print_usage
 
     # Returns nothing.
 
-    my ( $wiki, $lines );
+    my ( $file, $wiki, $lines );
+
+    if ( $options->{ 'data_in' } ) {
+        $file = $options->{ 'data_in' };
+    } else {
+        $file = join "", $ENV{ 'BP_DIR' }, "/bp_usage/", $options->{ 'script' }, ".wiki";
+    }
 
-    $wiki = Maasha::Gwiki::gwiki_read( "$options->{ 'path' }.wiki" );
+    $wiki = Maasha::Gwiki::gwiki_read( $file );
 
     if ( not $options->{ "help" } ) {
         @{ $wiki } = grep { $_->[ 0 ]->{ 'SECTION' } =~ /Biopiece|Synopsis|Usage|Options|Help/ } @{ $wiki };
@@ -1016,38 +1025,34 @@ sub script_list_biopieces
 {
     # Martin A. Hansen, January 2008.
 
-    # Prints the description from the usage for each of the biopieces.
+    # Prints the synopsis from the usage for each of the biopieces.
 
-    my ( $path,    # full path to usage directory
+    my ( $in,        # handle to in stream
+         $out,       # handle to out stream
+         $options,   # options hash
        ) = @_;
 
     # Returns nothing.
 
-    my ( @files, $file, $fh, $line, @lines, $program );
+    my ( @files, $file, $wiki, $program, $synopsis );
 
-    @files = Maasha::Common::ls_files( $path );
+    @files = Maasha::Common::ls_files( "$ENV{ 'BP_DIR' }/bp_usage" );
 
     foreach $file ( sort @files )
     {
-        $program = ( split "/", $file )[ -1 ];
-
-        $fh = Maasha::Common::read_open( $file );
-
-        while ( $line = <$fh> )
+        if ( $file =~ /\/([a-z0-9_]+)\.wiki$/ )
         {
-            chomp $line;
+            $program = $1;
 
-            if ( $line =~ /^Description:\s+(.+)/ )
-            {
-                @lines = Maasha::Common::wrap_line( $1, 60 );
+            $wiki = Maasha::Gwiki::gwiki_read( $file );
 
-                printf( "%-30s%s\n", $program, shift @lines );
+            @{ $wiki } = grep { $_->[ 0 ]->{ 'SECTION' } =~ /Synopsis/ }  @{ $wiki };
+            @{ $wiki } = grep { $_->[ 0 ]->{ 'FORMAT' }  =~ /paragraph/ } @{ $wiki };
 
-                map { printf( "%-30s%s\n", "", $_ ) } @lines;
-            }
-        }
+            $synopsis = $wiki->[ 0 ]->[ 0 ]->{ 'TEXT' };
 
-        close $fh;
+            printf( "%-30s%s\n", $program, $synopsis );
+        }
     }
 
     exit;
-- 
2.39.5