From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 2 Jun 2009 18:37:28 +0000 (+0000)
Subject: bleh blah
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=bd27b1017ee7cdfde9f7d93fbe1b0ef97312edd6;p=biopieces.git

bleh blah

git-svn-id: http://biopieces.googlecode.com/svn/trunk@472 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/bp_bin/read_mysql b/bp_bin/read_mysql
index fdf5bd2..0033207 100755
--- a/bp_bin/read_mysql
+++ b/bp_bin/read_mysql
@@ -1,6 +1,92 @@
-#!/usr/bin/env perl
+#!/usr/bin/env perl -w
+
+# Copyright (C) 2007-2009 Martin A. Hansen.
+
+# This program is free software; you can redistribute it and/or
+# modify it under the terms of the GNU General Public License
+# as published by the Free Software Foundation; either version 2
+# of the License, or (at your option) any later version.
+
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with this program; if not, write to the Free Software
+# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+
+# http://www.gnu.org/copyleft/gpl.html
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Read records from a MySQL query.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use warnings;
 use strict;
+use Maasha::Biopieces;
+use Maasha::SQL;
+use Maasha::UCSC;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $run_time_beg, $run_time_end, $default_user, $default_password, $options, $in, $out, $record, $dbh, $results );
+
+$default_user     = Maasha::UCSC::ucsc_get_user();
+$default_password = Maasha::UCSC::ucsc_get_password();
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'database', short => 'd', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
+        { long => 'query',    short => 'q', type => 'string', mandatory => 'yes', default => undef,             allowed => undef, disallowed => undef },
+        { long => 'user',     short => 'u', type => 'string', mandatory => 'no',  default => $default_user,     allowed => undef, disallowed => undef },
+        { long => 'password', short => 'p', type => 'string', mandatory => 'no',  default => $default_password, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) {
+    Maasha::Biopieces::put_record( $record, $out );
+}
+
+$dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
+
+$results = Maasha::SQL::query_hashref_list( $dbh, $options->{ "query" } );
+
+Maasha::SQL::disconnect( $dbh );
+
+map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    $run_time_beg = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::log_biopiece();
+}
+
+END
+{
+    Maasha::Biopieces::close_stream( $in );
+    Maasha::Biopieces::close_stream( $out );
+
+    $run_time_end = Maasha::Biopieces::run_time();
+
+    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__
diff --git a/bp_bin/read_phastcons b/bp_bin/read_phastcons
deleted file mode 100755
index 9449a0d..0000000
--- a/bp_bin/read_phastcons
+++ /dev/null
@@ -1,99 +0,0 @@
-#!/usr/bin/env perl -w
-
-# Copyright (C) 2007-2009 Martin A. Hansen.
-
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU General Public License
-# as published by the Free Software Foundation; either version 2
-# of the License, or (at your option) any later version.
-
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-
-# You should have received a copy of the GNU General Public License
-# along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
-
-# http://www.gnu.org/copyleft/gpl.html
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-# Read FASTA entries from one or more files.
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-use strict;
-use Maasha::Biopieces;
-use Maasha::Filesys;
-use Maasha::Fasta;
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-my ( $run_time_beg, $run_time_end, $options, $in, $out, $record, $data_in, $num, $entry );
-
-$options = Maasha::Biopieces::parse_options(
-    [
-        { long => 'data_in', short => 'i', type => 'files!', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
-        { long => 'num',     short => 'n', type => 'uint',   mandatory => 'no', default => undef, allowed => undef, disallowed => '0' },
-    ]   
-);
-
-$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
-$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
-
-while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-    Maasha::Biopieces::put_record( $record, $out );
-}
-
-if ( $options->{ 'data_in' } )
-{
-    $data_in = Maasha::Filesys::files_read_open( $options->{ 'data_in' } );
-
-    $num = 1;
-
-    while ( $entry = Maasha::Fasta::get_entry( $data_in ) ) 
-    {
-        if ( $record = Maasha::Fasta::fasta2biopiece( $entry ) ) {
-            Maasha::Biopieces::put_record( $record, $out );
-        }
-
-        last if $options->{ "num" } and $num == $options->{ "num" };
-
-        $num++;
-    }
-
-    close $data_in;
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-BEGIN
-{
-    $run_time_beg = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::log_biopiece();
-}
-
-END
-{
-    Maasha::Biopieces::close_stream( $in );
-    Maasha::Biopieces::close_stream( $out );
-
-    $run_time_end = Maasha::Biopieces::run_time();
-
-    Maasha::Biopieces::run_time_print( $run_time_beg, $run_time_end, $options );
-}
-
-
-# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
-
-
-__END__
diff --git a/code_perl/Maasha/BioRun.pm b/code_perl/Maasha/BioRun.pm
index 3f4fb1c..16b6df9 100644
--- a/code_perl/Maasha/BioRun.pm
+++ b/code_perl/Maasha/BioRun.pm
@@ -112,8 +112,6 @@ sub run_script
 
     if    ( $script eq "print_usage" )              { script_print_usage(               $in, $out, $options ) }
     elsif ( $script eq "read_stockholm" )           { script_read_stockholm(            $in, $out, $options ) }
-    elsif ( $script eq "read_phastcons" )           { script_read_phastcons(            $in, $out, $options ) }
-    elsif ( $script eq "read_mysql" )               { script_read_mysql(                $in, $out, $options ) }
     elsif ( $script eq "uppercase_seq" )            { script_uppercase_seq(             $in, $out, $options ) }
     elsif ( $script eq "complexity_seq" )           { script_complexity_seq(            $in, $out, $options ) }
     elsif ( $script eq "get_genome_align" )         { script_get_genome_align(          $in, $out, $options ) }
@@ -158,26 +156,6 @@ sub get_options
             num|n=s
         );
     }
-    elsif ( $script eq "read_phastcons" )
-    {
-        @options = qw(
-            data_in|i=s
-            num|n=s
-            min|m=s
-            dist|d=s
-            threshold|t=f
-            gap|g=s
-        );
-    }
-    elsif ( $script eq "read_mysql" )
-    {
-        @options = qw(
-            database|d=s
-            query|q=s
-            user|u=s
-            password|p=s
-        );
-    }
     elsif ( $script eq "get_genome_align" )
     {
         @options = qw(
@@ -467,94 +445,6 @@ sub script_read_stockholm
 }
 
 
-sub script_read_phastcons
-{
-    # Martin A. Hansen, December 2007.
-
-    # Read PhastCons format.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $data_in, $file, $num, $entry, @records, $record );
-
-    $options->{ "min" }       ||= 10;
-    $options->{ "dist" }      ||= 25;
-    $options->{ "threshold" } ||= 0.8;
-    $options->{ "gap" }       ||= 5;
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-
-    $num = 1;
-
-    foreach $file ( @{ $options->{ "files" } } )
-    {
-        $data_in = Maasha::Common::read_open( $file );
-
-        while ( $entry = Maasha::UCSC::fixedstep_get_entry( $data_in ) ) 
-        {
-            @records = Maasha::UCSC::phastcons_parse_entry( $entry, $options );
-
-            foreach $record ( @records )
-            {
-                $record->{ "REC_TYPE" } = "BED";
-                $record->{ "BED_LEN" }  = $record->{ "CHR_END" } - $record->{ "CHR_BEG" } + 1;
-
-                Maasha::Biopieces::put_record( $record, $out );
-
-                goto NUM if $options->{ "num" } and $num == $options->{ "num" };
-
-                $num++;
-            }
-        }
-
-        close $data_in;
-    }
-
-    NUM:
-
-    close $data_in if $data_in;
-}
-
-
-sub script_read_mysql
-{
-    # Martin A. Hansen, May 2008.
-
-    # Read a MySQL query into stream.
-
-    my ( $in,        # handle to in stream
-         $out,       # handle to out stream
-         $options,   # options hash
-       ) = @_;
-
-    # Returns nothing.
-
-    my ( $record, $dbh, $results );
-
-    $options->{ "user" }     ||= Maasha::UCSC::ucsc_get_user();
-    $options->{ "password" } ||= Maasha::UCSC::ucsc_get_password();
-
-    while ( $record = Maasha::Biopieces::get_record( $in ) ) {
-        Maasha::Biopieces::put_record( $record, $out );
-    }
-
-    $dbh = Maasha::SQL::connect( $options->{ "database" }, $options->{ "user" }, $options->{ "password" } );
-
-    $results = Maasha::SQL::query_hashref_list( $dbh, $options->{ "query" } );
-
-    Maasha::SQL::disconnect( $dbh );
-
-    map { Maasha::Biopieces::put_record( $_ ) } @{ $results };
-}
-
-
 sub script_complexity_seq
 {
     # Martin A. Hansen, May 2008.
diff --git a/code_perl/Maasha/UCSC.pm b/code_perl/Maasha/UCSC.pm
index 7445807..fad1401 100644
--- a/code_perl/Maasha/UCSC.pm
+++ b/code_perl/Maasha/UCSC.pm
@@ -1216,6 +1216,11 @@ sub phastcons_parse_entry
     # Given a PhastCons entry converts this to a
     # list of super blocks.
 
+#    $options->{ "min" }       ||= 10;
+#    $options->{ "dist" }      ||= 25;
+#    $options->{ "threshold" } ||= 0.8;
+#    $options->{ "gap" }       ||= 5;
+
     my ( $lines,   # list of lines
          $args,    # argument hash
        ) = @_;
@@ -1638,9 +1643,13 @@ sub ucsc_get_user
 
     # Returns a string.
 
-    my ( $fh, $line, $user );
+    my ( $file, $fh, $line, $user );
+
+    $file = "$ENV{ 'HOME' }/.hg.conf";
+
+    return if not -f $file;
 
-    $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+    $fh = Maasha::Common::read_open( $file );
 
     while ( $line = <$fh> )
     {
@@ -1669,9 +1678,13 @@ sub ucsc_get_password
 
     # Returns a string.
 
-    my ( $fh, $line, $password );
+    my ( $file, $fh, $line, $password );
+
+    $file = "$ENV{ 'HOME' }/.hg.conf";
+
+    return if not -f $file;
 
-    $fh = Maasha::Common::read_open( "$ENV{ 'HOME' }/.hg.conf" );
+    $fh = Maasha::Common::read_open( $file );
 
     while ( $line = <$fh> )
     {