Mercurial > repos > dereeper > admixture
changeset 4:58df6910f1c3 draft
planemo upload
| author | dereeper |
|---|---|
| date | Tue, 12 Apr 2016 09:31:56 -0400 |
| parents | 9f6977aae93a |
| children | 97c9c8daa3c3 |
| files | Admixture.pl admixture.sh admixture.xml admixture/Admixture.pl admixture/admixture.sh admixture/admixture.xml admixture/tool_dependencies.xml test-data/input.bed test-data/input.bim test-data/input.fam test-data/output test-data/outputs.Q tool_dependencies.xml |
| diffstat | 13 files changed, 7536 insertions(+), 200 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Admixture.pl Tue Apr 12 09:31:56 2016 -0400 @@ -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"); + + + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admixture.sh Tue Apr 12 09:31:56 2016 -0400 @@ -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 + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/admixture.xml Tue Apr 12 09:31:56 2016 -0400 @@ -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>
--- a/admixture/Admixture.pl Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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"); - - - -
--- a/admixture/admixture.sh Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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 - -
--- a/admixture/admixture.xml Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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>
--- a/admixture/tool_dependencies.xml Thu Jul 02 04:31:34 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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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Chr1:43132577 0 43132577 T C +0 Chr1:43141118 0 43141118 C T +0 Chr1:43141179 0 43141179 A T +0 Chr1:43154143 0 43154143 G A +0 Chr1:43158899 0 43158899 A T +0 Chr1:43179527 0 43179527 A T +0 Chr1:43214669 0 43214669 A T +0 Chr1:43229591 0 43229591 G A +0 Chr1:43249859 0 43249859 A T +0 Chr1:43269458 0 43269458 A T
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fam Tue Apr 12 09:31:56 2016 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output Tue Apr 12 09:31:56 2016 -0400 @@ -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 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs.Q Tue Apr 12 09:31:56 2016 -0400 @@ -0,0 +1,342 @@ +BULUPANDAK 0.820166 0.179834 +KHAODAM 0.999990 0.000010 +NIPPONBARE_D 0.748877 0.251123 +63-104 0.999990 0.000010 +ARAGUAIA 0.999990 0.000010 +ARIAS 0.999990 0.000010 +ARROZCEBADA 0.746417 0.253583 +BABER 0.999990 0.000010 +BAKUNGH 0.767720 0.232280 +BENGALYVAKARINA 0.827800 0.172200 +BICOBRANCO 0.671502 0.328498 +BINULAWAN 0.999990 0.000010 +CAAWA/FORTUNA6 0.855007 0.144993 +CAIAPO 0.844450 0.155550 +CANAROXA 0.833462 0.166538 +CANELADEFERRO 0.997417 0.002583 +CHALOYOE 0.999990 0.000010 +CIRAD394 0.761822 0.238178 +CIRAD403 0.735955 0.264045 +CIRAD409 0.999990 0.000010 +CIRAD488 0.999990 0.000010 +CNA-7_BO_1_1_33-13-6-1 0.778845 0.221155 +COLOMBIA1 0.952970 0.047030 +CT13582-15-5-M 0.870019 0.129981 +CUBA65 0.999990 0.000010 +CUIABANA 0.780953 0.219047 +DAM 0.999990 0.000010 +DAWASANRED 0.884809 0.115191 +DOURADOAGULHA 0.838808 0.161192 +DOURADOPRECOCE 0.999990 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+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 + + +==================================== + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Apr 12 09:31:56 2016 -0400 @@ -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>