agat_sp_filter_feature_by_attribute_value.pl

#!/usr/bin/env perl

use strict;
use warnings;
use Getopt::Long;
use File::Basename;
use POSIX qw(strftime);
use Scalar::Util qw(looks_like_number);
use Pod::Usage;
use IO::File;
use AGAT::AGAT;

my $header = get_agat_header();
my $config;
my $primaryTag=undef;
my $opt_output= undef;
my $opt_value = undef;
my $opt_attribute = undef;
my $opt_test = "=";
my $opt_gff = undef;
my $opt_verbose = undef;
my $opt_help;

# OPTION MANAGMENT
my @copyARGV=@ARGV;
if ( !GetOptions( 'f|ref|reffile|gff=s' => \$opt_gff,
                  'value=s'             => \$opt_value,
                  "p|type|l=s"          => \$primaryTag,
                  'a|attribute=s'       => \$opt_attribute,
                  't|test=s'            => \$opt_test,
                  'o|output=s'          => \$opt_output,
                  'v|verbose!'          => \$opt_verbose,
                  'c|config=s'               => \$config,
                  'h|help!'             => \$opt_help ) )
{
    pod2usage( { -message => 'Failed to parse command line',
                 -verbose => 1,
                 -exitval => 1 } );
}

if ($opt_help) {
    pod2usage( { -verbose => 99,
                 -exitval => 0,
                 -message => "$header\n" } );
}

if ( ! $opt_gff or ! defined($opt_value) or ! $opt_attribute ){
    pod2usage( {
           -message => "$header\nAt least 3 parameters are mandatory:\n1) Input reference gff file: --gff\n".
           "2) An attribute tag: -a\n3) A value (string or int) that will be used for filtering: --value\n\n",
           -verbose => 0,
           -exitval => 2 } );
}

# --- Manage config ---
$config = get_agat_config({config_file_in => $config});

###############
# Test options
if($opt_test ne "<" and $opt_test ne ">" and $opt_test ne "<=" and $opt_test ne ">=" and $opt_test ne "="){
  print "The test to apply is Wrong: $opt_test.\nWe want something among this list: <,>,<=,>=,! or =.";exit;
}
if( ! looks_like_number($opt_value) ){
  if($opt_test eq "="){$opt_test="eq";}
  elsif($opt_test eq "!"){$opt_test="ne";}
  else{ print "This test $opt_test is not possible with string value.";exit; }
}

###############
# Manage Output

## FOR GFF FILE
my $gffout_ok_file ;
my $fhout_discarded_file ;
my $ostreamReport_file;

if ($opt_output) {
  my ($outfile,$path,$ext) = fileparse($opt_output,qr/\.[^.]*/);

  # set file names
  $gffout_ok_file = $path.$outfile.$ext;
  $fhout_discarded_file = $path.$outfile."_discarded.txt";
  $ostreamReport_file = $path.$outfile."_report.txt";
}

my $gffout_ok = prepare_gffout($config, $gffout_ok_file);
my $fhout_discarded = prepare_fileout($fhout_discarded_file);
my $ostreamReport = prepare_fileout($ostreamReport_file);

# Manage $primaryTag
my @ptagList;
my $print_feature_string;
if(! $primaryTag or $primaryTag eq "all"){
  $print_feature_string = "all features";
  push(@ptagList, "all");
}
elsif($primaryTag =~/^level[123]$/){
  $print_feature_string .= "$primaryTag features ";
  push(@ptagList, $primaryTag);
}
else{
   @ptagList= split(/,/, $primaryTag);
   foreach my $tag (@ptagList){
      if($tag =~/^level[123]$/){
        $print_feature_string .= "$primaryTag features ";
      }
      else{
        $print_feature_string .= "$tag feature ";
      }
   }
}

# start with some interesting information
my $stringPrint = strftime "%m/%d/%Y at %Hh%Mm%Ss", localtime;
$stringPrint .= "\nusage: $0 @copyARGV\n";
$stringPrint .= "We will discard $print_feature_string that have the attribute $opt_attribute with the value $opt_test $opt_value.\n";

if ($opt_output){
  print $ostreamReport $stringPrint;
  print $stringPrint;
}
else{ print $stringPrint; }
                          #######################
# >>>>>>>>>>>>>>>>>>>>>>>>#        MAIN         #<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
                          #######################
my %all_cases = ('l1' => 0, 'l2' => 0, 'l3' => 0, 'all' => 0);
######################
### Parse GFF input #
my ($hash_omniscient, $hash_mRNAGeneLink) =  slurp_gff3_file_JD({ input => $opt_gff,
                                                                  config => $config
                                                                });
print("Parsing Finished\n");
### END Parse GFF input #
#########################
# sort by seq id
my $hash_sortBySeq = gather_and_sort_l1_by_seq_id($hash_omniscient);

my $removeit=undef;
#################
# == LEVEL 1 == #
#################
foreach my $seqid (sort { (($a =~ /(\d+)$/)[0] || 0) <=> (($b =~ /(\d+)$/)[0] || 0) } keys %{$hash_sortBySeq}){ # loop over all the feature level1

	foreach my $tag_l1 (sort {$a cmp $b} keys %{$hash_omniscient->{'level1'}}){
		foreach my $feature_l1 ( @{$hash_sortBySeq->{$seqid}{$tag_l1}} ){
			my $id_l1 = lc($feature_l1->_tag_value('ID'));

	    $removeit = check_feature($feature_l1, 'level1', \@ptagList, $opt_attribute, $opt_test, $opt_value);
			# we can remove feature L1 now because we are looping over $hash_sortBySeq not $hash_omniscient
	    if ($removeit){
	      my $cases = remove_l1_and_relatives($hash_omniscient, $feature_l1, $fhout_discarded);
				$all_cases{'l1'} += $cases->{'l1'};
				$all_cases{'l2'} += $cases->{'l2'};
				$all_cases{'l3'} += $cases->{'l3'};
				$all_cases{'all'} += $cases->{'all'};
				next;
	    }

	    #################
	    # == LEVEL 2 == #
	    #################
			my @list_l2_to_remove;
			my @list_l3_to_remove;
	    foreach my $tag_l2 (sort keys %{$hash_omniscient->{'level2'}}){ # primary_tag_key_level2 = mrna or mirna or ncrna or trna etc...

	      if ( exists_keys( $hash_omniscient, ('level2', $tag_l2, $id_l1) ) ){
	        my @list_fl2 = @{$hash_omniscient->{'level2'}{$tag_l2}{$id_l1}};
	        foreach my $feature_l2 ( @list_fl2 ) {

	          $removeit = check_feature($feature_l2,'level2', \@ptagList, $opt_attribute, $opt_test, $opt_value);
	          if ($removeit){
	            push @list_l2_to_remove, [$feature_l2, $tag_l1, $id_l1, $fhout_discarded];
	            next;
	          }
	          #################
	          # == LEVEL 3 == #
	          #################
	          my $id_l2 = lc($feature_l2->_tag_value('ID'));

	          foreach my $tag_l3 (sort keys %{$hash_omniscient->{'level3'}}){ # primary_tag_key_level3 = cds or exon or start_codon or utr etc...
	            if ( exists_keys( $hash_omniscient, ('level3', $tag_l3, $id_l2) ) ){
	              my @list_fl3 = @{$hash_omniscient->{'level3'}{$tag_l3}{$id_l2}};
	              foreach my $feature_l3 ( @list_fl3 ) {

	                $removeit = check_feature($feature_l3, 'level3', \@ptagList, $opt_attribute, $opt_test, $opt_value);
	                if ($removeit){
	                  push @list_l3_to_remove, [$feature_l3, $tag_l1, $id_l1, $tag_l2, $id_l2, $fhout_discarded];
	                }
	              }
	            }
	          }
	        }
	      }
	    }
			# Should be removed after looping over them to avoid problems
			if (@list_l2_to_remove) {
				foreach my $infos (@list_l2_to_remove) {
					my $cases = remove_l2_and_relatives( $hash_omniscient, @$infos);
					$all_cases{'l1'} += $cases->{'l1'};
					$all_cases{'l2'} += $cases->{'l2'};
					$all_cases{'l3'} += $cases->{'l3'};
					$all_cases{'all'} += $cases->{'all'};
				}
			}
			if (@list_l3_to_remove) {
				foreach my $infos (@list_l3_to_remove) {
					my $cases = remove_l3_and_relatives( $hash_omniscient, @$infos);
					$all_cases{'l1'} += $cases->{'l1'};
					$all_cases{'l2'} += $cases->{'l2'};
					$all_cases{'l3'} += $cases->{'l3'};
					$all_cases{'all'} += $cases->{'all'};
				}
			}
		}
  }
}

print_omniscient( {omniscient => $hash_omniscient, output => $gffout_ok} );

$stringPrint = $all_cases{'all'}." features removed:\n";
$stringPrint .= $all_cases{'l1'}." features level1 (e.g. gene) removed\n";
$stringPrint .= $all_cases{'l2'}." features level2 (e.g. mRNA) removed\n";
$stringPrint .= $all_cases{'l3'}." features level3 (e.g. exon) removed\n";
if ($opt_output){
  print $ostreamReport $stringPrint;
  print $stringPrint;
} else{ print $stringPrint; }

#######################################################################################################################
        ####################
         #     methods    #
          ################
           ##############
            ############
             ##########
              ########
               ######
                ####
                 ##

sub check_feature{
  my  ($feature, $level, $ptagList, $opt_attribute, $opt_test, $opt_value)=@_;

  my $removeit=undef;
  my $primary_tag=$feature->primary_tag;

  # check primary tag (feature type) to handle
  foreach my $ptag (@$ptagList){

    if($ptag eq "all"){
      $removeit = should_we_remove_feature($feature, $opt_attribute, $opt_test, $opt_value);
    }
    elsif(lc($ptag) eq $level){
      $removeit = should_we_remove_feature($feature, $opt_attribute, $opt_test, $opt_value);
    }
    elsif(lc($ptag) eq lc($primary_tag) ){
      $removeit = should_we_remove_feature($feature, $opt_attribute, $opt_test, $opt_value);
    }
  }
  return $removeit;
}

sub should_we_remove_feature{
  my ($feature, $opt_attribute, $opt_test, $opt_value)=@_;

  if ($feature->has_tag($opt_attribute)){

    # get list of values for the attribute
    my @values = $feature->get_tag_values($opt_attribute);

    # if we found among the values one pass the test we return 1
    foreach my $value (@values){

      if ($opt_test eq "eq"){
        if ($value eq $opt_value){return 1; }
      }
      elsif ($opt_test eq "ne"){
        if ($value ne $opt_value){return 1; }
      }
      elsif ($opt_test eq "="){
       if ($value == $opt_value){return 1; }
      }
      elsif ($opt_test eq "!"){
        if ($value != $opt_value){return 1; }
      }
      elsif ($opt_test eq ">"){
        if ($value > $opt_value){return 1; }
      }
      elsif ($opt_test eq "<"){
        if ($value < $opt_value){return 1; }
      }
      elsif ($opt_test eq "<="){
        if ($value <= $opt_value){return 1; }
      }
      elsif ($opt_test eq ">="){
        if ($value >= $opt_value){return 1; }
      }
    }
  }
  return 0;
}

__END__

=head1 NAME

agat_sp_select_feature_by_attribute_value.pl

=head1 DESCRIPTION

The script aims to filter features according to attribute value (9th column).
If the attribute tag is missing the feature will not be discarded.
If the attribute exists and the value pass the test, the feature is discarded.
Attribute are stored in the 9th column and have this shape: tag=value
/!\ Removing a level1 or level2 feature will automatically remove all linked subfeatures, and
removing all children of a feature will automatically remove this feature too.

=head1 SYNOPSIS

    agat_sp_select_feature_by_attribute_value.pl --gff infile.gff --value 1 -t "=" [ --output outfile ]
    agat_sp_select_feature_by_attribute_value.pl --help

=head1 OPTIONS

=over 8

=item B<-f>, B<--reffile>, B<--gff>  or B<-ref>

Input GFF3 file that will be read

=item  B<-a> or B<--attribute>

Attribute tag to specify the attribute to analyse (attribute example: tag=value).

=item B<-p>,  B<--type> or  B<-l>

primary tag option, case insensitive, list. Allow to specied the feature types that will be handled.
You can specified a specific feature by given its primary tag name (column 3) as: cds, Gene, MrNa
You can specify directly all the feature of a particular level:
      level2=mRNA,ncRNA,tRNA,etc
      level3=CDS,exon,UTR,etc
By default all feature are taking into account. fill the option by the value "all" will have the same behaviour.

=item B<--value>

Value to check in the attribute

=item B<-t> or B<--test>
Test to apply (> < = >= <=). default value "=". If you us one of these two character >, <, please don't forget to quote you parameter liket that "<=". Else your terminal will complain.

=item B<-o> or B<--output>

Output GFF file.  If no output file is specified, the output will be
written to STDOUT.

=item B<-v>

Verbose option for debugging purpose.

=item B<-c> or B<--config>

String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, 
otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose".
The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

=item B<-h> or B<--help>

Display this helpful text.

=back

=head1 FEEDBACK

=head2 Did you find a bug?

Do not hesitate to report bugs to help us keep track of the bugs and their
resolution. Please use the GitHub issue tracking system available at this
address:

            https://github.com/NBISweden/AGAT/issues

 Ensure that the bug was not already reported by searching under Issues.
 If you're unable to find an (open) issue addressing the problem, open a new one.
 Try as much as possible to include in the issue when relevant:
 - a clear description,
 - as much relevant information as possible,
 - the command used,
 - a data sample,
 - an explanation of the expected behaviour that is not occurring.

=head2 Do you want to contribute?

You are very welcome, visit this address for the Contributing guidelines:
https://github.com/NBISweden/AGAT/blob/master/CONTRIBUTING.md

=cut

AUTHOR - Jacques Dainat