[GenABEL-dev] Fwd: Re: Small patch for probabel.pl (against 0.2.0)

[Marijn Verkerk]

Small patch of probabel.pl for review!

Regards,
Marijn


-------- Original Message --------
Subject: 	Re: Small patch for probabel.pl (against 0.2.0) - small 
correction
Date: 	Tue, 14 Aug 2012 16:15:39 +0200
From: 	Marijn Verkerk <m.verkerk at erasmusmc.nl>
To: 	L.C. Karssen <l.karssen at erasmusmc.nl>, yurii.aulchenko at gmail.com



On 8/14/12 2:14 PM, Marijn Verkerk wrote:
> FYI
>
> This patch removes some redundancies in the code and makes probabel.pl
> compatible with a bit more complicated cohort configuration, i.e.
> where cohorts are located at a location with multiple references to
> the chromosome, see attachments.
>
> Best wishes,
> Marijn
>





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< $separator_filename = "_._chr_._";
---
> $chr_replacement = "_._chr_._";
38,41c38,41
< @mlinfo;
< @mldose;
< @mlprobe;
< @legend;
---
> @mlinfos;
> @mldoses;
> @mlprobes;
> @legends;
52,61c52,61
< 	{
< 	next if (/^#/);
< 	chomp($line);
< 	@line_array = split(/$separator_cfg/, $line);
< 	$cohorts{$line_array[0]} = $i;
< 	$mlinfo[$i]  = $line_array[1];
< 	$mldose[$i]  = $line_array[2];
< 	$mlprobe[$i] = $line_array[3];
< 	$legend[$i]  = $line_array[4];
< 	}
---
> {
>   next if (/^#/);
>   chomp($line);
>   @line_array = split(/$separator_cfg/, $line);
>   $cohorts{$line_array[0]} = $i;
>   $mlinfos[$i]  = $line_array[1];
>   $mldoses[$i]  = $line_array[2];
>   $mlprobes[$i] = $line_array[3];
>   $legends[$i]  = $line_array[4];
> }
140,145c140,143
< 
< @mlinfo_split = split(/$separator_filename/, $mlinfo[$cohort_position]);
< @mldose_split = split(/$separator_filename/, $mldose[$cohort_position]);
< @mlprobe_split = split(/$separator_filename/, $mlprobe[$cohort_position]);
< @legend_split = split(/$separator_filename/, $legend[$cohort_position]);
< 
---
> $mlinfo = $mlinfos[$cohort_position];
> $mldose = $mldoses[$cohort_position];
> $mlprobe = $mlprobes[$cohort_position];
> $legend = $legends[$cohort_position];
173,187c171,179
< 	{
< 	$mldose_probe_split1 = $mldose_split[0];
< 	$mldose_probe_split2 = $mldose_split[1];
< 	$model_option_num=1;
< 	}
< elsif($model eq "--allmodels")
< 	{
< 	$mldose_probe_split1 = $mlprobe_split[0];
< 	$mldose_probe_split2 = $mlprobe_split[1];
< 	$model_option_num=2;
< 	}
< else
< 	{
< 	die "error: Wrong key for model. You can use \"--additive\" or \"--allmodels\" only\n";
< 	}
---
> {
>   $mldose_probe = $mldose;
>   $model_option_num=1;
> } elsif($model eq "--allmodels") {
>   $mldose_probe = $mlprobe;
>   $model_option_num=2;
> } else {
>   die "error: Wrong key for model. You can use \"--additive\" or \"--allmodels\" only\n";
> }
195a188,189
> $hadhead=0;
> 
198c192,210
<     print `$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_split[0]$mlinfo_split[1] -d $mldose_probe_split1$mldose_probe_split2 -m $legend_split[0]$legend_split[1] --chrom $chr -o $phename $keys`;
---
>         
> 	$mlinfo_arg = $mlinfo;
>         $mlinfo_arg =~ s/$chr_replacement/X/g;
> 
>         $mldose_arg = $mldose;
>         $mldose_arg =~ s/$chr_replacement/X/g;
> 
>         $legend_arg = $legend;
>         $legend_arg =~ s/$chr_replacement/X/g;
> 
> 	if($hadhead==0) {
>           $head="";
>           $hadhead=1;
>         } else {
>           $head="--no-head";
>         }
> 	
> 	print `$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom X -o $phename $head $keys`;
> 
203,232c215,258
< print `$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_split[0]${chr}$mlinfo_split[1] -d $mldose_probe_split1${chr}$mldose_probe_split2 -m $legend_split[0]${chr}$legend_split[1] --chrom $chr -o $phename $keys`;
< 	for($chr=($startchr+1);$chr<=$endchr;$chr++)
< 		{
< 		print `$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_split[0]${chr}$mlinfo_split[1] -d $mldose_probe_split1${chr}$mldose_probe_split2 -m $legend_split[0]${chr}$legend_split[1] --chrom $chr -o $phename.$chr --no-head $keys`;
< 
< 		if($model_option_num==2)
< 			{
< 			`cat $phename.${chr}$_2df_file_postfix >> ${phename}${_2df_file_postfix}`;
< 			`rm $phename.${chr}$_2df_file_postfix`;
< 
< 			`cat $phename.${chr}$_add_file_postfix >> ${phename}${_add_file_postfix}`;
< 			`rm $phename.${chr}$_add_file_postfix`;
< 
< 			`cat $phename.${chr}$_domin_file_postfix >> ${phename}${_domin_file_postfix}`;
< 			`rm $phename.${chr}$_domin_file_postfix`;
< 
< 			`cat $phename.${chr}$_recess_file_postfix >> ${phename}${_recess_file_postfix}`;
< 			`rm $phename.${chr}$_recess_file_postfix`;
< 
< 			`cat $phename.${chr}$_over_domin_file_postfix >> ${phename}${_over_domin_file_postfix}`;
< 			`rm $phename.${chr}$_over_domin_file_postfix`;
< 			}
< 		else
< 			{
< 			`cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}`;
< 			print "cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}\n";
< 			`rm $phename.${chr}$_add_file_postfix`;
< 			print "rm $phename.${chr}$_add_file_postfix\n";
< 			}
< 		}
---
> 	
> for($chr=$startchr;$chr<=$endchr;$chr++)
> {
>       $mlinfo_arg = $mlinfo;
>       $mlinfo_arg =~ s/$chr_replacement/$chr/g;
> 
>       $mldose_arg = $mldose;
>       $mldose_arg =~ s/$chr_replacement/$chr/g;
> 
>       $legend_arg = $legend;
>       $legend_arg =~ s/$chr_replacement/$chr/g;
> 
>       if($hadhead==0) {
>         $head="";
>         $hadhead=1;
>       } else {
>         $head="--no-head";
>       }
>  
>       print `$prog -p $phename.PHE --ngpreds $model_option_num -i $mlinfo_arg -d $mldose_arg -m $legend_arg --chrom $chr -o $phename.$chr $head $keys`;
> 
>       if($model_option_num==2)
>       {
>         `cat $phename.${chr}$_2df_file_postfix >> ${phename}${_2df_file_postfix}`;
> 	`rm $phename.${chr}$_2df_file_postfix`;
> 
> 	`cat $phename.${chr}$_add_file_postfix >> ${phename}${_add_file_postfix}`;
> 	`rm $phename.${chr}$_add_file_postfix`;
> 
> 	`cat $phename.${chr}$_domin_file_postfix >> ${phename}${_domin_file_postfix}`;
> 	`rm $phename.${chr}$_domin_file_postfix`;
> 
> 	`cat $phename.${chr}$_recess_file_postfix >> ${phename}${_recess_file_postfix}`;
> 	`rm $phename.${chr}$_recess_file_postfix`;
> 
> 	`cat $phename.${chr}$_over_domin_file_postfix >> ${phename}${_over_domin_file_postfix}`;
> 	`rm $phename.${chr}$_over_domin_file_postfix`;
>       } else {		
> 	`cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}`;
> 	print "cat $phename.${chr}$_add_file_postfix >> $phename${_add_file_postfix}\n";
> 	`rm $phename.${chr}$_add_file_postfix`;
> 	print "rm $phename.${chr}$_add_file_postfix\n";
>       }
> }