[GenABEL-dev] [Genabel-commits] r630 - pkg/ProbABEL/src
Yurii Aulchenko
yurii.aulchenko at gmail.com
Fri Jan 7 20:20:24 CET 2011
Less cohorts, may be, but not less chromosomes :) Enigmatic it is ...
Yurii
On 1/7/11, L.C. Karssen <l.karssen at erasmusmc.nl> wrote:
> On Fri, 2011-01-07 at 16:30 +0100, Yurii Aulchenko wrote:
>> Great work, happy that things go on improving!
> Thanks!
>
>>
>> Did you update the "changes.log", or will we eventually generate that
>> based on commit-comments? (Some way to automate that???)
> I think we should try to automate that. Let's think of that and maybe
> look around how others do it.
>
>
>>
>> Btw my feeling is that few people use this pl except us -- do we
>> describe how to configure it in the manual? That may be the reason...
> It is mentioned in the manual. Maybe others have less cohorts?
>
> Lennart.
>
>
>>
>> Yurii
>>
>> On 1/7/11, noreply at r-forge.r-project.org <noreply at r-forge.r-project.org>
>> wrote:
>> > Author: lckarssen
>> > Date: 2011-01-07 14:01:11 +0100 (Fri, 07 Jan 2011)
>> > New Revision: 630
>> >
>> > Modified:
>> > pkg/ProbABEL/src/probabel.pl
>> > Log:
>> > Updates to the probabel.pl script. Tested for some time on our own
>> > servers.
>> > Details:
>> > - Added possibility to use the script for the X chromosome as well
>> > - Clarified part of the help text and error messages
>> > - slightly simpler configuration because now the base path to each of
>> > the pa-utilities can be set in one variable.
>> > - Removed some superfluous spaces and empty lines
>> > - Fixed a few minor spelling errors in the comments and help text.
>> >
>> >
>> > Modified: pkg/ProbABEL/src/probabel.pl
>> > ===================================================================
>> > --- pkg/ProbABEL/src/probabel.pl 2011-01-05 17:31:39 UTC (rev 629)
>> > +++ pkg/ProbABEL/src/probabel.pl 2011-01-07 13:01:11 UTC (rev 630)
>> > @@ -1,27 +1,33 @@
>> > -#! /usr/bin/perl
>> > +#! /usr/bin/perl
>> >
>> > -#=====================================================================================
>> > +#============================================================================
>> > #
>> > # Filename: probabel.pl
>> > #
>> > -# Description: Handy perl wraper for ProbABEL functions
>> > +# Description: Handy perl wrapper for ProbABEL functions
>> > #
>> > -# Version: 1.1
>> > +# Version: 1.4
>> > # Created: 28-Oct-2008
>> > # Revision: none
>> > -# last modification: 12-Jan-2009
>> > +# last modification: 07-Jan-2011
>> > #
>> > -# Author: Maksim V. Struchalin, Yurii S. Aulchenko
>> > -# Company: ErasmusMC, Epidemiology & Biostatistics
>> > Department,
>> > The Netherlands.
>> > -# Email: m.struchalin at erasmusmc.nl,
>> > i.aoultchenko at erasmusmc.nl
>> > +# Author: Lennart C. Karssen,
>> > +# Maksim V. Struchalin,
>> > +# Yurii S. Aulchenko
>> > +# Company: Erasmus MC,
>> > +# Epidemiology & Biostatistics Department,
>> > +# The Netherlands.
>> > +# Email: l.karssen at erasmusmc.nl,
>> > +# m.struchalin at erasmusmc.nl,
>> > +# i.aoultchenko at erasmusmc.nl
>> > #
>> > -#=====================================================================================
>> > +#============================================================================
>> >
>> >
>> >
>> >
>> > -$version="1.1";
>> > -$release_data="11-Jan-2009";
>> > +$version="1.4";
>> > +$release_data="07-Jan-2011";
>> >
>> > $_2df_file_postfix = "_2df.out.txt";
>> > $_add_file_postfix = "_add.out.txt";
>> > @@ -35,11 +41,11 @@
>> > $separator_cfg = ",";
>> > $separator_filename = "_._chr_._";
>> >
>> > +$base_path = "./";
>> > +$config = $base_path . "probabel_config.cfg";
>> >
>> > -$config = "probabel_config.cfg";
>> > -
>> > @method = ("linear","logistic","coxph");
>> > - at anprog = ("./palinear","./palogist","./pacoxph");
>> > + at anprog = ($base_path . "palinear", $base_path . "palogist", $base_path
>> > .
>> > "pacoxph");
>> >
>> > %cohorts;
>> > @mlinfo;
>> > @@ -72,52 +78,50 @@
>> > close(CFG);
>> >
>> >
>> > -
>> > -
>> > -if(@ARGV<6 || $ARGV[0] == "--help")
>> > +if(@ARGV<6 || $ARGV[0] eq "--help")
>> > {
>> > print "\nUsage:
>> > probabel.pl chrom-start chrom-end method cohort <--allmodels OR
>> > --additive> trait <other available keys of ProbABEL functions>\n";
>> > print "\n * chrom-start - the first chromosome number, chrom-end - the
>> > last one";
>> > print "\n * method can be ";
>> > foreach $me(@method) {print "\"".$me."\", "};
>> > - print "\n * use --allmodels if you need dominant, recessive and
>> > heterozygous models
>> > + print "\n * use --allmodels if you need dominant, recessive and
>> > heterozygous models
>> > and --additive if additive only\n";
>> > print " * Available cohorts is ";
>> > - foreach $coh(keys %cohorts) {print "\"".$coh."\", "};
>> > + foreach $coh(keys %cohorts) {print "\"".$coh."\", "};
>> > print "\n * example:
>> > - probabel.pl 1 22 linear \"ERF\" --additive filename1 filename2
>> > + probabel.pl 1 22 linear \"ERF\" --additive filename1 filename2
>> > (filename has to be saved as filename.PHE)\n\n";
>> > -
>> > -
>> > +
>> > +
>> > print "\n Details:\n";
>> > - print " Script probabel.pl is used for analysis of imputed data.
>> > - Firstly you have to create file with phenotypes which you are going
>> > to
>> > use.
>> > - The first column is ids in special order, the second - trait which
>> > you
>> > are going analyze, rest - covariates.
>> > + print " The probabel.pl script is used for analysis of imputed data.
>> > + First you have to create file with the phenotypes that you are going
>> > to
>> > use.
>> > + The first column contains ids in special order, the second: the
>> > trait
>> > which you are going analyze, the others containd covariates.
>> > Like this =>
>> > -
>> > - id phen1 covariate1 covariate2
>> > +
>> > + id phen1 covariate1 covariate2
>> > 1_2094 0 334 0
>> > 1_5060 1 56 1
>> > 1_4077 1 346 6
>> > .
>> > - .
>> > .
>> > -
>> > - That means model:
>> > + .
>> > +
>> > + This implies the model:
>> > phen1 ~ covariate1 + covariate2 + SNP
>> > -
>> > -
>> > - Then save it to folder where you are doing analysis. Name of file
>> > must
>> > be name_of_file.PHE.
>> > - Where name_of_file is any name.
>> > -
>> > - Then perform in bash (Linux) comand line
>> > +
>> > +
>> > + Then save it to folder where you are doing the analysis. The name of
>> > the
>> > file must be name_of_file.PHE, where name_of_file is any name.
>> > +
>> > + Then run the following on the Linux command line:
>> > probabel.pl 1 22 \"method\" \"cohort\" --model name_of_file
>> > - Change \"method\" \"cohort\" --model on appropriate values\n";
>> > - print "\n Version: $version";
>> > - print "\n Release data: $release_data";
>> > - print "\n\n Autors: Maksim Struchalin - m.struchalin\@erasmusmc.nl,
>> > - Yurii Aulchenko - i.aoultchenko\@erasmusmc.nl.\n\n";
>> > + Change \"method\" \"cohort\" --model to appropriate values\n";
>> > + print "\n Version: $version";
>> > + print "\n Release data: $release_data";
>> > + print "\n\n Authors: Lennart Karssen - l.karssen\@erasmusmc.nl,
>> > + Maksim Struchalin - m.struchalin\@erasmusmc.nl,
>> > + Yurii Aulchenko - i.aoultchenko\@erasmusmc.nl.\n\n";
>> > exit;
>> > }
>> >
>> > @@ -130,22 +134,18 @@
>> >
>> >
>> >
>> > -die "error: chrom-start is > 22" if($startchr > 22);
>> > -die "error: chrom-end is > 22" if($endchr > 22);
>> > +die "error: chrom-start is > 22" if($startchr > 22 && $startchr != "X")
>> > ;
>> > +die "error: chrom-end is > 22" if($endchr > 22 && $endchr != "X");
>> > die "error: chrom-start > chrom-end" if($startchr > $endchr);
>> >
>> >
>> > -
>> > -
>> > -
>> > -
>> > $cohort_position = $cohorts{$chohort};
>> >
>> >
>> > if(!defined($cohort_position))
>> > {
>> > -print "\nerror: Wrong cohort name
>> > -Available cohorts is ";
>> > +print "\nerror: Wrong cohort name, \"$chohort\" is not an available
>> > cohort.
>> > +Available cohorts are ";
>> > foreach $coh(keys %cohorts) {print "\"".$coh."\", "};
>> > print "\n\n";
>> > exit;
>> > @@ -176,7 +176,7 @@
>> > $keys="";
>> >
>> >
>> > -for ($i=6;$i<@ARGV;$i++)
>> > +for ($i=6;$i<@ARGV;$i++)
>> > {
>> > $keys = $keys.$ARGV[$i]." ";
>> > }
>> > @@ -207,12 +207,20 @@
>> >
>> > print "Start...\n";
>> >
>> > - $chr = $startchr;
>> > - print `$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 $keys`;
>> > +$chr = $startchr;
>> > +
>> > +# Separate command for the X chromosome.
>> > +if ($chr eq "X") {
>> > + 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 $keys`;
>> > + exit;
>> > +}
>> > +
>> > +# Commands for the autosomes
>> > +print `$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}`;
>> > @@ -220,7 +228,7 @@
>> >
>> > `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`;
>> >
>> >
>> > _______________________________________________
>> > Genabel-commits mailing list
>> > Genabel-commits at lists.r-forge.r-project.org
>> > https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-commits
>> >
>>
>
> --
> -----------------------------------------------
> L.C. Karssen
> Erasmus MC
> Department of Epidemiology
> Room Ee2224
>
> Postbus 2040
> 3000 CA Rotterdam
> The Netherlands
>
> phone: +31-10-7044217
> fax: +31-10-7044657
> email: l.karssen at erasmusmc.nl
> GPG key ID: 0E1D39E3
> -----------------------------------------------
>
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