[Genabel-commits] r783 - in pkg/ProbABEL: . src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Sep 14 20:37:32 CEST 2011
Author: lckarssen
Date: 2011-09-14 20:37:31 +0200 (Wed, 14 Sep 2011)
New Revision: 783
Added:
pkg/ProbABEL/src/probabel_config.cfg.example
Removed:
pkg/ProbABEL/src/probabel_config.cfg
Modified:
pkg/ProbABEL/configure.ac
pkg/ProbABEL/src/Makefile.am
pkg/ProbABEL/src/probabel.pl
Log:
* In ProbABEL's configure.ac script the version number was already set
to 0.2, changed it to 0.2-beta to avoid confusion about the present
status of the code.
* The probabel_config.cfg file is now renamed to have .example added to
it. This is to make sure that make install does not overwrite the
user's own version.
* Various edits related to the probabel.pl script:
- Some cleaning up (removal of unnecessary bits, addition of some comments)
- In src/Makefle.am:
+ substitute the path to the installed binaries
+ substitute the version number
Modified: pkg/ProbABEL/configure.ac
===================================================================
--- pkg/ProbABEL/configure.ac 2011-09-11 19:37:12 UTC (rev 782)
+++ pkg/ProbABEL/configure.ac 2011-09-14 18:37:31 UTC (rev 783)
@@ -2,8 +2,8 @@
# Process this file with autoconf to produce a configure script.
AC_PREREQ([2.67])
-AC_INIT(ProbABEL, 0.2-0, genabel-devel at r-forge.wu-wien.ac.at)
-AM_INIT_AUTOMAKE(ProbABEL, 0.2-0)
+AC_INIT(ProbABEL, 0.2-0-beta, genabel-devel at r-forge.wu-wien.ac.at)
+AM_INIT_AUTOMAKE(ProbABEL, 0.2-0-beta)
AC_CONFIG_SRCDIR([src/data.h])
AC_CONFIG_HEADERS([src/config.h])
Modified: pkg/ProbABEL/src/Makefile.am
===================================================================
--- pkg/ProbABEL/src/Makefile.am 2011-09-11 19:37:12 UTC (rev 782)
+++ pkg/ProbABEL/src/Makefile.am 2011-09-14 18:37:31 UTC (rev 783)
@@ -46,9 +46,11 @@
dist_bin_SCRIPTS = probabel.pl extIDS.pl
## Install the config file
-dist_sysconf_DATA = probabel_config.cfg
+dist_sysconf_DATA = probabel_config.cfg.example
-## Insert the correct path to the configure file in probabel.pl
+## Insert the correct values of several variables in the installed probabel.pl
install-exec-hook:
$(SED) -i "s;probabel_config.cfg;@sysconfdir@/probabel_config.cfg;" \
$(DESTDIR)$(bindir)/probabel.pl
+ $(SED) -i "s;\./;@bindir@/;" $(DESTDIR)$(bindir)/probabel.pl
+ $(SED) -i "s;PROBABEL_VERSION;@VERSION@;" $(DESTDIR)$(bindir)/probabel.pl
Modified: pkg/ProbABEL/src/probabel.pl
===================================================================
--- pkg/ProbABEL/src/probabel.pl 2011-09-11 19:37:12 UTC (rev 782)
+++ pkg/ProbABEL/src/probabel.pl 2011-09-14 18:37:31 UTC (rev 783)
@@ -1,34 +1,18 @@
#! /usr/bin/perl
-#============================================================================
+#==========================================================================
#
# Filename: probabel.pl
#
# Description: Handy perl wrapper for ProbABEL functions
#
-# Version: 1.5
-# Created: 28-Oct-2008
-# Revision: none
-# last modification: 02-Sep-2011
-#
-# Author: Lennart C. Karssen,
-# Maksim V. Struchalin,
-# Yurii S. Aulchenko
-# Company: Erasmus MC,
-# Department of Epidemiology,
-# The Netherlands.
-# Email: l.karssen at erasmusmc.nl,
-# m.struchalin at erasmusmc.nl,
-# i.aoultchenko at erasmusmc.nl
-#
-#============================================================================
+#==========================================================================
+#==========================================================================
+# Set variables
+$version="PROBABEL_VERSION";
-
-
-$version="1.5";
-$release_data="02-Sep-2011";
-
+# Define some filename postfixes
$_2df_file_postfix = "_2df.out.txt";
$_add_file_postfix = "_add.out.txt";
$_domin_file_postfix = "_domin.out.txt";
@@ -36,16 +20,19 @@
$_over_domin_file_postfix = "_over_domin.out.txt";
-
-
+# Separators in the config file
$separator_cfg = ",";
$separator_filename = "_._chr_._";
+# Set file locations
$base_path = "./";
+ at anprog = ($base_path . "palinear",
+ $base_path . "palogist",
+ $base_path . "pacoxph");
$config = "probabel_config.cfg";
- at method = ("linear","logistic","coxph");
- at anprog = ($base_path . "palinear", $base_path . "palogist", $base_path . "pacoxph");
+# Define the regression methods that are implemented
+ at method = ("linear", "logistic", "coxph");
%cohorts;
@mlinfo;
@@ -54,10 +41,11 @@
@legend;
+#==========================================================================
+# Read config file
+open(CFG,"$config") or die "Reading configuration file failed: $!" .
+ "\nDid you forget to edit and rename the probabel_config.cfg.example file?\n";
-#read config file
-open(CFG,"$config") or die "$!";
-
<CFG>; #skip the first line (header)
for(my $i=0 ; my $line = <CFG> ; $i++)
@@ -65,19 +53,17 @@
next if (/^#/);
chomp($line);
@line_array = split(/$separator_cfg/, $line);
-# foreach (@line_array) {print $_."\n"}
-# print "\n";
$cohorts{$line_array[0]} = $i;
$mlinfo[$i] = $line_array[1];
$mldose[$i] = $line_array[2];
$mlprobe[$i] = $line_array[3];
$legend[$i] = $line_array[4];
-# print "legend[$i]=".$legend[$i]."\n";
-# print "mlprobe[$i]=".$mlprobe[$i]."\n";
}
close(CFG);
+#==========================================================================
+# Print usage info if arguments are not correct
if(@ARGV<6 || $ARGV[0] eq "--help")
{
print "\nUsage:
@@ -96,8 +82,9 @@
print "\n Details:\n";
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.
+ First you have to create a 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 contains covariates.
Like this =>
id phen1 covariate1 covariate2
@@ -114,26 +101,25 @@
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:
+ Then run the following on the command line:
probabel.pl 1 22 \"method\" \"cohort\" --model name_of_file
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";
+ Yurii Aulchenko - yurii.aulchenko at gmail.com.\n\n";
exit;
}
+#==========================================================================
+# Put the command line arguments into variables and verify them
$startchr = $ARGV[0];
$endchr = $ARGV[1];
$method = $ARGV[2];
$chohort = $ARGV[3];
$model = $ARGV[4];
-
-
die "error: chrom-start is > 22" if($startchr > 22 && $startchr != "X") ;
die "error: chrom-end is > 22" if($endchr > 22 && $endchr != "X");
die "error: chrom-start > chrom-end" if($startchr > $endchr);
@@ -169,9 +155,6 @@
die "error: Wrong method. method has to be one of: @method\n" if (!$passed);
-
-
-
$phename = $ARGV[5];
$keys="";
@@ -204,7 +187,8 @@
}
-
+#==========================================================================
+# Start the analysis now that the input has been validated
print "Start...\n";
$chr = $startchr;
Deleted: pkg/ProbABEL/src/probabel_config.cfg
===================================================================
--- pkg/ProbABEL/src/probabel_config.cfg 2011-09-11 19:37:12 UTC (rev 782)
+++ pkg/ProbABEL/src/probabel_config.cfg 2011-09-14 18:37:31 UTC (rev 783)
@@ -1,3 +0,0 @@
-cohort,mlinfo_path,mldose_path,mlprobe_path,legend_path
-ERGO,script_test/merlin._._chr_._.collected.ped.out.mlinfo,script_test/merlin._._chr_._.collected.ped.out.mldose,script_test/merlin._._chr_._.collected.ped.out.mlprob,script_test/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
-ERGOPLUS,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mlinfo,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mldose,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mlprob,/mnt/impute/impute_b36/collected/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
Copied: pkg/ProbABEL/src/probabel_config.cfg.example (from rev 781, pkg/ProbABEL/src/probabel_config.cfg)
===================================================================
--- pkg/ProbABEL/src/probabel_config.cfg.example (rev 0)
+++ pkg/ProbABEL/src/probabel_config.cfg.example 2011-09-14 18:37:31 UTC (rev 783)
@@ -0,0 +1,3 @@
+cohort,mlinfo_path,mldose_path,mlprobe_path,legend_path
+ERGO,script_test/merlin._._chr_._.collected.ped.out.mlinfo,script_test/merlin._._chr_._.collected.ped.out.mldose,script_test/merlin._._chr_._.collected.ped.out.mlprob,script_test/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
+ERGOPLUS,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mlinfo,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mldose,/mnt/space/ergoplus/ergoplus.chr_._chr_._.mach.mlprob,/mnt/impute/impute_b36/collected/genotypes_chr_._chr_.__CEU_r22_nr.b36_fwd_legend.txt
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