| Previous changeset 3:9f6977aae93a (2015-07-02) Next changeset 5:97c9c8daa3c3 (2016-04-13) |
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Commit message:
planemo upload |
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added:
Admixture.pl admixture.sh admixture.xml test-data/input.bed test-data/input.bim test-data/input.fam test-data/output test-data/outputs.Q tool_dependencies.xml |
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removed:
admixture/Admixture.pl admixture/admixture.sh admixture/admixture.xml admixture/tool_dependencies.xml |
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| diff -r 9f6977aae93a -r 58df6910f1c3 Admixture.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Admixture.pl Tue Apr 12 09:31:56 2016 -0400 |
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| @@ -0,0 +1,147 @@ +#!/usr/bin/perl + +use strict; +use Getopt::Long; +use File::Basename; + +my $usage = qq~Usage:$0 <args> [<opts>] +where <args> are: + -i, --input <input basename (for PED, FAM, BIM)> + -o, --output <output> + -k, --kmin <K min. int> + -m, --maxK <K max. int> + -d, --directory <temporary directory> +~; +$usage .= "\n"; + +my ($input,$output,$kmin,$kmax,$directory); + + +GetOptions( + "input=s" => \$input, + "output=s" => \$output, + "kmin=s" => \$kmin, + "maxK=s" => \$kmax, + "directory=s" => \$directory, +); + + +die $usage + if ( !$input || !$output || !$kmin || !$kmax || !$directory ); + +if ($kmin =~/^(\d+)\s*$/){ + $kmin = $1; +} +else{ + die "Error: kmin must be an integer\n"; +} +if ($kmax =~/^(\d+)\s*$/){ + $kmax = $1; +} +else{ + die "Error: kmax must be an integer\n"; +} + + + +open(my $P2,"$input.fam"); +my $n = 0; +my $ind_num = 0; +my @individus; +while(<$P2>) +{ + my ($ind,$other) = split(/ /,$_); + push(@individus,$ind); +} +close($P2); + +my $basename = basename($input); + +################################### +# launch admixture for different K +################################### +my %errors; +for (my $k = $kmin; $k <= $kmax; $k++) +{ + system("admixture --cv $input.bed $k >>$directory/log.$k 2>&1"); + my $cv_error_line = `grep -h CV $directory/log.$k`; + if ($cv_error_line =~/: (\d+\.*\d*)$/) + { + $errors{$1} = $k; + } + system("cat $directory/log.$k >>$directory/logs"); + system("echo '\n\n====================================\n\n' >>$directory/logs"); + + open(my $O2,">$basename.$k.final.Q"); + open(my $O,"$basename.$k.Q"); + my %hash_groupes; + my %hash_indv; + my %group_of_ind; + my $i = 0; + while (<$O>){ + $i++; + my $line = $_; + $line =~s/\n//g; + $line =~s/\r//g; + my @infos = split(/\s+/,$line); + my $group = "admix"; + my $ind = $individus[$i]; + for (my $j = 0; $j <$k; $j++){ + my $val = $infos[$j]; + if ($val > 0.5){$group = "Q$j";} + } + if ($ind){ + $hash_indv{$ind} = join(" ",@infos); + $hash_groupes{$group}{"ind"} .= ",".$ind; + $group_of_ind{$ind} = $group; + } + } + close($O); + + foreach my $group(sort keys(%hash_groupes)){ + my @inds = split(",",$hash_groupes{$group}{"ind"}); + foreach my $ind(@inds){ + if ($ind =~/\w+/){ + #print $O3 "$ind;$group\n"; + print $O2 $ind." ".$hash_indv{$ind}. "\n"; + } + } + } + #close($O3); + close($O2); + + system("cat $basename.$k.final.Q >>$directory/outputs.Q"); + system("echo '\n\n====================================\n\n' >>$directory/outputs.Q"); + system("cat $basename.$k.P >>$directory/outputs.P"); + system("echo '\n\n====================================\n\n' >>$directory/outputs.P"); +} + +my @sorted_errors = sort {$a<=>$b} keys(%errors); +my $best_K = $errors{@sorted_errors[0]}; + + +open(BEST1,"$basename.$best_K.final.Q"); +open(BEST2,">$directory/output"); +print BEST2 "<Covariate>\n"; +print BEST2 "<Trait>"; +for (my $j=1;$j<=$best_K;$j++) +{ + print BEST2 " Q" . $j; +} +print BEST2 "\n"; +my $i = 0; +while(<BEST1>) +{ + my $line = $_; + $line =~s/ /\t/g; + print BEST2 $line; + $i++; +} +close(BEST1); +close(BEST2); + +system("cp -rf $directory/log.$best_K $directory/log"); + + + + |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admixture.sh Tue Apr 12 09:31:56 2016 -0400 |
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| @@ -0,0 +1,26 @@ +#!/bin/bash +bed=$1 +fam=$2 +bim=$3 +outputs=$4 +logs=$5 +best_k_output=$6 +best_k_logfile=$7 +kmin=$8 +kmax=$9 + +directory=`dirname $0` +mkdir tmpdir$$ +cp -rf $bed tmpdir$$/input.bed +cp -rf $fam tmpdir$$/input.fam +cp -rf $bim tmpdir$$/input.bim + + +perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ + +mv tmpdir$$/output $best_k_output +mv tmpdir$$/log $best_k_logfile +mv tmpdir$$/outputs.Q $outputs +mv tmpdir$$/logs $logs + + |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admixture.xml Tue Apr 12 09:31:56 2016 -0400 |
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| @@ -0,0 +1,77 @@ +<tool id="admixture" name="Admixture" version="1.23"> + <description>a population structure from large SNP genotype datasets</description> + <requirements> + <requirement type="package" version="1.23">admixture</requirement> + </requirements> + <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax + </command> + <inputs> + <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/> + <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/> + <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/> + <param type="text" name="kmin" label="K min" value="2"/> + <param type="text" name="kmax" label="K max" value="5"/> + </inputs> + <outputs> + <data format="txt" name="best_k_output" label="Best K Output"/> + <data format="txt" name="best_k_logfile" label="Best K Logfile"/> + <data format="txt" name="outputs" label="All Outputs"/> + <data format="txt" name="logs" label="All Logs"/> + </outputs> + + <tests> + <test> + <param name="bed" value="input.bed" /> + <param name="bim" value="input.bim" /> + <param name="fam" value="input.fam" /> + <param name="kmax" value="3" /> + + <output name="best_k_output" file="output" /> + <output name="outputs" file="outputs.Q" /> + </test> + + </tests> + + <help> + + +.. class:: infomark + +**Program encapsulated in Galaxy by Southgreen** + +.. class:: infomark + +**Admixture version 1.23** + +----- + +============== + Please cite: +============== + +"Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. + +----- + + +=========== + Overview: +=========== + +ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). + +----- + +For further informations, please visite the Admixture_ website. + + +.. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html + </help> + +<citations> +<citation type="doi" >10.1101/gr.094052.109</citation> +</citations> + + + +</tool> |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture/Admixture.pl --- a/admixture/Admixture.pl Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,112 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; -use File::Basename; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --input <input basename (for PED, FAM, BIM)> - -o, --output <output> - -k, --kmin <K min. int> - -m, --maxK <K max. int> - -d, --directory <temporary directory> -~; -$usage .= "\n"; - -my ($input,$output,$kmin,$kmax,$directory); - - -GetOptions( - "input=s" => \$input, - "output=s" => \$output, - "kmin=s" => \$kmin, - "maxK=s" => \$kmax, - "directory=s" => \$directory, -); - - -die $usage - if ( !$input || !$output || !$kmin || !$kmax || !$directory ); - -if ($kmin =~/^(\d+)\s*$/){ - $kmin = $1; -} -else{ - die "Error: kmin must be an integer\n"; -} -if ($kmax =~/^(\d+)\s*$/){ - $kmax = $1; -} -else{ - die "Error: kmax must be an integer\n"; -} - - - -open(my $P2,"$input.fam"); -my $n = 0; -my $ind_num = 0; -my @individus; -while(<$P2>) -{ - my ($ind,$other) = split(/ /,$_); - push(@individus,$ind); -} -close($P2); - -my $basename = basename($input); - -################################### -# launch admixture for different K -################################### -my %errors; -for (my $k = $kmin; $k <= $kmax; $k++) -{ - system("admixture --cv $input.bed $k >>$directory/log.$k 2>&1"); - my $cv_error_line = `grep -h CV $directory/log.$k`; - if ($cv_error_line =~/: (\d+\.*\d*)$/) - { - $errors{$1} = $k; - } - system("cat $directory/log.$k >>$directory/logs"); - system("echo '\n\n====================================\n\n' >>$directory/logs"); - system("cat $basename.$k.Q >>$directory/outputs.Q"); - system("echo '\n\n====================================\n\n' >>$directory/outputs.Q"); - system("cat $basename.$k.P >>$directory/outputs.P"); - system("echo '\n\n====================================\n\n' >>$directory/outputs.P"); -} - -my @sorted_errors = sort {$a<=>$b} keys(%errors); -my $best_K = $errors{@sorted_errors[0]}; - - -open(BEST1,"$basename.$best_K.Q"); -open(BEST2,">$directory/output"); -print BEST2 "<Covariate>\n"; -print BEST2 "<Trait>"; -for (my $j=1;$j<=$best_K;$j++) -{ - print BEST2 " Q" . $j; -} -print BEST2 "\n"; -my $i = 0; -while(<BEST1>) -{ - my $line = $_; - $line =~s/ /\t/g; - my $ind = $individus[$i]; - print BEST2 "$ind "; - print BEST2 $line; - $i++; -} -close(BEST1); -close(BEST2); - -system("cp -rf $directory/log.$best_K $directory/log"); - - - - |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture/admixture.sh --- a/admixture/admixture.sh Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,26 +0,0 @@ -#!/bin/bash -bed=$1 -fam=$2 -bim=$3 -outputs=$4 -logs=$5 -best_k_output=$6 -best_k_logfile=$7 -kmin=$8 -kmax=$9 - -directory=`dirname $0` -mkdir tmpdir$$ -cp -rf $bed tmpdir$$/input.bed -cp -rf $fam tmpdir$$/input.fam -cp -rf $bim tmpdir$$/input.bim - - -perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ - -mv tmpdir$$/output $best_k_output -mv tmpdir$$/log $best_k_logfile -mv tmpdir$$/outputs.Q $outputs -mv tmpdir$$/logs $logs - - |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture/admixture.xml --- a/admixture/admixture.xml Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,56 +0,0 @@ -<tool id="admixture" name="Admixture" version="1.23"> - <description>a population structure from large SNP genotype datasets</description> - <requirements> - <requirement type="package" version="1.23">admixture</requirement> - </requirements> - <command interpreter="bash">./admixture.sh $bed $fam $bim $outputs $logs $best_k_output $best_k_logfile $kmin $kmax - </command> - <inputs> - <param format="txt" name="bed" type="data" label="Allelic file in BED format" help="Allelic file in BED format"/> - <param format="txt" name="fam" type="data" label="Fam file" help="Fam file"/> - <param format="txt" name="bim" type="data" label="Bim file" help="Bim file"/> - <param type="text" name="kmin" label="K min" value="1"/> - <param type="text" name="kmax" label="K max" value="5"/> - </inputs> - <outputs> - <data format="txt" name="best_k_output" label="Best K Output"/> - <data format="txt" name="best_k_logfile" label="Best K Logfile"/> - <data format="txt" name="outputs" label="All Outputs"/> - <data format="txt" name="logs" label="All Logs"/> - </outputs> - <help> - - -.. class:: infomark - -**Program encapsulated in Galaxy by Southgreen** - -.. class:: infomark - -**Admixture version 1.23** - ------ - -============== - Please cite: -============== - -"Fast model-based estimation of ancestry in unrelated individuals.", **D.H. Alexander, J. Novembre, and K. Lange.**, Genome Research, 19:1655{1664, 2009. - ------ - -=========== - Overview: -=========== - -ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). - ------ - -For further informations, please visite the Admixture_ website. - - -.. _Admixture: http://www.genetics.ucla.edu/software/admixture/index.html - </help> - -</tool> |
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| diff -r 9f6977aae93a -r 58df6910f1c3 admixture/tool_dependencies.xml --- a/admixture/tool_dependencies.xml Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="admixture" version="1.23"> - <repository changeset_revision="61e04b2aa621" name="package_admixture_1_23" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu/" /> - </package> -</tool_dependency> |
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| diff -r 9f6977aae93a -r 58df6910f1c3 test-data/input.bed |
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| Binary file test-data/input.bed has changed |
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| diff -r 9f6977aae93a -r 58df6910f1c3 test-data/input.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.bim Tue Apr 12 09:31:56 2016 -0400 |
| b |
| b'@@ -0,0 +1,6603 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|
| b |
| diff -r 9f6977aae93a -r 58df6910f1c3 test-data/input.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fam Tue Apr 12 09:31:56 2016 -0400 |
| b |
| @@ -0,0 +1,167 @@ +AZUCENA AZUCENA 0 0 0 -9 +BULUPANDAK BULUPANDAK 0 0 0 -9 +GIZA171 GIZA171 0 0 0 -9 +IAC165 IAC165 0 0 0 -9 +KHAODAM KHAODAM 0 0 0 -9 +M202 M202 0 0 0 -9 +MOROBEREKAN MOROBEREKAN 0 0 0 -9 +NIPPONBARE_D NIPPONBARE_D 0 0 0 -9 +62667 62667 0 0 0 -9 +63-104 63-104 0 0 0 -9 +ARAGUAIA ARAGUAIA 0 0 0 -9 +ARIAS ARIAS 0 0 0 -9 +ARROZCEBADA ARROZCEBADA 0 0 0 -9 +BABER BABER 0 0 0 -9 +BAGANANASALAO BAGANANASALAO 0 0 0 -9 +BAKUNGH BAKUNGH 0 0 0 -9 +BENGALYVAKARINA BENGALYVAKARINA 0 0 0 -9 +BICOBRANCO BICOBRANCO 0 0 0 -9 +BINULAWAN BINULAWAN 0 0 0 -9 +CAAWA/FORTUNA6 CAAWA/FORTUNA6 0 0 0 -9 +CAIAPO CAIAPO 0 0 0 -9 +CANAROXA CANAROXA 0 0 0 -9 +CANELADEFERRO CANELADEFERRO 0 0 0 -9 +CHALOYOE CHALOYOE 0 0 0 -9 +CHAPHUMA CHAPHUMA 0 0 0 -9 +CICIHBETON CICIHBETON 0 0 0 -9 +CIRAD358 CIRAD358 0 0 0 -9 +CIRAD392 CIRAD392 0 0 0 -9 +CIRAD394 CIRAD394 0 0 0 -9 +CIRAD403 CIRAD403 0 0 0 -9 +CIRAD409 CIRAD409 0 0 0 -9 +CIRAD488 CIRAD488 0 0 0 -9 +CNA-7_BO_1_1_33-13-6-1 CNA-7_BO_1_1_33-13-6-1 0 0 0 -9 +COLOMBIA1 COLOMBIA1 0 0 0 -9 +CT13582-15-5-M CT13582-15-5-M 0 0 0 -9 +CUBA65 CUBA65 0 0 0 -9 +CUIABANA CUIABANA 0 0 0 -9 +CURINCA CURINCA 0 0 0 -9 +DAM DAM 0 0 0 -9 +DANGREY DANGREY 0 0 0 -9 +DAVAO DAVAO 0 0 0 -9 +DAWASANRED DAWASANRED 0 0 0 -9 +DINORADO DINORADO 0 0 0 -9 +DOURADOAGULHA DOURADOAGULHA 0 0 0 -9 +DOURADOPRECOCE DOURADOPRECOCE 0 0 0 -9 +ESPERANZA ESPERANZA 0 0 0 -9 +FOHISOMOTRA FOHISOMOTRA 0 0 0 -9 +GANIGI GANIGI 0 0 0 -9 +GEMJYAJYANAM GEMJYAJYANAM 0 0 0 -9 +GOGO GOGO 0 0 0 -9 +GOGOLEMPUK GOGOLEMPUK 0 0 0 -9 +GOGOLEMPAK GOGOLEMPAK 0 0 0 -9 +GOMPA2 GOMPA2 0 0 0 -9 +GRAZI GRAZI 0 0 0 -9 +GUARANI GUARANI 0 0 0 -9 +GUNDILKUNING GUNDILKUNING 0 0 0 -9 +HAWMOM HAWMOM 0 0 0 -9 +HD1-4 HD1-4 0 0 0 -9 +IAC25 IAC25 0 0 0 -9 +IAC47 IAC47 0 0 0 -9 +IDSA77 IDSA77 0 0 0 -9 +IGUAPECATETO IGUAPECATETO 0 0 0 -9 +INDANE INDANE 0 0 0 -9 +IR60080-46A IR60080-46A 0 0 0 -9 +IR63380-16 IR63380-16 0 0 0 -9 +IR63372-08 IR63372-08 0 0 0 -9 +IR65907-188-1-B IR65907-188-1-B 0 0 0 -9 +IR66421-096-2-1-1 IR66421-096-2-1-1 0 0 0 -9 +IR68704-145-1-1-B IR68704-145-1-1-B 0 0 0 -9 +IR71525-19-1-1 IR71525-19-1-1 0 0 0 -9 +IRAT104 IRAT104 0 0 0 -9 +IRAT109 IRAT109 0 0 0 -9 +IRAT112 IRAT112 0 0 0 -9 +IRAT13 IRAT13 0 0 0 -9 +IRAT144 IRAT144 0 0 0 -9 +IRAT170 IRAT170 0 0 0 -9 +IRAT177 IRAT177 0 0 0 -9 +IRAT2 IRAT2 0 0 0 -9 +IRAT212 IRAT212 0 0 0 -9 +IRAT216 IRAT216 0 0 0 -9 +IRAT234 IRAT234 0 0 0 -9 +IRAT257 IRAT257 0 0 0 -9 +IRAT335 IRAT335 0 0 0 -9 +IRAT362 IRAT362 0 0 0 -9 +IRAT364 IRAT364 0 0 0 -9 +IRAT366 IRAT366 0 0 0 -9 +IRAT380 IRAT380 0 0 0 -9 +JAOHAW JAOHAW 0 0 0 -9 +JIMBRUKJOLOWORO JIMBRUKJOLOWORO 0 0 0 -9 +JUMALI JUMALI 0 0 0 -9 +JUMULA2 JUMULA2 0 0 0 -9 +KAKANI2 KAKANI2 0 0 0 -9 +KANIRANGA KANIRANGA 0 0 0 -9 +KARASUKARASURANKASU KARASUKARASURANKASU 0 0 0 -9 +KEDAYAN KEDAYAN 0 0 0 -9 +KENDINGA5H KENDINGA5H 0 0 0 -9 +KETANKONIR KETANKONIR 0 0 0 -9 +KETANLUMBU KETANLUMBU 0 0 0 -9 +KETANMENAH KETANMENAH 0 0 0 -9 +KHAOKAPXANG KHAOKAPXANG 0 0 0 -9 +KINANDANGPATONG KINANDANGPATONG 0 0 0 -9 +KOMOJAMANITRA KOMOJAMANITRA 0 0 0 -9 +KU115 KU115 0 0 0 -9 +KUROKA KUROKA 0 0 0 -9 +LAMBAYQUE1 LAMBAYQUE1 0 0 0 -9 +LUDAN LUDAN 0 0 0 -9 +MAHAE MAHAE 0 0 0 -9 +MAINTIMOLOTSY1226 MAINTIMOLOTSY1226 0 0 0 -9 +MALAGKITPIRURUTONG MALAGKITPIRURUTONG 0 0 0 -9 +MANANELATRA520 MANANELATRA520 0 0 0 -9 +MANDRIRAVINA3512 MANDRIRAVINA3512 0 0 0 -9 +MARAVILHA MARAVILHA 0 0 0 -9 +MITSANGANAHIJERY MITSANGANAHIJERY 0 0 0 -9 +MOLOK MOLOK 0 0 0 -9 +NABESHI NABESHI 0 0 0 -9 +NEPHOAVANG NEPHOAVANG 0 0 0 -9 +NHTA10 NHTA10 0 0 0 -9 +NHTA5 NHTA5 0 0 0 -9 +NPE253 NPE253 0 0 0 -9 +NPE826 NPE826 0 0 0 -9 +ORYZICASABANA6 ORYZICASABANA6 0 0 0 -9 +OS4 OS4 0 0 0 -9 +OS6 OS6 0 0 0 -9 +P5589-1-1-3-P P5589-1-1-3-P 0 0 0 -9 +PACHOLINHA PACHOLINHA 0 0 0 -9 +PADIBOENAR PADIBOENAR 0 0 0 -9 +PADIKASALLE PADIKASALLE 0 0 0 -9 +PALAWAN PALAWAN 0 0 0 -9 +PATEBLANCMAN1 PATEBLANCMAN1 0 0 0 -9 +PCT11_0_0_2_BO_1_55-1-3-1 PCT11_0_0_2_BO_1_55-1-3-1 0 0 0 -9 +PCT4_SA_4_1_1076-2-4-1-5 PCT4_SA_4_1_1076-2-4-1-5 0 0 0 -9 +PEHPINUO PEHPINUO 0 0 0 -9 +POENOETHITAM POENOETHITAM 0 0 0 -9 +PULULAPA PULULAPA 0 0 0 -9 +RATHAL RATHAL 0 0 0 -9 +REKETMAUN REKETMAUN 0 0 0 -9 +RT1031-69 RT1031-69 0 0 0 -9 +SENG SENG 0 0 0 -9 +SPEAKER SPEAKER 0 0 0 -9 +TANDUI TANDUI 0 0 0 -9 +TREMBESE TREMBESE 0 0 0 -9 +TRESMESES TRESMESES 0 0 0 -9 +TSIPALA89 TSIPALA89 0 0 0 -9 +VARYLAVA90 VARYLAVA90 0 0 0 -9 +VARYLAVADEBETAFO VARYLAVADEBETAFO 0 0 0 -9 +VARYMADINIKA3566 VARYMADINIKA3566 0 0 0 -9 +VARYMALADY VARYMALADY 0 0 0 -9 +VARYSOMOTRASIHANAKA VARYSOMOTRASIHANAKA 0 0 0 -9 +WAB56-125 WAB56-125 0 0 0 -9 +WAB56-50 WAB56-50 0 0 0 -9 +WAB706-3-4-K4-KB-1 WAB706-3-4-K4-KB-1 0 0 0 -9 +YANCAOUSSA YANCAOUSSA 0 0 0 -9 +YANGKUMRED YANGKUMRED 0 0 0 -9 +YUNLU7 YUNLU7 0 0 0 -9 +IR47686-09-01-B-1 IR47686-09-01-B-1 0 0 0 -9 +IR53236-275-1 IR53236-275-1 0 0 0 -9 +IR65261-19-1-B IR65261-19-1-B 0 0 0 -9 +IR65907-206-4-B IR65907-206-4-B 0 0 0 -9 +IR66421-105-1-1 IR66421-105-1-1 0 0 0 -9 +IR71524-44-1-1 IR71524-44-1-1 0 0 0 -9 +VIETNAM1 VIETNAM1 0 0 0 -9 +VIETNAM3 VIETNAM3 0 0 0 -9 +IR47684-05-1-B IR47684-05-1-B 0 0 0 -9 +PRIMAVERA PRIMAVERA 0 0 0 -9 +CHUAN3 CHUAN3 0 0 0 -9 +CHUAN4 CHUAN4 0 0 0 -9 +EARLYMUTANTIAC165 EARLYMUTANTIAC165 0 0 0 -9 |
| b |
| diff -r 9f6977aae93a -r 58df6910f1c3 test-data/output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Tue Apr 12 09:31:56 2016 -0400 |
| b |
| @@ -0,0 +1,168 @@ +<Covariate> +<Trait> Q1 Q2 Q3 +GIZA171 0.586741 0.000010 0.413249 +IAC165 0.945312 0.006465 0.048224 +M202 0.999980 0.000010 0.000010 +MOROBEREKAN 0.831922 0.000010 0.168068 +62667 0.983237 0.016753 0.000010 +BAGANANASALAO 0.736051 0.263939 0.000010 +CHAPHUMA 0.801557 0.000010 0.198433 +CICIHBETON 0.999980 0.000010 0.000010 +CIRAD358 0.569210 0.000010 0.430780 +DANGREY 0.999980 0.000010 0.000010 +DAVAO 0.999980 0.000010 0.000010 +DINORADO 0.992108 0.007882 0.000010 +GOGO 0.999980 0.000010 0.000010 +GRAZI 0.844812 0.097165 0.058023 +HAWMOM 0.586615 0.000010 0.413375 +HD1-4 0.999980 0.000010 0.000010 +IR60080-46A 0.825891 0.000010 0.174099 +JIMBRUKJOLOWORO 0.999980 0.000010 0.000010 +JUMULA2 0.747177 0.163796 0.089027 +KAKANI2 0.790361 0.070580 0.139059 +KANIRANGA 0.855150 0.125292 0.019558 +KEDAYAN 0.999980 0.000010 0.000010 +KETANMENAH 0.650538 0.000010 0.349452 +KINANDANGPATONG 0.999980 0.000010 0.000010 +KUROKA 0.999980 0.000010 0.000010 +LAMBAYQUE1 0.671645 0.000010 0.328345 +LUDAN 0.709814 0.231278 0.058908 +MAINTIMOLOTSY1226 0.999980 0.000010 0.000010 +NABESHI 0.614509 0.000010 0.385481 +NEPHOAVANG 0.999980 0.000010 0.000010 +NHTA10 0.881379 0.118611 0.000010 +NHTA5 0.873563 0.000010 0.126427 +NPE253 0.712232 0.157112 0.130656 +NPE826 0.999980 0.000010 0.000010 +ORYZICASABANA6 0.999980 0.000010 0.000010 +PADIKASALLE 0.596822 0.000010 0.403168 +PALAWAN 0.538069 0.000010 0.461921 +POENOETHITAM 0.999980 0.000010 0.000010 +PULULAPA 0.629810 0.000010 0.370180 +RT1031-69 0.604237 0.000010 0.395753 +SPEAKER 0.999980 0.000010 0.000010 +YUNLU7 0.999980 0.000010 0.000010 +IR47686-09-01-B-1 0.657103 0.000010 0.342887 +VIETNAM3 0.999980 0.000010 0.000010 +IR47684-05-1-B 0.999980 0.000010 0.000010 +CHUAN4 0.999980 0.000010 0.000010 +EARLYMUTANTIAC165 0.999980 0.000010 0.000010 +CIRAD409 0.000010 0.759299 0.240691 +CIRAD488 0.000010 0.600168 0.399822 +COLOMBIA1 0.000010 0.626735 0.373255 +CT13582-15-5-M 0.000010 0.999980 0.000010 +DAM 0.000010 0.785028 0.214962 +IGUAPECATETO 0.000010 0.502238 0.497752 +IR63380-16 0.000010 0.541676 0.458314 +IR65907-188-1-B 0.000010 0.999980 0.000010 +IR66421-096-2-1-1 0.000010 0.999980 0.000010 +IR68704-145-1-1-B 0.230784 0.621690 0.147526 +IR71525-19-1-1 0.028760 0.689950 0.281290 +IRAT234 0.000010 0.999980 0.000010 +MITSANGANAHIJERY 0.000010 0.833207 0.166783 +PEHPINUO 0.000010 0.525577 0.474413 +WAB56-50 0.000010 0.590115 0.409875 +WAB706-3-4-K4-KB-1 0.000010 0.741529 0.258461 +IR66421-105-1-1 0.000010 0.999980 0.000010 +IR71524-44-1-1 0.095900 0.567619 0.336482 +PRIMAVERA 0.000010 0.999980 0.000010 +BULUPANDAK 0.138642 0.000010 0.861348 +KHAODAM 0.000010 0.000010 0.999980 +NIPPONBARE_D 0.121567 0.000010 0.878423 +63-104 0.000010 0.000010 0.999980 +ARAGUAIA 0.000010 0.000010 0.999980 +ARIAS 0.000010 0.271697 0.728293 +ARROZCEBADA 0.172047 0.042241 0.785712 +BABER 0.000010 0.000010 0.999980 +BAKUNGH 0.180348 0.000010 0.819642 +BENGALYVAKARINA 0.116979 0.000010 0.883011 +BICOBRANCO 0.210938 0.000010 0.789052 +BINULAWAN 0.000010 0.000010 0.999980 +CAAWA/FORTUNA6 0.082859 0.000010 0.917131 +CAIAPO 0.115889 0.000010 0.884101 +CANAROXA 0.134469 0.000010 0.865521 +CANELADEFERRO 0.000010 0.000010 0.999980 +CHALOYOE 0.000010 0.000010 0.999980 +CIRAD392 0.442360 0.000010 0.557630 +CIRAD394 0.204730 0.107281 0.687989 +CIRAD403 0.242768 0.126952 0.630280 +CNA-7_BO_1_1_33-13-6-1 0.196055 0.081135 0.722809 +CUBA65 0.000010 0.487001 0.512989 +CUIABANA 0.155072 0.000010 0.844918 +CURINCA 0.471804 0.000010 0.528186 +DAWASANRED 0.053031 0.000010 0.946959 +DOURADOAGULHA 0.085429 0.000010 0.914561 +DOURADOPRECOCE 0.000010 0.000010 0.999980 +ESPERANZA 0.000010 0.000010 0.999980 +FOHISOMOTRA 0.000010 0.359984 0.640006 +GANIGI 0.000010 0.000010 0.999980 +GEMJYAJYANAM 0.197535 0.000010 0.802455 +GOGOLEMPUK 0.220531 0.000010 0.779459 +GOGOLEMPAK 0.450796 0.000010 0.549194 +GOMPA2 0.454524 0.000010 0.545466 +GUARANI 0.000010 0.000010 0.999980 +GUNDILKUNING 0.000010 0.000010 0.999980 +IAC25 0.000010 0.000010 0.999980 +IAC47 0.000010 0.000010 0.999980 +IDSA77 0.000010 0.000010 0.999980 +INDANE 0.000010 0.000010 0.999980 +IR63372-08 0.000010 0.402550 0.597440 +IRAT104 0.000010 0.430660 0.569330 +IRAT109 0.000010 0.000010 0.999980 +IRAT112 0.155698 0.109413 0.734889 +IRAT13 0.000010 0.000010 0.999980 +IRAT144 0.000010 0.012649 0.987341 +IRAT170 0.191251 0.036820 0.771930 +IRAT177 0.000010 0.000010 0.999980 +IRAT2 0.000010 0.000010 0.999980 +IRAT212 0.000010 0.000010 0.999980 +IRAT216 0.212135 0.023321 0.764544 +IRAT257 0.000010 0.000010 0.999980 +IRAT335 0.000010 0.000010 0.999980 +IRAT362 0.000010 0.270513 0.729477 +IRAT364 0.000010 0.321994 0.677996 +IRAT366 0.000010 0.000010 0.999980 +IRAT380 0.000010 0.000010 0.999980 +JAOHAW 0.168986 0.099515 0.731499 +JUMALI 0.312901 0.000010 0.687089 +KARASUKARASURANKASU 0.304195 0.000010 0.695795 +KENDINGA5H 0.190313 0.000010 0.809677 +KETANKONIR 0.127600 0.000010 0.872390 +KETANLUMBU 0.303188 0.000010 0.696802 +KHAOKAPXANG 0.219799 0.000010 0.780191 +KOMOJAMANITRA 0.000010 0.088058 0.911932 +KU115 0.080829 0.000010 0.919161 +MAHAE 0.161806 0.000010 0.838184 +MALAGKITPIRURUTONG 0.000010 0.000010 0.999980 +MANANELATRA520 0.116010 0.000010 0.883980 +MANDRIRAVINA3512 0.000010 0.000010 0.999980 +MARAVILHA 0.000010 0.000010 0.999980 +MOLOK 0.224580 0.076683 0.698737 +OS4 0.000010 0.384119 0.615871 +OS6 0.000010 0.000010 0.999980 +P5589-1-1-3-P 0.000010 0.000010 0.999980 +PACHOLINHA 0.000010 0.382637 0.617353 +PADIBOENAR 0.000010 0.000010 0.999980 +PATEBLANCMAN1 0.062371 0.000010 0.937619 +PCT11_0_0_2_BO_1_55-1-3-1 0.145774 0.000010 0.854216 +RATHAL 0.169700 0.004321 0.825979 +REKETMAUN 0.179511 0.000010 0.820479 +SENG 0.000010 0.000010 0.999980 +TANDUI 0.000010 0.000010 0.999980 +TREMBESE 0.221145 0.000010 0.778845 +TRESMESES 0.397909 0.000010 0.602081 +TSIPALA89 0.000010 0.000010 0.999980 +VARYLAVA90 0.072332 0.000010 0.927658 +VARYLAVADEBETAFO 0.000010 0.000010 0.999980 +VARYMADINIKA3566 0.063055 0.127148 0.809797 +VARYMALADY 0.154619 0.000010 0.845371 +VARYSOMOTRASIHANAKA 0.161759 0.000010 0.838231 +WAB56-125 0.060129 0.000010 0.939861 +YANCAOUSSA 0.000010 0.139600 0.860390 +YANGKUMRED 0.134426 0.000010 0.865564 +IR53236-275-1 0.000010 0.000010 0.999980 +IR65261-19-1-B 0.102795 0.000010 0.897195 +VIETNAM1 0.000010 0.112662 0.887328 +CHUAN3 0.290550 0.026546 0.682904 +PCT4_SA_4_1_1076-2-4-1-5 0.123261 0.473604 0.403136 +IR65907-206-4-B 0.169741 0.341301 0.488957 |
| b |
| diff -r 9f6977aae93a -r 58df6910f1c3 test-data/outputs.Q --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs.Q Tue Apr 12 09:31:56 2016 -0400 |
| b |
| b'@@ -0,0 +1,342 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\t0.999980\n+CAAWA/FORTUNA6\t0.082859\t0.000010\t0.917131\n+CAIAPO\t0.115889\t0.000010\t0.884101\n+CANAROXA\t0.134469\t0.000010\t0.865521\n+CANELADEFERRO\t0.000010\t0.000010\t0.999980\n+CHALOYOE\t0.000010\t0.000010\t0.999980\n+CIRAD392\t0.442360\t0.000010\t0.557630\n+CIRAD394\t0.204730\t0.107281\t0.687989\n+CIRAD403\t0.242768\t0.126952\t0.630280\n+CNA-7_BO_1_1_33-13-6-1\t0.196055\t0.081135\t0.722809\n+CUBA65\t0.000010\t0.487001\t0.512989\n+CUIABANA\t0.155072\t0.000010\t0.844918\n+CURINCA\t0.471804\t0.000010\t0.528186\n+DAWASANRED\t0.053031\t0.000010\t0.946959\n+DOURADOAGULHA\t0.085429\t0.000010\t0.914561\n+DOURADOPRECOCE\t0.000010\t0.000010\t0.999980\n+ESPERANZA\t0.000010\t0.000010\t0.999980\n+FOHISOMOTRA\t0.000010\t0.359984\t0.640006\n+GANIGI\t0.000010\t0.000010\t0.999980\n+GEMJYAJYANAM\t0.197535\t0.000010\t0.802455\n+GOGOLEMPUK\t0.220531\t0.000010\t0.779459\n+GOGOLEMPAK\t0.450796\t0.000010\t0.549194\n+GOMPA2\t0.454524\t0.000010\t0.545466\n+GUARANI\t0.000010\t0.000010\t0.999980\n+GUNDILKUNING\t0.000010\t0.000010\t0.999980\n+IAC25\t0.000010\t0.000010\t0.999980\n+IAC47\t0.000010\t0.000010\t0.999980\n+IDSA77\t0.000010\t0.000010\t0.999980\n+INDANE\t0.000010\t0.000010\t0.999980\n+IR63372-08\t0.000010\t0.402550\t0.597440\n+IRAT104\t0.000010\t0.430660\t0.569330\n+IRAT109\t0.000010\t0.000010\t0.999980\n+IRAT112\t0.155698\t0.109413\t0.734889\n+IRAT13\t0.000010\t0.000010\t0.999980\n+IRAT144\t0.000010\t0.012649\t0.987341\n+IRAT170\t0.191251\t0.036820\t0.771930\n+IRAT177\t0.000010\t0.000010\t0.999980\n+IRAT2\t0.000010\t0.000010\t0.999980\n+IRAT212\t0.000010\t0.000010\t0.999980\n+IRAT216\t0.212135\t0.023321\t0.764544\n+IRAT257\t0.000010\t0.000010\t0.999980\n+IRAT335\t0.000010\t0.000010\t0.999980\n+IRAT362\t0.000010\t0.270513\t0.729477\n+IRAT364\t0.000010\t0.321994\t0.677996\n+IRAT366\t0.000010\t0.000010\t0.999980\n+IRAT380\t0.000010\t0.000010\t0.999980\n+JAOHAW\t0.168986\t0.099515\t0.731499\n+JUMALI\t0.312901\t0.000010\t0.687089\n+KARASUKARASURANKASU\t0.304195\t0.000010\t0.695795\n+KENDINGA5H\t0.190313\t0.000010\t0.809677\n+KETANKONIR\t0.127600\t0.000010\t0.872390\n+KETANLUMBU\t0.303188\t0.000010\t0.696802\n+KHAOKAPXANG\t0.219799\t0.000010\t0.780191\n+KOMOJAMANITRA\t0.000010\t0.088058\t0.911932\n+KU115\t0.080829\t0.000010\t0.919161\n+MAHAE\t0.161806\t0.000010\t0.838184\n+MALAGKITPIRURUTONG\t0.000010\t0.000010\t0.999980\n+MANANELATRA520\t0.116010\t0.000010\t0.883980\n+MANDRIRAVINA3512\t0.000010\t0.000010\t0.999980\n+MARAVILHA\t0.000010\t0.000010\t0.999980\n+MOLOK\t0.224580\t0.076683\t0.698737\n+OS4\t0.000010\t0.384119\t0.615871\n+OS6\t0.000010\t0.000010\t0.999980\n+P5589-1-1-3-P\t0.000010\t0.000010\t0.999980\n+PACHOLINHA\t0.000010\t0.382637\t0.617353\n+PADIBOENAR\t0.000010\t0.000010\t0.999980\n+PATEBLANCMAN1\t0.062371\t0.000010\t0.937619\n+PCT11_0_0_2_BO_1_55-1-3-1\t0.145774\t0.000010\t0.854216\n+RATHAL\t0.169700\t0.004321\t0.825979\n+REKETMAUN\t0.179511\t0.000010\t0.820479\n+SENG\t0.000010\t0.000010\t0.999980\n+TANDUI\t0.000010\t0.000010\t0.999980\n+TREMBESE\t0.221145\t0.000010\t0.778845\n+TRESMESES\t0.397909\t0.000010\t0.602081\n+TSIPALA89\t0.000010\t0.000010\t0.999980\n+VARYLAVA90\t0.072332\t0.000010\t0.927658\n+VARYLAVADEBETAFO\t0.000010\t0.000010\t0.999980\n+VARYMADINIKA3566\t0.063055\t0.127148\t0.809797\n+VARYMALADY\t0.154619\t0.000010\t0.845371\n+VARYSOMOTRASIHANAKA\t0.161759\t0.000010\t0.838231\n+WAB56-125\t0.060129\t0.000010\t0.939861\n+YANCAOUSSA\t0.000010\t0.139600\t0.860390\n+YANGKUMRED\t0.134426\t0.000010\t0.865564\n+IR53236-275-1\t0.000010\t0.000010\t0.999980\n+IR65261-19-1-B\t0.102795\t0.000010\t0.897195\n+VIETNAM1\t0.000010\t0.112662\t0.887328\n+CHUAN3\t0.290550\t0.026546\t0.682904\n+PCT4_SA_4_1_1076-2-4-1-5\t0.123261\t0.473604\t0.403136\n+IR65907-206-4-B\t0.169741\t0.341301\t0.488957\n+\n+\n+====================================\n+\n+\n' |
| b |
| diff -r 9f6977aae93a -r 58df6910f1c3 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 12 09:31:56 2016 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="admixture" version="1.23"> + <repository changeset_revision="61e04b2aa621" name="package_admixture_1_23" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |