X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bp_bin%2Fgrab;h=b034f2de42ca047a93550cecf9bcaab9f2d457c2;hb=48bea5c28b89dc5586d0bddb338ccd6ba23aa1f9;hp=fdf5bd287f78613d2aea83bb9b15f855cad57e77;hpb=e8e32d43d674573ff4a66fe77780cc18cb02d430;p=biopieces.git

diff --git a/bp_bin/grab b/bp_bin/grab
index fdf5bd2..b034f2d 100755
--- a/bp_bin/grab
+++ b/bp_bin/grab
@@ -1,6 +1,316 @@
 #!/usr/bin/env perl
 
+# 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 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+# Grab records in stream.
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
 use warnings;
 use strict;
+use Data::Dumper;
+use Maasha::Biopieces;
+use Maasha::Common;
+use Maasha::Patscan;
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+my ( $options, $in, $out, $record, $keys, $vals_only, $keys_only, $invert,
+     $patterns, $regex, %lookup_hash, $key, $op, $val, $found, $total, $grabbed );
+
+$options = Maasha::Biopieces::parse_options(
+    [
+        { long => 'patterns',         short => 'p', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'patterns_in',      short => 'P', type => 'file!',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'regex',            short => 'r', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'eval',             short => 'e', type => 'string', mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'exact_in',         short => 'E', type => 'file!',  mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'invert',           short => 'i', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'case_insensitive', short => 'c', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'keys',             short => 'k', type => 'list',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'keys_only',        short => 'K', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+        { long => 'vals_only',        short => 'V', type => 'flag',   mandatory => 'no', default => undef, allowed => undef, disallowed => undef },
+    ]   
+);
+
+$in  = Maasha::Biopieces::read_stream( $options->{ "stream_in" } );
+$out = Maasha::Biopieces::write_stream( $options->{ "stream_out" } );
+
+$keys      = $options->{ 'keys' };
+$vals_only = $options->{ 'vals_only' };
+$keys_only = $options->{ 'keys_only' };
+$invert    = $options->{ 'invert' };
+
+if ( $options->{ 'patterns' } )
+{
+    $patterns = $options->{ 'patterns' };
+}
+elsif ( defined $options->{ 'patterns_in' } and -f $options->{ 'patterns_in' } )
+{
+    $patterns = Maasha::Patscan::read_patterns( $options->{ 'patterns_in' } );
+}
+elsif ( $options->{ 'regex' } )
+{
+    if ( $options->{ 'case_insensitive' } ) {
+        $regex = qr/$options->{ 'regex' }/i;
+    } else {
+        $regex = qr/$options->{ 'regex' }/;
+    }
+}
+elsif ( defined $options->{ 'exact_in' } and -f $options->{ 'exact_in' } )
+{
+    $patterns = Maasha::Patscan::read_patterns( $options->{ 'exact_in' } );
+
+    map { $lookup_hash{ $_ } = 1 } @{ $patterns };
+
+    undef $patterns;
+}
+elsif ( $options->{ 'eval' } )
+{
+    if ( $options->{ 'eval' } =~ /^([^><=! ]+)\s*(>=|<=|>|<|==|=|!=|eq|ne)\s*(.+)$/ )
+    {
+        $key = $1;
+        $op  = $2;
+        $val = $3;
+    }
+    else
+    {
+        Maasha::Common::error( qq(Bad eval string: $options->{ 'eval' }) );
+    }
+} 
+
+$total   = 0;
+$grabbed = 0;
+
+while ( $record = Maasha::Biopieces::get_record( $in ) ) 
+{
+    $found = 0;
+
+    if ( %lookup_hash ) {
+        $found = grab_lookup( \%lookup_hash, $record, $keys, $vals_only, $keys_only );
+    } elsif ( $patterns ) {
+        $found = grab_patterns( $patterns, $record, $keys, $vals_only, $keys_only );
+    } elsif ( $regex ) {
+        $found = grab_regex( $regex, $record, $keys, $vals_only, $keys_only );
+    } elsif ( $op ) {
+        $found = grab_eval( $key, $op, $val, $record );
+    }
+
+    if ( $found and not $invert )
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+        $grabbed += 1;
+    }
+    elsif ( not $found and $invert )
+    {
+        Maasha::Biopieces::put_record( $record, $out );
+        $grabbed += 1;
+    }
+
+    $total += 1;
+}
+
+Maasha::Biopieces::close_stream( $in );
+Maasha::Biopieces::close_stream( $out );
+
+if ( $options->{ 'verbose' } )
+{
+    print STDERR "Records grabbed: $grabbed\n";
+    print STDERR "Records missed: " . ( $total - $grabbed ) . "\n";
+    print STDERR "Patterns used: " . ( scalar @{$patterns} ) . "\n" if defined $patterns;
+    print STDERR "Patterns used: " . ( scalar keys %lookup_hash ) . "\n" if %lookup_hash;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> SUBROUTINES <<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+sub grab_lookup
+{
+    # Martin A. Hansen, November 2009.
+
+    # Uses keys from a lookup hash to search records. Optionally, a list of
+    # keys can be given so the lookup is limited to these, also, flags
+    # can be given to limit lookup to keys or vals only. Returns 1 if lookup
+    # succeeded, else 0.
+
+    my ( $lookup_hash,   # hashref with patterns
+         $record,        # hashref
+         $keys,          # list of keys   - OPTIONAL
+         $vals_only,     # only vals flag - OPTIONAL
+         $keys_only,     # only keys flag - OPTIONAL
+       ) = @_;
+
+    # Returns boolean.
+
+    if ( $keys )
+    {
+        map { return 1 if defined $record->{ $_ } and exists $lookup_hash->{ $record->{ $_ } } } @{ $keys };
+    }
+    else
+    {
+        if ( not $vals_only ) {
+            map { return 1 if exists $lookup_hash->{ $_ } } keys %{ $record };
+        }
+
+        if ( not $keys_only ) {
+            map { return 1 if defined $record->{ $_ } and exists $lookup_hash->{ $record->{ $_ } } } keys %{ $record };
+        }
+    }
+
+    return 0;
+}
+
+
+sub grab_patterns
+{
+    # Martin A. Hansen, November 2009.
+
+    # Uses patterns to match records containing the pattern as a substring.
+    # Returns 1 if the record is matched, else 0.
+
+    my ( $patterns,   # list of patterns
+         $record,     # hashref
+         $keys,       # list of keys   - OPTIONAL
+         $vals_only,  # only vals flag - OPTIONAL
+         $keys_only,  # only keys flag - OPTIONAL
+       ) = @_;
+
+    # Returns boolean.
+
+    my ( $pattern, $key );
+
+    foreach $pattern ( @{ $patterns } )
+    {
+        if ( $keys )
+        {
+            foreach $key ( @{ $keys } )
+            {
+                return 0 if not exists $record->{ $key };
+                return 1 if index( $record->{ $key }, $pattern ) >= 0;
+            }
+        }
+        else
+        {
+            if ( not $vals_only ) {
+                map { return 1 if index( $_, $pattern ) >= 0 } keys %{ $record };
+            }
+
+            if ( not $keys_only ) {
+                map { return 1 if index( $record->{ $_ }, $pattern ) >= 0 } keys %{ $record };
+            }
+        }
+    }
+
+    return 0;
+}
+
+
+sub grab_regex
+{
+    # Martin A. Hansen, November 2009.
+
+    # Uses regex to match records.
+    # Returns 1 if the record is matched, else 0.
+
+    my ( $regex,      # regex to match
+         $record,     # hashref
+         $keys,       # list of keys   - OPTIONAL
+         $vals_only,  # only vals flag - OPTIONAL
+         $keys_only,  # only keys flag - OPTIONAL
+       ) = @_;
+
+    # Returns boolean.
+
+    if ( $keys )
+    {
+        map { return 1 if exists $record->{ $_ } and $record->{ $_ } =~ /$regex/ } @{ $keys };
+    }
+    else
+    {
+        if ( not $vals_only ) {
+            map { return 1 if $_ =~ /$regex/ } keys %{ $record };
+        }
+
+        if ( not $keys_only ) {
+            map { return 1 if $record->{ $_ } =~ /$regex/ } keys %{ $record };
+        }
+    }
+
+    return 0;
+}
+
+
+sub grab_eval
+{
+    # Martin A. Hansen, November 2009.
+
+    # Test if the value of a given record key evaluates according
+    # to a given operator. Returns 1 if eval is OK, else 0.
+
+    my ( $key,     # record key
+         $op,      # operator
+         $val,     # value
+         $record,  # hashref
+       ) = @_;
+    
+    # Returns boolean.
+
+    if ( defined $record->{ $key } ) 
+    {
+        return 1 if ( $op eq "<"  and $record->{ $key } <  $val );
+        return 1 if ( $op eq ">"  and $record->{ $key } >  $val );
+        return 1 if ( $op eq ">=" and $record->{ $key } >= $val );
+        return 1 if ( $op eq "<=" and $record->{ $key } <= $val );
+        return 1 if ( $op eq "="  and $record->{ $key } == $val );
+        return 1 if ( $op eq "==" and $record->{ $key } == $val );
+        return 1 if ( $op eq "!=" and $record->{ $key } != $val );
+        return 1 if ( $op eq "eq" and $record->{ $key } eq $val );
+        return 1 if ( $op eq "ne" and $record->{ $key } ne $val );
+    }
+
+    return 0;
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
+
+BEGIN
+{
+    Maasha::Biopieces::status_set();
+}
+
+
+END
+{
+    Maasha::Biopieces::status_log();
+}
+
+
+# >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
+
 
-use Maasha::BioRun;
+__END__