comparison rapsodyn/mpileupfilterandstat.pl @ 7:3f7b0788a1c4 draft

Uploaded

6:1776b8ddd87e

#!/usr/bin/perl
use strict;
use Getopt::Long;

#
# Filter a pileup file on forward/reverse presence and %read having the variant

my $MIN_DEPTH=0;
my $MAX_DEPTH=500;
my $VERBOSE=0;
my $ONLY_UNFILTERED_VARIANT="OFF";
my $DO_STAT="NO";


my $STAT_MIN_DEPTH_MIN = 2;
my $STAT_MIN_DEPTH_MAX = 10;
my $STAT_MIN_DEPTH_STEP = 2;

#Extraction des variants
my $nb_line=0;
while (my $line=<IF>){
	$nb_line++;
	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
		print "$nb_line\n";
	}
	my $error_code=0;

		$after = $tbl_line[$i+1];
	}		
	my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
	if ($error_code == 0){
		print $line{"line"};
	}
	else {
		push(@error,$error_code,"\t",$line{"line"});
	}
}

### LOG
open(LF,">$logfile") or die ("Can't open $logfile\n");

if ($DO_STAT eq "YES"){
	for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
		for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
			for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ 
				for (my $idx_dist=$STAT_DIST_MIN;$idx_dist<=$STAT_DIST_MAX;$idx_dist = $idx_dist + $STAT_DIST_STEP){
					for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){

		}
	}
}


for (my $i=0;$i<=$#error;$i++){
	print LF $error[$i];
}
close (LF);

7:3f7b0788a1c4

#!/usr/bin/perl
#V1.0.0
use strict;
use Getopt::Long;

#
# Filter a pileup file on forward/reverse presence and %read having the variant

my $MIN_DEPTH=0;
my $MAX_DEPTH=500;
my $VERBOSE=0;
my $ONLY_UNFILTERED_VARIANT="OFF";
my $DO_STAT="NO";

my $nb_variant_checked=0;
my $nb_variant_selected=0;


my $STAT_MIN_DEPTH_MIN = 2;
my $STAT_MIN_DEPTH_MAX = 10;
my $STAT_MIN_DEPTH_STEP = 2;

#Extraction des variants
my $nb_line=0;
while (my $line=<IF>){
	$nb_variant_checked++;
	$nb_line++;
	if (($nb_line % 1000000 == 0)&&($VERBOSE==1)){
		print "$nb_line\n";
	}
	my $error_code=0;

		$after = $tbl_line[$i+1];
	}		
	my $error_code = check_error($tbl_line[$i],$before,$after,\%USR_PARAM);
	if ($error_code == 0){
		print $line{"line"};
		$nb_variant_selected++;
	}
	else {
		push(@error,$error_code,"\t",$line{"line"});
	}
}

### LOG
open(LF,">$logfile") or die ("Can't open $logfile\n");
print LF "\n####\t MPileup filtering \n";
print LF "Variant checked  :\t$nb_variant_checked\n";
if ($DO_STAT eq "NO"){
	print LF "Variant selected :\t$nb_variant_selected\n";
}
elsif ($DO_STAT eq "YES"){
	for (my $idx_min_depth=$STAT_MIN_DEPTH_MIN;$idx_min_depth<=$STAT_MIN_DEPTH_MAX;$idx_min_depth = $idx_min_depth + $STAT_MIN_DEPTH_STEP ){
		for (my $idx_max_depth=$STAT_MAX_DEPTH_MIN;$idx_max_depth<=$STAT_MAX_DEPTH_MAX;$idx_max_depth = $idx_max_depth + $STAT_MAX_DEPTH_STEP ){
			for (my $idx_freq = $STAT_FREQ_MIN;$idx_freq<=$STAT_FREQ_MAX;$idx_freq= $idx_freq+$STAT_FREQ_STEP){ 
				for (my $idx_dist=$STAT_DIST_MIN;$idx_dist<=$STAT_DIST_MAX;$idx_dist = $idx_dist + $STAT_DIST_STEP){
					for (my $idx_fr=0;$idx_fr<=1;$idx_fr++){

		}
	}
}


#for (my $i=0;$i<=$#error;$i++){
#	print LF $error[$i];
#}
close (LF);