-#!/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__
+++ /dev/null
-#!/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__
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 ) }
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(
}
-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.
# 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
) = @_;
# 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> )
{
# 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> )
{
projects / biopieces.git / commitdiff