# HG changeset patch
# User dereeper
# Date 1509615767 14400
# Node ID 6d1122b573446ef9a86465135fe60e081d1eb680
# Parent  2bc9b3ee5eea5ed8b9ba702abcb8eff3d1ad50a4
Uploaded

diff -r 2bc9b3ee5eea -r 6d1122b57344 Plink.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Plink.pl	Thu Nov 02 05:42:47 2017 -0400
@@ -0,0 +1,242 @@
+
+#!/usr/bin/perl
+
+use strict;
+use Getopt::Long;
+use Bio::SeqIO;
+
+my $usage = qq~Usage:$0 <args> [<opts>]
+
+where <args> are:
+
+    -i, --input          <VCF input>
+    -o, --out            <Output basename>
+      
+      <opts> are:
+
+    -s, --samples        <Samples to be analyzed. Comma separated list>
+    -c, --chromosomes    <List of chromosomes to be analyzed.>
+    -e, --export         <Output format (VCF/freq/plink. Default: VCF>
+    -f, --frequency      <Minimum MAF. Default: 0.001>
+    -m, --max_freq       <Maximum MAF. Default: 0.5>
+    -a, --allow_missing  <Allowed missing data proportion per site. Must be comprised between 0 and 1. Default: 1>
+    -t, --type           <Type of polymorphisms to keep (ALL/SNP). Default: ALL>
+    -b, --bounds         <Lower bound and upper bound for a range of sites to be processed (start,end). Default: 1, 100000000>
+    -r, --remove_filt    <Remove all sites with a FILTER flag other than PASS (true/false). Default: false>
+    -d, --distance       <Thin sites so that no two sites are within the specified distance from one another. Default: 0>
+~;
+$usage .= "\n";
+
+my ($input,$out);
+
+my $PLINK_EXE = "plink";
+
+
+#my $indel_size_max = 500;
+#my $indel_size_min = 1;
+my $frequency_max = 0.5;
+my $frequency_min = 0.001;
+my $pos_max = 100000000000;
+my $pos_min = 0;
+my $filter_snp_type = "all";
+my $remove_filt = "False";
+
+my $missing_data = 1;
+my $export = "VCF";
+my $type = "ALL";
+my $bounds;
+my $samples;
+my $chromosomes;
+my $thin;
+
+GetOptions(
+	"input=s"        => \$input,
+	"out=s"          => \$out,
+	"samples=s"      => \$samples,
+	"chromosomes=s"  => \$chromosomes,
+	"frequency=s"    => \$frequency_min,
+	"max_freq=s"     => \$frequency_max,
+	"allow_missing=s"=> \$missing_data,
+	"export=s"       => \$export,
+	"type=s"         => \$type,
+	"bounds=s"       => \$bounds,
+	"remove_filt=s"  => \$remove_filt,
+	"distance=s"         => \$thin
+);
+
+
+die $usage
+  if ( !$input || !$out);
+
+if ($samples && $samples =~/^([\w\,\-\.]+)\s*$/){
+	$samples = $1;
+}
+elsif ($samples){
+	die "Error: Samples must be a comma separated list of string\n";
+}
+if ($bounds && $bounds =~/^([\d\,]+)\s*$/){
+	$bounds = $1;
+}
+elsif($bounds){
+	die "Error: Bounds must be a comma separated list of integers\n";
+}
+
+my $minfreq_cmd = "";
+if ($frequency_min && $frequency_min > 0 && $frequency_min =~/^([\d\.]+)\s*$/){
+	$frequency_min = $1;
+	$minfreq_cmd = "--maf $frequency_min";
+}
+elsif ($frequency_min == 0){
+	$minfreq_cmd = "";
+}
+elsif ($frequency_min){
+	die "Error: frequency must be an integer\n";
+}
+if ($thin && $thin =~/^([\d\.]+)\s*$/){
+        $thin = $1;
+}
+elsif ($thin){
+        die "Error: frequency must be an integer\n";
+}
+my $maxfreq_cmd = "";
+if ($frequency_max && $frequency_max =~/^([\d\.]+)\s*$/){
+	$frequency_max = $1;
+	if ($frequency_max < 0.5){
+		$maxfreq_cmd = "--max-maf $frequency_max";		
+	}
+}
+elsif($frequency_max){
+	die "Error: frequency must be an integer\n";
+}
+if ($missing_data =~/^([\d\.]+)\s*$/){
+	$missing_data = $1;
+	#$missing_data = 1 - $missing_data;	
+}
+elsif ($missing_data){
+	die "Error: Missing data must be an integer\n";
+}
+if ($export && $export =~/^([\w]+)\s*$/){
+	$export = $1;
+}
+elsif($export){
+	die "Error: Export must be a string\n";
+}
+if ($type && $type =~/^([\w]+)\s*$/){
+	$type = $1;
+}
+elsif($type){
+	die "Error: Type must be a string\n";
+}
+
+
+my @dnasamples;
+if ($samples)
+{
+	@dnasamples = split(",",$samples);
+}
+my @boundaries;
+if ($bounds)
+{
+	@boundaries = split(",",$bounds);
+}
+
+
+my $experiment = "chromosomes";
+my $table = "";
+my %genes;
+my @snp_ids;
+my @snp_ids_and_positions;
+my @snp_ids_and_positions_all;
+my $gene;
+my $snp_num = 0;
+my %ref_sequences;
+my %snps_of_gene;
+
+my $indiv_cmd = "";
+if (@dnasamples)
+{
+	if (scalar @dnasamples > 1)
+	{
+		open(my $S,">$out.samples");
+		foreach my $samp(@dnasamples){
+			print $S "$samp	$samp\n";
+		}
+		close($S);
+		$indiv_cmd = "--keep $out.samples ";
+	}
+	else
+	{
+		$indiv_cmd = "--indv " . join(" --indv ",@dnasamples);
+	}
+}
+
+my $chrom_cmd = "";
+if ($chromosomes)
+{
+	$chrom_cmd = "--chr ".$chromosomes
+}
+
+my $export_cmd = "--recode vcf-iid";
+if ($export eq "bcf"){
+	$export_cmd = "--recode bcf";
+}
+if ($export eq "freq"){
+	$export_cmd = "--freq";
+}
+if ($export eq "plink"){
+	$export_cmd = "--make-bed";
+}
+if ($export eq "bed"){
+        $export_cmd = "--make-bed";
+} 
+
+
+my $bounds_cmd = "";
+if (@boundaries && $chrom_cmd=~/\w/ && $chrom_cmd !~/,/)
+{
+        $bounds_cmd = "--from-bp $boundaries[0] --to-bp $boundaries[1]";
+}
+
+
+ 
+my $type_cmd = "";
+if ($type eq "SNP")
+{
+	$type_cmd = "--snps-only";
+}
+
+my $filt_cmd = "";
+if ($remove_filt eq "true")
+{
+	$filt_cmd = "--remove-filtered-all";
+}
+
+my $thin_cmd = "";
+if ($thin){
+	$thin_cmd = "--bp-space $thin";
+}
+
+#my $bcf_input = $input;
+#$bcf_input =~s/vcf/bcf/g;
+my $bcf_input;
+my $bed_input = $input;
+$bed_input =~s/\.bed//g;
+
+if (-e "$bed_input.bed"){
+        system("$PLINK_EXE --bfile $bed_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");
+	# for first 1000 SNPs
+	system("$PLINK_EXE --bfile $bed_input --out $out.recode $type_cmd --recode vcf-fid $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr --thin-count 800 1>$out.2.plink.stdout 2>$out.2.plink.stderr");
+}
+elsif (-e $bcf_input){
+	system("$PLINK_EXE --bcf $bcf_input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.plink.stdout 2>$out.plink.stderr");
+}
+else
+{
+	system("$PLINK_EXE --vcf $input --out $out $type_cmd $export_cmd $chrom_cmd $indiv_cmd $minfreq_cmd $maxfreq_cmd --geno $missing_data $thin_cmd $bounds_cmd --allow-extra-chr 1>$out.3.plink.stdout 2>$out.3.plink.stderr");
+
+}
+
+
+
+
+	
diff -r 2bc9b3ee5eea -r 6d1122b57344 find_indiv.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/find_indiv.py	Thu Nov 02 05:42:47 2017 -0400
@@ -0,0 +1,20 @@
+import sys
+import os
+import re
+
+def get_field_samples_options(dataset):
+	options = []
+	line=os.popen("grep '#CHROM' %s"%dataset.file_name).read()[:-1].split('\t')
+	index=line.index('FORMAT')
+	for opt in line[index+1:] :
+		options.append((opt,opt, True))
+	return options
+
+def get_field_chrs_options(dataset):
+        options = []
+        chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n')
+        for line in chrs:
+		opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
+                options.append((opt,opt, True))
+        return options
+
diff -r 2bc9b3ee5eea -r 6d1122b57344 plink.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plink.sh	Thu Nov 02 05:42:47 2017 -0400
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+
+tool_path=$(dirname $0)
+
+filein=$1
+fileout_label=$(date "+%Y%m%d%H%M%S")
+fileout=$2
+filelog=$3
+frequency=$4
+max_freq=$5
+allow_missing=$6
+type=${7}
+bound_start=${8}
+bound_end=${9}
+
+cp -rf $filein input$$.vcf
+
+if [ "${10}" != "None" ]
+then samples="--samples ${10}"
+fi
+
+if [ "${11}" != "None" ]
+then chromosomes="--chromosomes ${11}"
+fi
+
+if [ "$bound_start" -gt "$bound_end" ]
+then tmp=$bound_start ; bound_start=$bound_end ; bound_end=$tmp ; echo "Warning : Lower bound must be lower than greater bound!" >&2
+fi
+
+
+export="VCF"
+
+perl $tool_path/Plink.pl --input input$$.vcf --out $fileout_label --export $export --frequency $frequency --max_freq $max_freq --allow_missing $allow_missing --type $type --bounds $bound_start','$bound_end $samples $chromosomes
+
+
+#echo ${16} >>$fileout_label.log
+#echo ${15} >>$fileout_label.log
+#echo ${17} >>$fileout_label.log
+#echo ${18} >>$fileout_label.log
+
+if [ "$export" = "VCF" ]
+then cp  $fileout_label.vcf $fileout ; rm $fileout_label.vcf
+else cp  $fileout_label.bed $fileout; cp $fileout_label.bed ${15} ; cp $fileout_label.bim ${18} ;rm $fileout_label.bed $fileout_label.fam $fileout_label.bim
+fi
+
+cp $fileout_label.log $filelog
+rm $fileout_label.log
+
diff -r 2bc9b3ee5eea -r 6d1122b57344 plink.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plink.xml	Thu Nov 02 05:42:47 2017 -0400
@@ -0,0 +1,83 @@
+<tool id="sniplay_plink" name="plink" version="1.0">
+    
+    <!-- [REQUIRED] Tool description displayed after the tool name -->
+    <description> - Filter large VCF file</description>
+    
+    <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
+    <requirements>
+        <requirement type="binary">perl</requirement>
+	<requirement type="package" version="1.90b4">plink</requirement>
+    </requirements>
+    
+
+    <!-- [STRONGLY RECOMMANDED] Exit code rules -->
+    <stdio>
+        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
+        <exit_code range="1:" level="fatal" />
+    </stdio>    
+
+    <!-- [REQUIRED] The command to execute -->
+    <command interpreter="bash">
+	./plink.sh $vcf $fileout $filelog $frequency $max_freq $allow_missing $type_p $bound_start $bound_end
+	#if str( $samples ) == "":
+	'None'
+	#else
+	$samples
+	#end if
+	#if str( $chromosomes ) == "":
+	'None'
+	#else
+	$chromosomes
+	#end if
+    </command>
+    <code file="find_indiv.py"/>
+    <!-- [REQUIRED] Input files and tool parameters -->
+    <inputs>
+	<param name="vcf" type="data" format="vcf" optional="false" label="VCF input" />
+
+	<param name="samples" type="select" label="Samples" multiple="true" dynamic_options="get_field_samples_options(vcf)" help="Samples to be analyzed." />
+	<!--<param name="samples" type="text" label="Samples" multiple="true" help="Samples to be analyzed." />-->
+        <!--<param name="chromosomes" type="select" label="Chromosomes" multiple="true" dynamic_options="get_field_chrs_options(input)" help="Chromosomes to be analyzed." />-->
+	<param name="frequency" type="float" value="0" label="Minimum MAF" help="Minimum Minor Allele Frequency (MAF)" />
+	<param name="max_freq" type="float" value="0.5" label="Maximum MAF" help="Maximum Minor Allele Frequency (MAF)" />
+	<param name="allow_missing" type="float" value="1" min="0" max="1" label="Missing data proportion" help="Allowed missing data proportion per site. Must be comprised between 0 and 1." />
+        <param name="type_p" type="select" label="Polymorphisms" help="Type of polymorphisms to keep." >
+            <option value="ALL" selected="true">All</option>
+            <option value="SNP">SNPs only</option>
+        </param>
+        <param name="chromosomes" type="text" label="Chromosomes" multiple="true" help="Chromosomes to be analyzed. (Comma-separated list of reference sequences, ex: Chr1,Chr2)" />
+	<param name="bound_start" type="integer" value="1" label="Lower bound" help="Lower bound for a range of sites to be processed." />
+	<param name="bound_end" type="integer" value="100000000" label="Upper bound" help="Upper bound for a range of sites to be processed." />
+    </inputs>
+    
+    <!-- [REQUIRED] Output files -->
+    <outputs>
+	<data name="fileout" format="vcf" label="Plink filtered VCF"/>
+	<data name="filelog" format="txt" label="Plink logfile" />
+    </outputs>
+    
+    
+    <!-- [OPTIONAL] Help displayed in Galaxy -->
+    <help>
+
+.. class:: infomark
+
+**Authors**     Shaun Purcell : plink_
+
+.. _plink: https://www.cog-genomics.org/plink2
+
+ | **Please cite** "PLINK: a toolset for whole-genome association and population-based linkage analysis.", Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC, **American Journal of Human Genetics**, 2007 
+
+.. class:: infomark
+
+**Galaxy integration** Dereeper Alexis (IRD), Andres Gwendoline (Institut Français de Bioinformatique).
+
+.. class:: infomark
+
+**Support** For any questions about Galaxy integration, please send an e-mail to support.abims@sb-roscoff.fr
+
+
+
+    </help>
+
+</tool>