| Previous changeset 3:345f88a8f483 (2015-07-10) Next changeset 5:ec22fcacb66c (2016-02-15) |
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Commit message:
planemo upload |
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modified:
MDSplot/mdsplot.sh MDSplot/mdsplot.xml PedToFasta/Ped2Fasta.pl PedToFasta/pedToFasta.xml Rooting/rooting.xml SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml VCF2Hapmap/vcf2FastaAndHapmap.sh VCF2Hapmap/vcf2FastaAndHapmap.xml check_gwas_inputs/CheckGWASInputs.xml egglib/CalculateDiversityIndexes.xml hapmap2mlmm/HapmapToMLMMFiles.xml ped2bed/ped2bed.xml tool_dependencies.xml |
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added:
test-data/MDSplot-input.map test-data/MDSplot-input.ped test-data/MDSplot-output.ibs_matrix.txt test-data/MDSplot-output.mds_plot.txt test-data/SNPden-hapmap test-data/SNPden-result.txt test-data/SNPden-result_bysample.txt test-data/egglib-alignment.fa test-data/egglib-result.txt test-data/gwas-hapmap test-data/gwas-result.hapmap test-data/gwas-result.stats test-data/gwas-result.trait test-data/gwas-trait test-data/hapmap2mlmm-hapmap test-data/hapmap2mlmm-result_genot test-data/hapmap2mlmm-result_snp.hapmap test-data/ped2bed-input.map test-data/ped2bed-input.ped test-data/ped2bed-result.bed test-data/ped2bed-result.bim test-data/ped2bed-result.fam test-data/ped2fasta-result.fa test-data/ped2fasta-sample.ped test-data/rooting-newick test-data/rooting-out_tree test-data/vcf2fastaAndHapmap-reference.fa test-data/vcf2fastaAndHapmap-reference.gff test-data/vcf2fastaAndHapmap-result1.hapmap test-data/vcf2fastaAndHapmap-result2.flanking.txt test-data/vcf2fastaAndHapmap-result2.hapmap test-data/vcf2fastaAndHapmap-result3.flanking.txt test-data/vcf2fastaAndHapmap-result3.gene_alignment.fas test-data/vcf2fastaAndHapmap-result3.hapmap test-data/vcf2fastaAndHapmap-sample.vcf |
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removed:
MDSplot/MDSbasedOnIBSmatrix.pl.org MDSplot/test-data/analyse.ibs_matrix.txt MDSplot/test-data/analyse.log MDSplot/test-data/analyse.mds_plot.txt MDSplot/test-data/input.map MDSplot/test-data/input.ped PedToFasta/test-data/result.fa PedToFasta/test-data/sample.ped Rooting/test-data/newick Rooting/test-data/out_tree Rooting/test-data/out_tree.log SNP_density/test-data/hapmap SNP_density/test-data/result.txt SNP_density/test-data/result_bysample.txt |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/MDSbasedOnIBSmatrix.pl.org --- a/MDSplot/MDSbasedOnIBSmatrix.pl.org Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,77 +0,0 @@ -#!/usr/bin/perl - -use strict; -use Switch; -use Getopt::Long; -use Bio::SeqIO; - -my $PLINK_EXE= "/apps/www/sniplay.cirad.fr/tools/plink/plink-1.07-x86_64/plink"; - -my $usage = qq~Usage:$0 <args> [<opts>] -where <args> are: - -i, --in <input> - -o, --out <output> -~; -$usage .= "\n"; - -my ($in,$out); - - -GetOptions( - "in=s" => \$in, - "out=s" => \$out -); - -die $usage - if ( !$in || !$out); - - -my $plink_command = $PLINK_EXE . " --file $in --noweb --cluster --matrix --mds-plot 2 --out $out >>$in.plink.log 2>&1"; -system($plink_command); - -my $awk_cmd = "awk \{\'print \$1\'\} $in.ped"; -my $inds = `$awk_cmd`; -my @individuals = split("\n",$inds); - - -open(my $OUT,">$out.mds_plot.txt"); -my $go = 0; -open(my $O,"$out.mds"); -while(<$O>) -{ - if ($go) - { - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - my $ind = $i[1]; - print $OUT "$ind ".$i[4]." ".$i[5]."\n"; - } - if (/C1/){$go = 1;} -} -close($O); -close($OUT); - - -my $j = 0; -open(my $IBS,">$out.ibs_matrix.txt"); -print $IBS "Individuals " . join("\t",@individuals)."\n"; -open(my $O2,"$out.mibs"); -while(<$O2>) -{ - my $line = $_; - $line =~s/\n//g; - $line =~s/\r//g; - my @i = split(/\s+/,$line); - print $IBS $individuals[$j]. " ". join("\t",@i)."\n"; - $j++; -} -close($O2); -close($IBS); - - - - - - |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/mdsplot.sh --- a/MDSplot/mdsplot.sh Fri Jul 10 10:38:43 2015 -0400 +++ b/MDSplot/mdsplot.sh Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -3,10 +3,10 @@ tool_path=$(dirname $0) ped=$1 map=$2 -fileout_label=$3 -fileout_matrix=$4 -fileout_plot=$5 -fileout_log=$6 +fileout_label=$(date "+%Y%m%d%H%M%S") +fileout_matrix=$3 +fileout_plot=$4 +fileout_log=$5 rsync -a $ped input.ped rsync -a $map input.map |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/mdsplot.xml --- a/MDSplot/mdsplot.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/MDSplot/mdsplot.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -8,6 +8,13 @@ <requirement type="binary">perl</requirement> <requirement type="package" version="1.07">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> + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> @@ -18,7 +25,7 @@ <!-- [REQUIRED] The command to execute --> <command interpreter="bash"> - mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log + mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log </command> <!-- [REQUIRED] Input files and tool parameters --> @@ -35,22 +42,15 @@ <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> </outputs> - <!-- [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> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> - <param name="fileped" value="input.ped" /> - <param name="filemap" value="input.map" /> - <output name="fileout_matrix" file="output.ibs_matrix.txt" /> - <output name="fileout_plot" file="output.mds_plot.txt" /> - <output name="fileout_log" file="output.log" /> + <param name="fileped" value="MDSplot-input.ped" /> + <param name="filemap" value="MDSplot-input.map" /> + <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" /> + <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" /> </test> <!-- [HELP] Multiple tests can be defined with different parameters --> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/test-data/analyse.ibs_matrix.txt --- a/MDSplot/test-data/analyse.ibs_matrix.txt Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,94 +0,0 @@\n-Individuals\tIRAT112\tIAC25\tIAC165\tKARASUKARASURANKASU\tDOURADOPRECOCE\tCUIABANA\tBICOBRANCO\tCAAWA/FORTUNA6\tCANELADEFERRO\tCIRAD358\tCOLOMBIA1\tCIRAD409\tBAGANANASALAO\tBAKUNGH\tFOHISOMOTRA\tKAKANI2\tGUARANI\tDOURADOAGULHA\tIRAT13\tDAWASANRED\tGRAZI\tIRAT144\tIAC47\tMOROBEREKAN\tIRAT362\tGIZA171\tIDSA77\tIRAT216\tIRAT177\tCHAPHUMA\tCIRAD392\tARROZCEBADA\tINDANE\tDINORADO\t63-104\tIR63380-16\tCANAROXA\tCICIHBETON\tIR68704-145-1-1-B\tHAWMOM\tIRAT364\tIRAT212\tKHAODAM\t62667\tIRAT234\tNIPPONBARE_D\tJUMULA2\tCUBA65\tBABER\tCIRAD488\tBENGALYVAKARINA\tESPERANZA\tBULUPANDAK\tARIAS\tGOMPA2\tCT13582-15-5-M\tIRAT335\tM202\tIR65907-188-1-B\tIR71525-19-1-1\tCNA-7_BO_1_1_33-13-6-1\tIRAT257\tIRAT109\tKANIRANGA\tIR66421-096-2-1-1\tGOGO\tGEMJYAJYANAM\tDANGREY\tBINULAWAN\tCAIAPO\tIGUAPECATETO\tIRAT170\tIRAT380\tARAGUAIA\tGOGOLEMPAK\tJAOHAW\tCHALOYOE\tGANIGI\tGUNDILKUNING\tIRAT2\tIRAT366\tIRAT104\tDAVAO\tHD1-4\tCURINCA\tDAM\tCIRAD403\tJUMALI\tJIMBRUKJOLOWORO\tGOGOLEMPUK\tCIRAD394\tIR63372-08\tIR60080-46A\n-IRAT112\t1\t0.93691\t0.937407\t0.734724\t0.943368\t0.819672\t0.903626\t0.850969\t0.842524\t0.802285\t0.717834\t0.836562\t0.804272\t0.832588\t0.81073\t0.614009\t0.946846\t0.943368\t0.944362\t0.688525\t0.807253\t0.712866\t0.929955\t0.782414\t0.902136\t0.692499\t0.817188\t0.796821\t0.943865\t0.697963\t0.790859\t0.787879\t0.704918\t0.833582\t0.917039\t0.769001\t0.938897\t0.682563\t0.814704\t0.707402\t0.859911\t0.787879\t0.709389\t0.945355\t0.883259\t0.703924\t0.697963\t0.843517\t0.725286\t0.725782\t0.84302\t0.876304\t0.69995\t0.74466\t0.651267\t0.836066\t0.958271\t0.651764\t0.755092\t0.859911\t0.861898\t0.905614\t0.892201\t0.739692\t0.828117\t0.80924\t0.650273\t0.644312\t0.860407\t0.853949\t0.922504\t0.944858\t0.81073\t0.908097\t0.756085\t0.674118\t0.744163\t0.785892\t0.698957\t0.944858\t0.80775\t0.857427\t0.838053\t0.931446\t0.831098\t0.721311\t0.798808\t0.592151\t0.739692\t0.757079\t0.767014\t0.781918\t0.899155\n-IAC25\t0.93691\t1\t0.958768\t0.723299\t0.965723\t0.825137\t0.93691\t0.836562\t0.850969\t0.772976\t0.713363\t0.807253\t0.791853\t0.819175\t0.814208\t0.602583\t0.934426\t0.966716\t0.904123\t0.676105\t0.817685\t0.706408\t0.948336\t0.811724\t0.892697\t0.693989\t0.819672\t0.784401\t0.902633\t0.677596\t0.806259\t0.812221\t0.717337\t0.813214\t0.876801\t0.757576\t0.923497\t0.706905\t0.806259\t0.69995\t0.833582\t0.777447\t0.693989\t0.904123\t0.896672\t0.703428\t0.694486\t0.813214\t0.728763\t0.747144\t0.82464\t0.864878\t0.710383\t0.758073\t0.643815\t0.834575\t0.925981\t0.674118\t0.745653\t0.839543\t0.845504\t0.900149\t0.851962\t0.764034\t0.817685\t0.814704\t0.655738\t0.644809\t0.819175\t0.834575\t0.90313\t0.90462\t0.838053\t0.928465\t0.751615\t0.666667\t0.733731\t0.800298\t0.707402\t0.902633\t0.805266\t0.846995\t0.822653\t0.955787\t0.809737\t0.700944\t0.788376\t0.591654\t0.750124\t0.751615\t0.790363\t0.769498\t0.879781\n-IAC165\t0.937407\t0.958768\t1\t0.722802\t0.929459\t0.839543\t0.932439\t0.862891\t0.85544\t0.786388\t0.739692\t0.817685\t0.790363\t0.817685\t0.822653\t0.596125\t0.968703\t0.929459\t0.920517\t0.677596\t0.832091\t0.704918\t0.9846\t0.822156\t0.92002\t0.688525\t0.834078\t0.794834\t0.921013\t0.685047\t0.805763\t0.823646\t0.717834\t0.826627\t0.895181\t0.769995\t0.945852\t0.688525\t0.825633\t0.694486\t0.846001\t0.77993\t0.697466\t0.920517\t0.90611\t0.694983\t0.689021\t0.809737\t0.723299\t0.745653\t0.810233\t0.87233\t0.692002\t0.76155\t0.636364\t0.849975\t0.91853\t0.66766\t0.755092\t0.866865\t0.855936\t0.916542\t0.868356\t0.746647\t0.822156\t0.813214\t0.651267\t0.632389\t0.82464\t0.844014\t0.927471\t0.921013\t0.832588\t0.963736\t0.774963\t0.661202\t0.743169\t0.796821\t0.702931\t0.921013\t0.800795\t0.864382\t0.80924\t0.98609\t0.821162\t0.709389\t0.797814\t0.588177\t0.735718\t0.774963\t0.783905\t0.780924\t0.901143\n-KARASUKARASURANKASU\t0.734724\t0.723299\t0.722802\t1\t0.73075\t0.748137\t0.745653\t0.766518\t0.747144\t0.796324\t0.673125\t0.738202\t0.774466\t0.753105\t0.780924\t0.630899\t0.731247\t0.73075\t0.769498\t0.802782\t0.769498\t0.677099\t0.73224\t0.749627\t0.754098\t0.817685\t0.715847\t0.721311\t0.769001\t0.837059\t0.777943\t0.775956\t0.827124\t0.740189\t0.778937\t0.707402\t0.743169\t0.675609\t0.704421\t0.80775\t0.780427\t0.748137\t0.879285\t0.770492\t0.759066\t0.828117\t0.731744\t0.743169\t0.761053\t0.669151\t0.764531\t0.71237\t0.693989\t0.737705\t0.668157\t0.735718\t0.723795\t0.781918\t0.728266\t0.764531\t0.750621\t0.741679\t0.731247\t0.689'..b'\t0.74764\t0.723795\t0.61997\t0.77546\t0.692002\t0.730253\t0.850969\t0.703428\t0.672628\t0.654247\t0.640835\t0.722305\t0.694983\t0.726279\t0.74615\t0.727769\t0.724292\t0.71535\t0.653751\t0.740189\t0.724292\t0.656731\t0.687531\t0.811227\t0.726279\t0.688525\t0.723795\t0.800795\t0.680079\t0.663189\t0.748137\t0.658718\t0.663189\t0.791356\t0.721311\t0.737705\t0.759563\t0.631396\t0.682067\t0.741679\t0.647789\t0.671634\t0.77844\t0.689021\t0.774466\t0.682563\t0.865872\t0.707899\t0.814208\t0.616493\t0.60457\t0.774963\t0.726776\t0.736711\t0.724292\t0.733234\t0.709389\t0.77993\t0.691008\t0.679583\t0.775956\t0.727769\t0.723299\t0.796821\t0.777943\t0.763537\t0.734724\t0.651267\t0.678589\t0.643815\t0.600099\t1\t0.77993\t0.680576\t0.641828\t0.739195\n-GOGOLEMPUK\t0.757079\t0.751615\t0.774963\t0.710383\t0.756085\t0.791356\t0.783905\t0.780924\t0.771485\t0.801788\t0.63686\t0.69995\t0.750124\t0.79533\t0.835072\t0.597615\t0.789369\t0.756085\t0.782911\t0.727769\t0.801788\t0.685544\t0.787382\t0.852459\t0.776453\t0.693989\t0.669647\t0.673125\t0.782414\t0.71535\t0.717834\t0.79533\t0.730253\t0.754595\t0.77546\t0.685047\t0.790363\t0.748634\t0.706905\t0.729757\t0.795827\t0.765524\t0.725782\t0.783905\t0.815201\t0.697466\t0.689518\t0.729757\t0.73075\t0.693492\t0.795827\t0.715847\t0.777943\t0.738202\t0.645802\t0.72926\t0.762047\t0.643318\t0.674118\t0.813711\t0.751118\t0.782911\t0.733731\t0.840537\t0.772976\t0.789866\t0.73224\t0.718331\t0.780427\t0.743169\t0.761053\t0.783408\t0.722802\t0.749627\t0.998013\t0.734228\t0.721808\t0.838053\t0.785892\t0.783408\t0.808246\t0.853949\t0.759066\t0.787879\t0.660705\t0.728763\t0.675112\t0.577745\t0.77993\t1\t0.677099\t0.675112\t0.791356\n-CIRAD394\t0.767014\t0.790363\t0.783905\t0.761053\t0.778937\t0.725782\t0.783905\t0.742176\t0.750621\t0.693492\t0.725286\t0.755589\t0.71535\t0.742673\t0.705912\t0.677099\t0.764531\t0.778937\t0.803775\t0.700944\t0.727273\t0.718331\t0.781421\t0.717337\t0.811227\t0.834078\t0.755092\t0.759563\t0.803279\t0.692499\t0.865872\t0.736711\t0.685544\t0.76155\t0.813214\t0.787382\t0.784401\t0.674118\t0.73075\t0.680079\t0.723299\t0.794337\t0.706905\t0.804769\t0.793343\t0.838549\t0.783905\t0.729757\t0.722802\t0.748137\t0.752111\t0.770492\t0.676602\t0.714357\t0.733234\t0.783905\t0.742176\t0.79235\t0.745653\t0.735221\t0.813711\t0.766021\t0.764531\t0.699454\t0.790859\t0.761053\t0.690512\t0.685544\t0.738698\t0.789866\t0.76304\t0.804272\t0.824143\t0.758569\t0.676105\t0.69846\t0.723795\t0.693989\t0.680576\t0.803279\t0.655241\t0.752608\t0.728266\t0.781918\t0.745156\t0.702931\t0.763537\t0.645306\t0.680576\t0.677099\t1\t0.773472\t0.781421\n-IR63372-08\t0.781918\t0.769498\t0.780924\t0.735221\t0.76006\t0.712866\t0.778937\t0.796821\t0.74764\t0.697466\t0.868356\t0.944362\t0.747144\t0.729757\t0.717834\t0.605564\t0.781421\t0.761053\t0.834575\t0.707899\t0.728266\t0.642822\t0.77844\t0.702434\t0.835072\t0.700944\t0.945852\t0.981123\t0.835072\t0.700447\t0.763537\t0.741679\t0.710383\t0.74466\t0.836066\t0.93542\t0.798311\t0.619473\t0.846001\t0.698957\t0.757079\t0.721808\t0.720815\t0.835569\t0.773472\t0.71237\t0.683557\t0.742673\t0.707899\t0.690512\t0.719324\t0.769498\t0.61699\t0.697466\t0.634873\t0.85544\t0.759066\t0.690015\t0.963239\t0.767014\t0.849478\t0.757079\t0.798311\t0.660705\t0.837556\t0.750124\t0.663686\t0.672628\t0.745653\t0.764034\t0.753105\t0.835072\t0.760556\t0.79235\t0.674118\t0.687531\t0.711873\t0.691008\t0.627919\t0.835072\t0.670144\t0.746647\t0.72926\t0.77993\t0.938897\t0.709886\t0.981123\t0.592648\t0.641828\t0.675112\t0.773472\t1\t0.812221\n-IR60080-46A\t0.899155\t0.879781\t0.901143\t0.753105\t0.867362\t0.807253\t0.869349\t0.878291\t0.845007\t0.808743\t0.738202\t0.861898\t0.787879\t0.817188\t0.84004\t0.617486\t0.924491\t0.868356\t0.946846\t0.702931\t0.799801\t0.769001\t0.898659\t0.818679\t0.934426\t0.704918\t0.801788\t0.82613\t0.946349\t0.722305\t0.799305\t0.812221\t0.714357\t0.837059\t0.919523\t0.797317\t0.925484\t0.702931\t0.846001\t0.725782\t0.861401\t0.84302\t0.742673\t0.947839\t0.865872\t0.711376\t0.719324\t0.835072\t0.725782\t0.741182\t0.80775\t0.858917\t0.721311\t0.762047\t0.672628\t0.882265\t0.880278\t0.680079\t0.806259\t0.942871\t0.891207\t0.923\t0.903626\t0.743169\t0.832588\t0.813711\t0.674615\t0.66468\t0.842027\t0.871336\t0.87233\t0.947342\t0.812221\t0.871833\t0.790363\t0.718331\t0.743666\t0.798311\t0.722305\t0.947342\t0.79533\t0.910581\t0.837556\t0.901143\t0.785892\t0.726776\t0.828117\t0.603577\t0.739195\t0.791356\t0.781421\t0.812221\t1\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/test-data/analyse.log --- a/MDSplot/test-data/analyse.log Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,56 +0,0 @@ - -@----------------------------------------------------------@ -| PLINK! | v1.07 | 10/Aug/2009 | -|----------------------------------------------------------| -| (C) 2009 Shaun Purcell, GNU General Public License, v2 | -|----------------------------------------------------------| -| For documentation, citation & bug-report instructions: | -| http://pngu.mgh.harvard.edu/purcell/plink/ | -@----------------------------------------------------------@ - -Skipping web check... [ --noweb ] -Writing this text to log file [ analyse.log ] -Analysis started: Tue Jan 20 09:30:56 2015 - -Options in effect: - --file input - --noweb - --cluster - --matrix - --mds-plot 2 - --out analyse - -2013 (of 2013) markers to be included from [ input.map ] -93 individuals read from [ input.ped ] -93 individuals with nonmissing phenotypes -Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) -Missing phenotype value is also -9 -0 cases, 93 controls and 0 missing -93 males, 0 females, and 0 of unspecified sex -Before frequency and genotyping pruning, there are 2013 SNPs -Converting data to SNP-major format -93 founders and 0 non-founders found -Total genotyping rate in remaining individuals is 1 -0 SNPs failed missingness test ( GENO > 1 ) -0 SNPs failed frequency test ( MAF < 0 ) -Converting data to Individual-major format -After frequency and genotyping pruning, there are 2013 SNPs -After filtering, 0 cases, 93 controls and 0 missing -After filtering, 93 males, 0 females, and 0 of unspecified sex - - **Warning** this analysis typically requires whole-genome level data - to give accurate results - -Clustering individuals based on genome-wide IBS -Merge distance p-value constraint = 0 -IBS(g) calculation: 0 of 4278 IBS(g) calculation: 100 of 4278 IBS(g) calculation: 200 of 4278 IBS(g) calculation: 300 of 4278 IBS(g) calculation: 400 of 4278 IBS(g) calculation: 500 of 4278 IBS(g) calculation: 600 of 4278 IBS(g) calculation: 700 of 4278 IBS(g) calculation: 800 of 4278 IBS(g) calculation: 900 of 4278 IBS(g) calculation: 1000 of 4278 IBS(g) calculation: 1100 of 4278 IBS(g) calculation: 1200 of 4278 IBS(g) calculation: 1300 of 4278 IBS(g) calculation: 1400 of 4278 IBS(g) calculation: 1500 of 4278 IBS(g) calculation: 1600 of 4278 IBS(g) calculation: 1700 of 4278 IBS(g) calculation: 1800 of 4278 IBS(g) calculation: 1900 of 4278 IBS(g) calculation: 2000 of 4278 IBS(g) calculation: 2100 of 4278 IBS(g) calculation: 2200 of 4278 IBS(g) calculation: 2300 of 4278 IBS(g) calculation: 2400 of 4278 IBS(g) calculation: 2500 of 4278 IBS(g) calculation: 2600 of 4278 IBS(g) calculation: 2700 of 4278 IBS(g) calculation: 2800 of 4278 IBS(g) calculation: 2900 of 4278 IBS(g) calculation: 3000 of 4278 IBS(g) calculation: 3100 of 4278 IBS(g) calculation: 3200 of 4278 IBS(g) calculation: 3300 of 4278 IBS(g) calculation: 3400 of 4278 IBS(g) calculation: 3500 of 4278 IBS(g) calculation: 3600 of 4278 IBS(g) calculation: 3700 of 4278 IBS(g) calculation: 3800 of 4278 IBS(g) calculation: 3900 of 4278 IBS(g) calculation: 4000 of 4278 IBS(g) calculation: 4100 of 4278 IBS(g) calculation: 4200 of 4278 Writing IBS similarity matrix to [ analyse.mibs ] -Of these, 4278 are pairable based on constraints -Writing cluster progress to [ analyse.cluster0 ] -Writing cluster solution (1) [ analyse.cluster1 ] -Writing cluster solution (2) [ analyse.cluster2 ] -Writing cluster solution (3) [ analyse.cluster3 ] -Writing MDS solution to [ analyse.mds ] -MDS plot of individuals (not clusters) - -Analysis finished: Tue Jan 20 09:30:57 2015 - |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/test-data/analyse.mds_plot.txt --- a/MDSplot/test-data/analyse.mds_plot.txt Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,93 +0,0 @@ -IRAT112 -0.0969382 0.0376036 -IAC25 -0.0918126 0.0501177 -IAC165 -0.104815 0.0453876 -KARASUKARASURANKASU 0.107782 -0.0683546 -DOURADOPRECOCE -0.0831697 0.0516412 -CUIABANA 0.0327877 0.0497752 -BICOBRANCO -0.0554177 0.0501857 -CAAWA/FORTUNA6 -0.052355 0.0170584 -CANELADEFERRO -0.0142283 0.0598394 -CIRAD358 0.0497841 0.0645487 -COLOMBIA1 -0.110347 -0.172742 -CIRAD409 -0.113614 -0.105898 -BAGANANASALAO 0.0247582 0.0186246 -BAKUNGH 0.0199022 0.0613692 -FOHISOMOTRA 0.0344309 0.0697592 -KAKANI2 0.147713 -0.0780455 -GUARANI -0.0892761 0.0387007 -DOURADOAGULHA -0.0831373 0.0514523 -IRAT13 -0.0757215 0.00312413 -DAWASANRED 0.131309 -0.102364 -GRAZI 0.0177091 0.0870472 -IRAT144 0.0146443 0.0067734 -IAC47 -0.0968934 0.0477667 -MOROBEREKAN 0.0395544 0.0952695 -IRAT362 -0.0921075 -0.00860852 -GIZA171 0.14498 -0.0932001 -IDSA77 -0.122827 -0.120219 -IRAT216 -0.120205 -0.136803 -IRAT177 -0.0762395 0.00230332 -CHAPHUMA 0.149543 -0.0680637 -CIRAD392 0.0187265 -0.047646 -ARROZCEBADA 0.0110416 0.0787137 -INDANE 0.108691 -0.0338065 -DINORADO -0.00819237 0.0386578 -63-104 -0.053974 -0.00204494 -IR63380-16 -0.0968028 -0.0931822 -CANAROXA -0.0756689 0.0253328 -CICIHBETON 0.108857 0.142633 -IR68704-145-1-1-B -0.103292 -0.071382 -HAWMOM 0.129651 -0.0473323 -IRAT364 -0.0118523 0.0472973 -IRAT212 0.0231616 -0.00146178 -KHAODAM 0.123936 -0.0654516 -62667 -0.0752552 0.00278556 -IRAT234 -0.0346607 0.0551203 -NIPPONBARE_D 0.133199 -0.0963396 -JUMULA2 0.104558 -0.0524994 -CUBA65 -0.0124835 0.013679 -BABER 0.090299 -0.0460696 -CIRAD488 -0.0201481 -0.0262103 -BENGALYVAKARINA 0.028631 0.0637662 -ESPERANZA -0.108888 -0.00812147 -BULUPANDAK 0.119762 0.143912 -ARIAS 0.0327948 0.0827878 -GOMPA2 0.133341 -0.0543414 -CT13582-15-5-M -0.0922561 -0.0543988 -IRAT335 -0.0886849 0.0522465 -M202 0.13463 -0.106462 -IR65907-188-1-B -0.0755893 -0.136821 -IR71525-19-1-1 -0.0353444 0.0478985 -CNA-7_BO_1_1_33-13-6-1 -0.0823478 -0.0435581 -IRAT257 -0.0606191 0.0564989 -IRAT109 -0.1006 -0.00959445 -KANIRANGA 0.0705459 0.129888 -IR66421-096-2-1-1 -0.00859728 -0.0570793 -GOGO 0.0232414 0.0351889 -GEMJYAJYANAM 0.170032 -0.0857315 -DANGREY 0.175792 -0.113683 -BINULAWAN -0.0208225 0.0611919 -CAIAPO -0.0149329 -0.0122987 -IGUAPECATETO -0.0740464 0.0552386 -IRAT170 -0.0756928 0.00297643 -IRAT380 -0.0210318 -0.00092536 -ARAGUAIA -0.123443 0.0273298 -GOGOLEMPAK 0.0598291 0.107462 -JAOHAW 0.17563 -0.0587865 -CHALOYOE 0.0904761 -0.0565325 -GANIGI 0.0526286 0.0960475 -GUNDILKUNING 0.116788 0.130234 -IRAT2 -0.0762849 0.00262428 -IRAT366 0.0273652 0.13551 -IRAT104 -0.00310702 0.0636479 -DAVAO -0.00538403 0.0564886 -HD1-4 -0.0960109 0.0459137 -CURINCA -0.128876 -0.121141 -DAM 0.129029 -0.0660183 -CIRAD403 -0.117849 -0.134651 -JUMALI 0.123992 -0.0843623 -JIMBRUKJOLOWORO 0.0549906 0.135017 -GOGOLEMPUK 0.0597267 0.10733 -CIRAD394 0.0040454 -0.0885135 -IR63372-08 -0.0951857 -0.140804 -IR60080-46A -0.0732581 0.0197832 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/test-data/input.map --- a/MDSplot/test-data/input.map Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,2013 +0,0 @@\n-Chr1 Chr1:4299 0 4299\n-Chr1 Chr1:26710 0 26710\n-Chr1 Chr1:56184 0 56184\n-Chr1 Chr1:93272 0 93272\n-Chr1 Chr1:93274 0 93274\n-Chr1 Chr1:146252 0 146252\n-Chr1 Chr1:171433 0 171433\n-Chr1 Chr1:186286 0 186286\n-Chr1 Chr1:198907 0 198907\n-Chr1 Chr1:205550 0 205550\n-Chr1 Chr1:206108 0 206108\n-Chr1 Chr1:214680 0 214680\n-Chr1 Chr1:214775 0 214775\n-Chr1 Chr1:215711 0 215711\n-Chr1 Chr1:217307 0 217307\n-Chr1 Chr1:238821 0 238821\n-Chr1 Chr1:240448 0 240448\n-Chr1 Chr1:240579 0 240579\n-Chr1 Chr1:300528 0 300528\n-Chr1 Chr1:312532 0 312532\n-Chr1 Chr1:337330 0 337330\n-Chr1 Chr1:351841 0 351841\n-Chr1 Chr1:353617 0 353617\n-Chr1 Chr1:405193 0 405193\n-Chr1 Chr1:405217 0 405217\n-Chr1 Chr1:409167 0 409167\n-Chr1 Chr1:415515 0 415515\n-Chr1 Chr1:424861 0 424861\n-Chr1 Chr1:425116 0 425116\n-Chr1 Chr1:429660 0 429660\n-Chr1 Chr1:439393 0 439393\n-Chr1 Chr1:456979 0 456979\n-Chr1 Chr1:479030 0 479030\n-Chr1 Chr1:479033 0 479033\n-Chr1 Chr1:525146 0 525146\n-Chr1 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| b |
| diff -r 345f88a8f483 -r 10627af23f10 MDSplot/test-data/input.ped --- a/MDSplot/test-data/input.ped Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,93 +0,0 @@\n-IRAT112\t1\t0\t0\t1\t1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t1 1\t2 2\t1 1\t4 4\t1 1\t1 1\t4 4\t2 2\t4 4\t1 1\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t3 3\t4 4\t4 4\t2 2\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t2 2\t4 4\t2 2\t1 1\t1 1\t3 3\t3 3\t4 4\t4 4\t3 3\t3 3\t2 2\t1 1\t2 2\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t3 3\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t4 4\t4 4\t3 3\t4 4\t1 1\t3 3\t3 3\t3 3\t1 1\t2 2\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t3 3\t2 2\t3 3\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t2 2\t4 4\t4 4\t1 1\t4 4\t2 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4\t4 4\t1 1\t1 1\t2 2\t3 3\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t2 2\t4 4\t4 4\t1 1\t2 2\t4 4\t3 3\t4 4\t4 4\t4 4\t1 1\t3 3\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t1 1\t1 1\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t4 4\t1 1\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t2 2\t4 4\t3 3\t1 1\t2 2\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t1 1\t3 3\t1 1\t2 2\t3 3\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t3 3\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t3 3\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t3 3\t1 1\t1 1\t2 2\t4 4\t1 1\t1 1\t2 2\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 PedToFasta/pedToFasta.xml --- a/PedToFasta/pedToFasta.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/PedToFasta/pedToFasta.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -7,6 +7,12 @@ <requirements> <requirement type="binary">perl</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> <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> @@ -31,18 +37,12 @@ <data name="fileout" type="data" format="fasta" label="${fileout_label}.fa" /> </outputs> - <!-- [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> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> - <param name="filein" value="sample.ped" /> - <output name="fileout" file="result.fa" /> + <param name="filein" value="ped2fasta-sample.ped" /> + <output name="fileout" file="ped2fasta-result.fa" /> </test> </tests> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 PedToFasta/test-data/result.fa --- a/PedToFasta/test-data/result.fa Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
|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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 PedToFasta/test-data/sample.ped --- a/PedToFasta/test-data/sample.ped Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
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tG\tG\tA\tA\tT\tT\tC\tT\tC\tA\tT\tA\tC\tA\tG\tT\tC\tC\tT\tG\tA\tG\tA\tA\tG\tC\tT\tT\tC\tT\tC\tG\tT\tG\tA\tT\tC\tC\tT\tA\tG\tT\tC\tT\tC\tA\tG\tC\tT\tA\tC\tT\tG\tG\tA\tA\tG\tC\tT\tA\tG\tC\tT\tT\tA\tT\tA\tC\tT\tG\tA\tA\tG\tA\tG\tG\tA\tC\tT\tG\tA\tC\tT\tT\tC\tC\tG\tA\tT\tA\tC\tC\tA\tT\tA\tC\tT\tT\tA\tC\tA\tT\tC\tA\tT\tC\tG\tT\tC\tT\tC\tG\tA\tT\tA\tT\tA\tT\tA\tT\tC\tG\tA\tA\tG\tA\tG\tG\tA\tC\tT\tT\tA\tC\tT\tG\tT\tG\tC\tT\tG\tG\tA\tT\tC\tG\tC\tG\tC\tC\tT\tC\tT\tT\tC\tA\tT\tG\tA\tG\tA\tG\tA\tA\tC\tA\tC\tA\tG\tC\tG\tT\tC\tT\tC\tT\tG\tC\tT\tA\tG\tG\tT\tC\tT\tC\tT\tC\tA\tC\tT\tT\tG\tA\tG\tT\tC\tC\tT\tT\tC\tT\tG\tG\tA\tC\tT\tG\tC\tC\tA\tT\tC\tT\tC\tT\tA\tT\tC\tG\tA\tG\tC\tA\tT\tG\tA\tA\tG\tT\tA\tA\tG\tC\tT\tG\tT\tA\tG\tC\tT\tA\tG\tT\tC\tT\tC\tT\tC\tA\tG\tT\tC\tA\tG\tG\tT\tC\tT\tT\tC\tT\tC\tA\tG\tC\tT\tT\tG\tC\tT\tC\tT\tC\tT\tC\tT\tG\tA\tG\tC\tC\tT\tG\tT\tT\tA\tC\tT\tA\tC\tT\tA\tG\tC\tA\tC\tG\tA\tA\tG\tC\tT\tA\tG\tC\tA\tT\tG\tG\tA\tA\tC\tA\tG\tT\tC\tG\tC\tG\tA\tC\tT\tC\tG\tA\tG\tC\tT\tC\tT\tT\tC\tG\tA\tC\tA\tT\tC\tT\tG\tA\tG\tG\tA\tG\tA\tA\tT\tA\tG\tC\tT\tC\tT\tG\tA\tG\tA\tG\tA\tA\tG\tT\tC\tT\tC\tA\tT\tT\tC\tT\tC\tA\tT\tA\tG\tG\tA\tT\tG\tA\tT\tG\tT\tT\tG\tA\tG\tT\tC\tA\tG\tA\tT\tA\tG\tA\tT\tC\tT\tC\tG\tC\tA\tC\tT\tG\tA\tG\tA\tG\tC\tC\tA\tG\tA\tA\tT\tT\tA\tA\tT\tC\tG\tC\tA\tA\tG\tC\tA\tC\tG\tG\tA\tG\tT\tC\tT\tT\tA\tA\tG\tG\tA\tC\tT\tT\tC\tC\tT\tA\tT\tC\tT\tA\tG\tT\tC\tC\tG\tC\tT\tA\tG\tA\tC\tT\tA\tA\tC\tA\tG\tG\tC\tA\tT\tA\tG\tC\tT\tT\tG\tT\tG\tA\tG\tA\tG\tT\tA\tC\tG\tG\tC\tC\tT\tT\tC\tT\tC\tC\tT\tT\tC\tG\tA\tT\tC\tT\tC\tT\tC\tC\tA\tC\tT\tC\tT\tT\tC\tT\tC\tA\tC\tA\tG\tC\tT\tG\tT\tT\tC\tT\tC\tA\tG\tT\tA\tC\tT\tT\tC\tC\tT\tA\tG\tC\tT\tC\tT\tC\tT\tC\tT\tC\tT\tC\tT\tG\tA\tA\tC\tC\tT\tC\tT\tC\tT\tG\tA\tG\tA\tG\tA\tC\tT\tT\tC\tC\tT\tT\tC\tA\tG\tA\tG\tC\tT\tT\tG\tT\tA\tG\tA\tC\tT\tG\tA\tA\tG\tG\tA\tC\tT\tA\tT\tA\tT\tT\tC\tT\tG\tA\tC\tG\tA\tG\tT\tC\tG\tC\tT\tT\tC\tT\tC\tT\tC\tT\tC\tG\tA\tC\tT\tT\tA\tG\tA\tG\tA\tA\tG\tA\tG\tT\tG\tG\tC\tT\tC\tC\tG\tT\tC\tC\tA\tG\tA\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 Rooting/rooting.xml --- a/Rooting/rooting.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/Rooting/rooting.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_rooting" name="Rooting" version="1.1"> +<tool id="sniplay_rooting" name="Rooting" version="1.0.2"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Midpoint rooting of newick tree </description> @@ -8,6 +8,13 @@ <requirement type="binary">perl</requirement> <requirement type="package">Rootings_54.jar</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> + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> @@ -23,7 +30,7 @@ <!-- [REQUIRED] Input files and tool parameters --> <inputs> - <param name="filein" type="data" format="txt" optional="false" label="Newick tree input" /> + <param name="filein" type="data" format="txt" optional="false" label="Fasta alignment input" /> <param name="fileout_label" type="text" value="out tree" label="Output name" help="Output name for files" /> </inputs> @@ -33,20 +40,13 @@ <data name="fileout" type="data" format="txt" label="${fileout_label}" /> </outputs> - <!-- [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> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> - <param name="filein" value="newick" /> - <output name="fileout" file="out_tree" /> - <output name="fileout_log" file="out_tree.log" /> + <param name="filein" value="rooting-newick" /> + <output name="fileout" file="rooting-out_tree" /> </test> <!-- [HELP] Multiple tests can be defined with different parameters --> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 Rooting/test-data/newick --- a/Rooting/test-data/newick Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,2 +0,0 @@ -(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); - |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 Rooting/test-data/out_tree --- a/Rooting/test-data/out_tree Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,1 +0,0 @@ -(ref:0.575788,(((((((((((((((((((((((PALAWAN:0.032789,KENDINGA5H:0.028863):0.031721,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.004581,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004869,DINORADO:0.065206):0.004898,((LUDAN:0.05423,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):8.8E-5):0.006838,CAAWA/FORT:0.05563):0.011439,CANELADEFE:0.050931):0.002897,PACHOLINHA:0.042509):0.002988,TRESMESES:0.028972):0.001209,((OS4:0.021016,OS6:0.01567):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.006303,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.004673,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.14437):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.04316,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.01418,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.05797):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.00344,(((((KUROKA:0.096901,IRAT144:0.032372):0.04063,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.03418):0.01106,CAIAPO:0.07222):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.001457,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.01125,(((IAC47:0.007321,(IAC165:5.0E-4,VARYLAVA90:0.00165):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.007912,IRAT234:0.037316):0.005647,MANDRIRAVI:0.049833):0.002593,RT1031-69:0.04352):0.005079,((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.00474):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):8.58E-4,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.02711,GRAZI:0.022678):7.63E-4):0.00987,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:0.0,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):9.71E-4):0.009442):0.002985):0.008281,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.02162,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.05943,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.001416,((GANIGI:0.040448,PULULAPA:0.03984):0.020258,GOGO:0.060904):0.005609):0.018877,CUIABANA:0.066182):0.020665,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.03265):0.012575,VIETNAM1:0.049323):0.00311,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.01445):0.01097):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.00624,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.043699,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.015245,(((JUMALI:0.07765,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607):0.14713500000000007); |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml --- a/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="sniplay_density" name="SNP density" version="1.2.0"> +<tool id="sniplay_density" name="SNP density" version="1.3.0"> <!-- [REQUIRED] Tool description displayed after the tool name --> <description> Calculate SNP densities along chromosome from HapMap</description> @@ -8,6 +8,12 @@ <requirement type="binary">perl</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> + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> <!-- @@ -19,7 +25,7 @@ <command interpreter="bash"> calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step </command> - + <!-- [REQUIRED] Input files and tool parameters --> <inputs> <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> @@ -32,22 +38,14 @@ <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> </outputs> - - <!-- [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> - - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> + <tests> - <!-- [HELP] Test files have to be in the ~/test-data directory --> -<!-- - <test> - <param name="input" value="input_test.txt" /> - <output name="output" file="output_test.txt" /> + <test> + <param name="filein" value="SNPden-hapmap" /> + <param name="step" value="200000" /> + <output name="fileout" file="SNPden-result.txt" /> + <output name="fileout_bysample" file="SNPden-result_bysample.txt" /> </test> ---> <!-- [HELP] Multiple tests can be defined with different parameters --> <!-- <test> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 SNP_density/test-data/hapmap --- a/SNP_density/test-data/hapmap Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,3584 +0,0 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r1:3939962\t[C/A]\tchr1\t3939962\tCc01_g02140:1177\texon\tNON_SYNONYMOUS_CODING\tGcc/Tcc\tA/S\t12.5%\t4\tCC\tCA\tCC\tCC\n-chr1:3939959\t[G/T]\tchr1\t3939959\tCc01_g02140:1180\texon\tNON_SYNONYMOUS_CODING\tCtt/Att\tL/I\t25.0%\t4\tGG\tTT\tGG\tGG\n-chr1:3939916\t[C/T]\tchr1\t3939916\tCc01_g02140:1223\texon\tNON_SYNONYMOUS_CODING\taGt/aAt\tS/N\t25.0%\t4\tCC\tTT\tCC\tCC\n-chr1:3938977\t[G/C]\tchr1\t3938977\tCc01_g02140:1335\texon\tSYNONYMOUS_CODING\ttcC/tcG\tS/S\t12.5%\t4\tGG\tGC\tGG\tGG\n-chr1:3938798\t[T/G]\tchr1\t3938798\tCc01_g02140:1369\texon\tNON_SYNONYMOUS_CODING\tAgt/Cgt\tS/R\t37.5%\t4\tTT\tGG\tTG\tTT\n-chr1:3938797\t[C/G]\tchr1\t3938797\tCc01_g02140:1370\texon\tNON_SYNONYMOUS_CODING\taGt/aCt\tS/T\t12.5%\t4\tCC\tCC\tCC\tCG\n-chr1:3938792\t[G/A]\tchr1\t3938792\tCc01_g02140:1375\texon\tSYNONYMOUS_CODING\tCta/Tta\tL/L\t12.5%\t4\tGG\tGG\tGG\tAG\n-chr1:3938784\t[C/T]\tchr1\t3938784\tCc01_g02140:1383\texon\tSYNONYMOUS_CODING\tccG/ccA\tP/P\t25.0%\t4\tCC\tTC\tCT\tCC\n-chr1:3938738\t[C/T]\tchr1\t3938738\tCc01_g02140:1429\texon\tNON_SYNONYMOUS_CODING\tGtt/Att\tV/I\t12.5%\t4\tCC\tCC\tCT\tCC\n-chr1:3938734\t[T/C]\tchr1\t3938734\tCc01_g02140:1433\texon\tNON_SYNONYMOUS_CODING\tcAa/cGa\tQ/R\t25.0%\t4\tTT\tTT\tTC\tCT\n-chr1:3938731\t[A/G]\tchr1\t3938731\tCc01_g02140:1436\texon\tNON_SYNONYMOUS_CODING\tgTg/gCg\tV/A\t12.5%\t4\tAA\tAA\tAG\tAA\n-chr1:3938674\t[C/T]\tchr1\t3938674\tCc01_g02140:1493\texon\tNON_SYNONYMOUS_CODING\taGt/aAt\tS/N\t12.5%\t4\tCC\tCC\tCT\tCC\n-chr1:3950327\t[A/C]\tchr1\t3950327\tCc01_g02150:300\texon\tNON_SYNONYMOUS_CODING\tcaT/caG\tH/Q\t37.5%\t4\tAA\tCC\tAC\tAA\n-chr1:3949508\t[G/T]\tchr1\t3949508\tCc01_g02150:438\texon\tSYNONYMOUS_CODING\ttcC/tcA\tS/S\t12.5%\t4\tGG\tGT\tGG\tGG\n-chr1:3949500\t[T/C]\tchr1\t3949500\tCc01_g02150:446\texon\tNON_SYNONYMOUS_CODING\ttAt/tGt\tY/C\t12.5%\t4\tTT\tTT\tTC\tTT\n-chr1:3949478\t[G/A]\tchr1\t3949478\tCc01_g02150:468\texon\tSYNONYMOUS_CODING\tcgC/cgT\tR/R\t12.5%\t4\tGG\tGG\tGA\tGG\n-chr1:3949470\t[C/T]\tchr1\t3949470\tCc01_g02150:476\texon\tNON_SYNONYMOUS_CODING\taGg/aAg\tR/K\t25.0%\t4\tCC\tTT\tCC\tCC\n-chr1:3949465\t[C/G]\tchr1\t3949465\tCc01_g02150:481\texon\tNON_SYNONYMOUS_CODING\tGgt/Cgt\tG/R\t37.5%\t4\tCC\tGG\tCG\tCC\n-chr1:3949086\t[C/T]\tchr1\t3949086\tCc01_g02150:541\texon\tNON_SYNONYMOUS_CODING\tGtc/Atc\tV/I\t12.5%\t4\tCC\tCC\tCT\tCC\n-chr1:3967535\t[C/T]\tchr1\t3967535\tCc01_g02160:57\texon\tSYNONYMOUS_CODING\tcgG/cgA\tR/R\t12.5%\t4\tCC\tCT\tCC\tCC\n-chr1:3967530\t[A/T]\tchr1\t3967530\tCc01_g02160:62\texon\tNON_SYNONYMOUS_CODING\tcTg/cAg\tL/Q\t12.5%\t4\tAA\tAA\tAA\tAT\n-chr1:3967524\t[G/A]\tchr1\t3967524\tCc01_g02160:68\texon\tNON_SYNONYMOUS_CODING\tcCa/cTa\tP/L\t37.5%\t4\tGG\tAG\tGA\tAG\n-chr1:3967512\t[A/G]\tchr1\t3967512\tCc01_g02160:80\texon\tNON_SYNONYMOUS_CODING\taTa/aCa\tI/T\t12.5%\t4\tAA\tAA\tAG\tAA\n-chr1:3967435\t[A/G]\tchr1\t3967435\tCc01_g02160:157\texon\tNON_SYNONYMOUS_CODING\tTcc/Ccc\tS/P\t25.0%\t4\tAA\tAG\tAA\tAG\n-chr1:3967421\t[G/A]\tchr1\t3967421\tCc01_g02160:171\texon\tSYNONYMOUS_CODING\tacC/acT\tT/T\t12.5%\t4\tGG\tAG\tGG\tGG\n-chr1:3967412\t[A/C]\tchr1\t3967412\tCc01_g02160:180\texon\tSTOP_GAINED\ttaT/taG\tY/0\t37.5%\t4\tAA\tAC\tAC\tAC\n-chr1:3967382\t[A/G]\tchr1\t3967382\tCc01_g02160:210\texon\tSYNONYMOUS_CODING\tccT/ccC\tP/P\t25.0%\t4\tAA\tGA\tGA\tAA\n-chr1:3967354\t[G/T]\tchr1\t3967354\tCc01_g02160:238\texon\tNON_SYNONYMOUS_CODING\tCaa/Aaa\tQ/K\t12.5%\t4\tGG\tGG\tGG\tGT\n-chr1:3967352\t[T/C]\tchr1\t3967352\tCc01_g02160:240\texon\tSYNONYMOUS_CODING\tcaA/caG\tQ/Q\t37.5%\t4\tTT\tCC\tCT\tCC\n-chr1:3967310\t[G/C]\tchr1\t3967310\tCc01_g02160:282\texon\tNON_SYNONYMOUS_CODING\tatC/atG\tI/M\t37.5%\t4\tGG\tGC\tGC\tGC\n-chr1:3967300\t[C/T]\tchr1\t3967300\tCc01_g02160:292\texon\tNON_SYNONYMOUS_CODING\tGat/Aat\tD/N\t12.5%\t4\tCC\tCC\tCC\tTC\n-chr1:3967295\t[G/A]\tchr1\t3967295\tCc01_g02160:297\texon\tSYNONYMOUS_CODING\tatC/atT\tI/I\t12.5%\t4\tGG\tGG\tGA\tGG\n-chr1:3966909\t[T/A]\tchr1\t3966909\tCc01_g02160:683\texon\tNON_SYNONYMOUS_CODING\ttAt/tTt\tY/F\t12.5%\t4\tTT\tTA\tTT\tTT\n-chr1:3966784\t[G/A]\tchr1\t3966784\tCc01_g02160:808\texon\tNON_SYNONYMOUS_CODING\tCtt/Ttt\tL/F\t16.7%\t3\tGG\tNN\tGA\tGG\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 SNP_density/test-data/result.txt --- a/SNP_density/test-data/result.txt Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -Chromosome Position SNPs -chr1 200000 355 -chr1 400000 228 -chr1 600000 63 -chr1 800000 191 -chr1 1000000 88 -chr1 1200000 90 -chr1 1400000 190 -chr1 1600000 267 -chr1 1800000 226 -chr1 2000000 163 -chr1 2200000 357 -chr1 2400000 132 -chr1 2600000 158 -chr1 2800000 104 -chr1 3000000 146 -chr1 3200000 331 -chr1 3400000 181 -chr1 3600000 36 -chr1 3800000 167 -chr1 4000000 110 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 SNP_density/test-data/result_bysample.txt --- a/SNP_density/test-data/result_bysample.txt Fri Jul 10 10:38:43 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -Chromosome BA58 BA59 BD54 -chr1 220 197 225 -chr1 130 119 133 -chr1 43 43 40 -chr1 139 167 141 -chr1 62 72 78 -chr1 35 76 38 -chr1 98 123 82 -chr1 133 205 135 -chr1 94 141 151 -chr1 112 116 117 -chr1 228 238 204 -chr1 86 95 96 -chr1 60 106 82 -chr1 60 74 64 -chr1 106 112 115 -chr1 199 220 228 -chr1 151 94 64 -chr1 18 32 27 -chr1 87 90 100 -chr1 54 75 47 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 VCF2Hapmap/vcf2FastaAndHapmap.sh --- a/VCF2Hapmap/vcf2FastaAndHapmap.sh Fri Jul 10 10:38:43 2015 -0400 +++ b/VCF2Hapmap/vcf2FastaAndHapmap.sh Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -5,19 +5,19 @@ filein=$1 -fileout_label=$2 -fileout=$3 -option=$4 +fileout_label=$(date "+%Y%m%d%H%M%S") +fileout=$2 +option=$3 option_text='' if [ "$option" != "none" ] -then fileout_seq=$5 - fileout_fa1=$6 - filefasta=$7 +then fileout_seq=$4 + fileout_fa1=$5 + filefasta=$6 if [ "$option" == "fasta_gff" ] - then filegff=$8 + then filegff=$7 fi fi |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 VCF2Hapmap/vcf2FastaAndHapmap.xml --- a/VCF2Hapmap/vcf2FastaAndHapmap.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/VCF2Hapmap/vcf2FastaAndHapmap.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -8,6 +8,12 @@ <requirement type="binary">perl</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> + <!-- [OPTIONAL] Command to be executed to get the tool's version string --> <version_command> <!-- @@ -17,7 +23,7 @@ <!-- [REQUIRED] The command to execute --> <command interpreter="bash"> - vcf2FastaAndHapmap.sh $filein $fileout_label $fileout $optional.file_opt + vcf2FastaAndHapmap.sh $filein $fileout $optional.file_opt #if str( $optional.file_opt ) != "none": $fileout_seq $fileout_fa1 $filefasta #if str( $optional.file_opt ) == "fasta_gff": @@ -58,27 +64,29 @@ </data> </outputs> - <!-- [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> - <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <test> - <param name="filein" value="sample.vcf" /> - <param name="otpional.file_opt" value="none" /> - <output name="fileout" file="result1.hapmap" /> + <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" /> + <param name="file_opt" value="none" /> + <output name="fileout" file="vcf2fastaAndHapmap-result1.hapmap" /> </test> <test> - <param name="filein" value="sample.vcf" /> - <param name="otpional.file_opt" value="fasta" /> - <param name="filefasta" value="reference.fa" /> - <output name="fileout" file="result2.hapmap" /> - <output name="fileout_seq" file="result2.flanking.txt" /> - <output name="fileout_fa1" file="result2.gene_alignment.fas" /> + <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" /> + <param name="file_opt" value="fasta" /> + <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" /> + <output name="fileout" file="vcf2fastaAndHapmap-result2.hapmap" /> + <output name="fileout_seq" file="vcf2fastaAndHapmap-result2.flanking.txt" /> + </test> + <test> + <param name="filein" value="vcf2fastaAndHapmap-sample.vcf" /> + <param name="file_opt" value="fasta_gff" /> + <param name="filefasta" value="vcf2fastaAndHapmap-reference.fa" /> + <param name="filegff" value="vcf2fastaAndHapmap-reference.gff" /> + <output name="fileout" file="vcf2fastaAndHapmap-result3.hapmap" /> + <output name="fileout_seq" file="vcf2fastaAndHapmap-result3.flanking.txt" /> + <output name="fileout_fa1" file="vcf2fastaAndHapmap-result3.gene_alignment.fas" /> </test> </tests> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 check_gwas_inputs/CheckGWASInputs.xml --- a/check_gwas_inputs/CheckGWASInputs.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/check_gwas_inputs/CheckGWASInputs.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -1,30 +1,40 @@ -<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.1"> +<tool id="check_GWAS_inputs" name="Check GWAS Inputs" version="1.0"> <description>checks concordance between input files for GWAS analysis</description> + + <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> + <requirements> + <requirement type="binary">perl</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> + <command interpreter="bash">./CheckGWASInputs.sh $hapmap $trait $out_hapmap $out_trait $stats </command> <inputs> - <param format="txt" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> - <param format="txt" name="trait" type="data" label="Trait file" help="Phenotypic file"/> + <param format="text" name="hapmap" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> + <param format="text" name="trait" type="data" label="Trait file" help="Phenotypic file"/> </inputs> <outputs> <data format="txt" name="out_hapmap" label="Hapmap output"/> <data format="txt" name="out_trait" label="Trait output"/> <data format="txt" name="stats" label="Logfile and statistics"/> </outputs> - <!-- [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> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- <test> + <param name="hapmap" value="gwas-hapmap" /> + <param name="trait" value="gwas-trait" /> + <output name="out_hapmap" file="gwas-result.hapmap" /> + <output name="out_trait" file="gwas-result.trait" /> + <output name="stats" file="gwas-result.stats" /> </test> ---> </tests> <help> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 egglib/CalculateDiversityIndexes.xml --- a/egglib/CalculateDiversityIndexes.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/egglib/CalculateDiversityIndexes.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -1,6 +1,11 @@ <tool id="calculate_diversity" name="Diversity by gene" version="2.1.6"> <description>calculates various diversity indexes with EggLib.</description> - <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log + <!-- [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> + <command interpreter="bash">./CalculateDiversityIndexes.sh $input $output $log </command> <inputs> <param format="fasta" name="input" type="data" label="Fasta alignment" help="..."/> @@ -9,20 +14,15 @@ <data format="txt" name="output" label="Diversity"/> <data format="txt" name="log" label="Logfile"/> </outputs> - <!-- [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> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- <test> + <param name="input" value="egglib-alignment.fa" /> + <output name="output" file="egglib-result.txt" /> </test> ---> </tests> <help> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 hapmap2mlmm/HapmapToMLMMFiles.xml --- a/hapmap2mlmm/HapmapToMLMMFiles.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/hapmap2mlmm/HapmapToMLMMFiles.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -1,6 +1,11 @@ <tool id="hapmap_to_mlmm_files" name="HapmapToMLMMFiles" version="1.1"> - <description>converts a hapmap file into MLMM input files</description> - <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot + <description>converts a hapmap file into MLMM input files</description> + <!-- [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> + <command interpreter="bash">./HapmapToMLMMFiles.sh $input $snp_info $genot </command> <inputs> <param format="txt" name="input" type="data" label="Allelic file in Hapmap format" help="Allelic file in Hapmap format"/> @@ -9,20 +14,17 @@ <data format="txt" name="snp_info" label="SNP Info file"/> <data format="txt" name="genot" label="Genotyping file for MLMM"/> </outputs> - <!-- [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> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- + <test> + <param name="input" value="hapmap2mlmm-hapmap" /> + <output name="snp_info" file="hapmap2mlmm-result_snp.hapmap" /> + <output name="genot" file="hapmap2mlmm-result_genot" /> </test> ---> </tests> <help> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 ped2bed/ped2bed.xml --- a/ped2bed/ped2bed.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/ped2bed/ped2bed.xml Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| @@ -3,7 +3,12 @@ <requirements> <requirement type="package" version="1.07">plink</requirement> </requirements> - <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs + <!-- [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> + <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs </command> <inputs> <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/> @@ -15,20 +20,18 @@ <data format="txt" name="bim" label="Bim file"/> <data format="txt" name="logs" label="All Logs"/> </outputs> - <!-- [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> <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> <tests> <!-- [HELP] Test files have to be in the ~/test-data directory --> <!-- [HELP] Multiple tests can be defined with different parameters --> -<!-- <test> + <param name="ped" value="ped2bed-input.ped" /> + <param name="map" value="ped2bed-input.map" /> + <output name="bed" file="ped2bed-result.bed" /> + <output name="fam" file="ped2bed-result.fam" /> + <output name="bim" file="ped2bed-result.bim" /> </test> ---> </tests> <help> |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/MDSplot-input.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MDSplot-input.map Tue Dec 15 05:18:02 2015 -0500 |
| b |
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| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/MDSplot-input.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MDSplot-input.ped Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,93 @@\n+IRAT112\t1\t0\t0\t1\t1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t1 1\t2 2\t1 1\t4 4\t1 1\t1 1\t4 4\t2 2\t4 4\t1 1\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t3 3\t4 4\t4 4\t2 2\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t2 2\t4 4\t2 2\t1 1\t1 1\t3 3\t3 3\t4 4\t4 4\t3 3\t3 3\t2 2\t1 1\t2 2\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t3 3\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t4 4\t4 4\t3 3\t4 4\t1 1\t3 3\t3 3\t3 3\t1 1\t2 2\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t3 3\t2 2\t3 3\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t2 2\t4 4\t4 4\t1 1\t4 4\t2 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4\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t3 3\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t2 2\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t3 3\t1 1\t2 2\t1 1\t1 1\t4 4\t4 4\t2 2\t1 1\t1 1\t2 2\t4 4\t1 1\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t3 3\t2 2\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t3 3\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t2 2\t4 4\t1 1\t3 3\t3 3\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t3 3\t1 1\t3 3\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3'..b' 1\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t3 3\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t2 2\t4 4\t1 1\t4 4\t1 1\t4 4\t2 2\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t3 3\t2 2\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t4 4\t1 1\t2 2\t4 4\t1 1\t3 3\t1 1\t1 1\t3 3\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t3 3\t3 3\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t3 3\t4 4\t3 3\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t4 4\t2 2\t2 2\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t4 4\t3 3\t1 1\t3 3\t3 3\t3 3\t4 4\t4 4\t2 2\t1 1\t2 2\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t2 2\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t2 2\t3 3\t4 4\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t2 2\t1 1\t3 3\t3 3\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t2 2\t4 4\t1 1\t2 2\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t3 3\t1 1\t4 4\t4 4\t3 3\t3 3\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t3 3\t3 3\t2 2\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t4 4\t4 4\t1 1\t3 3\t2 2\t2 2\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t3 3\t3 3\t1 1\t2 2\t2 2\t4 4\t2 2\t3 3\t1 1\t1 1\t3 3\t3 3\t1 1\t4 4\t1 1\t1 1\t3 3\t4 4\t2 2\t4 4\t4 4\t3 3\t2 2\t3 3\t3 3\t4 4\t4 4\t2 2\t2 2\t4 4\t2 2\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t3 3\t1 1\t1 1\t3 3\t1 1\t4 4\t3 3\t3 3\t1 1\t4 4\t1 1\t3 3\t3 3\t3 3\t1 1\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t3 3\t4 4\t1 1\t1 1\t2 2\t4 4\t3 3\t2 2\t3 3\t1 1\t1 1\t4 4\t4 4\t4 4\t3 3\t2 2\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t1 1\t1 1\t4 4\t1 1\t3 3\t1 1\t3 3\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t3 3\t3 3\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t2 2\t4 4\t2 2\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t2 2\t4 4\t1 1\t1 1\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t3 3\t4 4\t1 1\t4 4\t3 3\t3 3\t3 3\t1 1\t4 4\t3 3\t3 3\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t3 3\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t2 2\t4 4\t1 1\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t2 2\t3 3\t4 4\t2 2\t4 4\t4 4\t2 2\t1 1\t2 2\t1 1\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t3 3\t4 4\t2 2\t1 1\t2 2\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t3 3\t1 1\t1 1\t4 4\t4 4\t1 1\t2 2\t4 4\t1 1\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t4 4\t3 3\t3 3\t4 4\t4 4\t2 2\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t3 3\t4 4\t3 3\t4 4\t4 4\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t3 3\t2 2\t4 4\t4 4\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t2 2\t3 3\t2 2\t4 4\t1 1\t1 1\t4 4\t3 3\t2 2\t4 4\t2 2\t1 1\t3 3\t4 4\t1 1\t1 1\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t3 3\t4 4\t2 2\t4 4\t1 1\t1 1\t4 4\t2 2\t4 4\t4 4\t4 4\t3 3\t1 1\t1 1\t3 3\t1 1\t2 2\t1 1\t3 3\t2 2\t1 1\t2 2\t1 1\t1 1\t1 1\t2 2\t1 1\t4 4\t3 3\t1 1\t3 3\t1 1\t1 1\t3 3\t4 4\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t3 3\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t2 2\t4 4\t4 4\t1 1\t2 2\t4 4\t3 3\t4 4\t4 4\t4 4\t1 1\t3 3\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t1 1\t1 1\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t4 4\t1 1\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t2 2\t4 4\t3 3\t1 1\t2 2\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t1 1\t3 3\t1 1\t2 2\t3 3\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t3 3\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t3 3\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t3 3\t1 1\t1 1\t2 2\t4 4\t1 1\t1 1\t2 2\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/MDSplot-output.ibs_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MDSplot-output.ibs_matrix.txt Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,94 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/MDSplot-output.mds_plot.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/MDSplot-output.mds_plot.txt Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,93 @@ +Pop1 IRAT112 -0.0969382 0.0376036 +Pop1 IAC25 -0.0918126 0.0501177 +Pop1 IAC165 -0.104815 0.0453876 +Pop1 KARASUKARASURANKASU 0.107782 -0.0683546 +Pop1 DOURADOPRECOCE -0.0831697 0.0516412 +Pop1 CUIABANA 0.0327877 0.0497752 +Pop1 BICOBRANCO -0.0554177 0.0501857 +Pop1 CAAWA/FORTUNA6 -0.052355 0.0170584 +Pop1 CANELADEFERRO -0.0142283 0.0598394 +Pop1 CIRAD358 0.0497841 0.0645487 +Pop1 COLOMBIA1 -0.110347 -0.172742 +Pop1 CIRAD409 -0.113614 -0.105898 +Pop1 BAGANANASALAO 0.0247582 0.0186246 +Pop1 BAKUNGH 0.0199022 0.0613692 +Pop1 FOHISOMOTRA 0.0344309 0.0697592 +Pop1 KAKANI2 0.147713 -0.0780455 +Pop1 GUARANI -0.0892761 0.0387007 +Pop1 DOURADOAGULHA -0.0831373 0.0514523 +Pop1 IRAT13 -0.0757215 0.00312413 +Pop1 DAWASANRED 0.131309 -0.102364 +Pop1 GRAZI 0.0177091 0.0870472 +Pop1 IRAT144 0.0146443 0.0067734 +Pop1 IAC47 -0.0968934 0.0477667 +Pop1 MOROBEREKAN 0.0395544 0.0952695 +Pop1 IRAT362 -0.0921075 -0.00860852 +Pop1 GIZA171 0.14498 -0.0932001 +Pop1 IDSA77 -0.122827 -0.120219 +Pop1 IRAT216 -0.120205 -0.136803 +Pop1 IRAT177 -0.0762395 0.00230332 +Pop1 CHAPHUMA 0.149543 -0.0680637 +Pop1 CIRAD392 0.0187265 -0.047646 +Pop1 ARROZCEBADA 0.0110416 0.0787137 +Pop1 INDANE 0.108691 -0.0338065 +Pop1 DINORADO -0.00819237 0.0386578 +Pop1 63-104 -0.053974 -0.00204494 +Pop1 IR63380-16 -0.0968028 -0.0931822 +Pop1 CANAROXA -0.0756689 0.0253328 +Pop1 CICIHBETON 0.108857 0.142633 +Pop1 IR68704-145-1-1-B -0.103292 -0.071382 +Pop1 HAWMOM 0.129651 -0.0473323 +Pop1 IRAT364 -0.0118523 0.0472973 +Pop1 IRAT212 0.0231616 -0.00146178 +Pop1 KHAODAM 0.123936 -0.0654516 +Pop1 62667 -0.0752552 0.00278556 +Pop1 IRAT234 -0.0346607 0.0551203 +Pop1 NIPPONBARE_D 0.133199 -0.0963396 +Pop1 JUMULA2 0.104558 -0.0524994 +Pop1 CUBA65 -0.0124835 0.013679 +Pop1 BABER 0.090299 -0.0460696 +Pop1 CIRAD488 -0.0201481 -0.0262103 +Pop1 BENGALYVAKARINA 0.028631 0.0637662 +Pop1 ESPERANZA -0.108888 -0.00812147 +Pop1 BULUPANDAK 0.119762 0.143912 +Pop1 ARIAS 0.0327948 0.0827878 +Pop1 GOMPA2 0.133341 -0.0543414 +Pop1 CT13582-15-5-M -0.0922561 -0.0543988 +Pop1 IRAT335 -0.0886849 0.0522465 +Pop1 M202 0.13463 -0.106462 +Pop1 IR65907-188-1-B -0.0755893 -0.136821 +Pop1 IR71525-19-1-1 -0.0353444 0.0478985 +Pop1 CNA-7_BO_1_1_33-13-6-1 -0.0823478 -0.0435581 +Pop1 IRAT257 -0.0606191 0.0564989 +Pop1 IRAT109 -0.1006 -0.00959445 +Pop1 KANIRANGA 0.0705459 0.129888 +Pop1 IR66421-096-2-1-1 -0.00859728 -0.0570793 +Pop1 GOGO 0.0232414 0.0351889 +Pop1 GEMJYAJYANAM 0.170032 -0.0857315 +Pop1 DANGREY 0.175792 -0.113683 +Pop1 BINULAWAN -0.0208225 0.0611919 +Pop1 CAIAPO -0.0149329 -0.0122987 +Pop1 IGUAPECATETO -0.0740464 0.0552386 +Pop1 IRAT170 -0.0756928 0.00297643 +Pop1 IRAT380 -0.0210318 -0.00092536 +Pop1 ARAGUAIA -0.123443 0.0273298 +Pop1 GOGOLEMPAK 0.0598291 0.107462 +Pop1 JAOHAW 0.17563 -0.0587865 +Pop1 CHALOYOE 0.0904761 -0.0565325 +Pop1 GANIGI 0.0526286 0.0960475 +Pop1 GUNDILKUNING 0.116788 0.130234 +Pop1 IRAT2 -0.0762849 0.00262428 +Pop1 IRAT366 0.0273652 0.13551 +Pop1 IRAT104 -0.00310702 0.0636479 +Pop1 DAVAO -0.00538403 0.0564886 +Pop1 HD1-4 -0.0960109 0.0459137 +Pop1 CURINCA -0.128876 -0.121141 +Pop1 DAM 0.129029 -0.0660183 +Pop1 CIRAD403 -0.117849 -0.134651 +Pop1 JUMALI 0.123992 -0.0843623 +Pop1 JIMBRUKJOLOWORO 0.0549906 0.135017 +Pop1 GOGOLEMPUK 0.0597267 0.10733 +Pop1 CIRAD394 0.0040454 -0.0885135 +Pop1 IR63372-08 -0.0951857 -0.140804 +Pop1 IR60080-46A -0.0732581 0.0197832 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/SNPden-hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNPden-hapmap Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| b'@@ -0,0 +1,3584 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/SNPden-result.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNPden-result.txt Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,21 @@ +Chromosome Position SNPs +chr1 200000 355 +chr1 400000 228 +chr1 600000 63 +chr1 800000 191 +chr1 1000000 88 +chr1 1200000 90 +chr1 1400000 190 +chr1 1600000 267 +chr1 1800000 226 +chr1 2000000 163 +chr1 2200000 357 +chr1 2400000 132 +chr1 2600000 158 +chr1 2800000 104 +chr1 3000000 146 +chr1 3200000 331 +chr1 3400000 181 +chr1 3600000 36 +chr1 3800000 167 +chr1 4000000 110 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/SNPden-result_bysample.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNPden-result_bysample.txt Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,21 @@ +Chromosome BA58 BA59 BD54 +chr1 197 220 225 +chr1 119 130 133 +chr1 43 43 40 +chr1 167 139 141 +chr1 72 62 78 +chr1 76 35 38 +chr1 123 98 82 +chr1 205 133 135 +chr1 141 94 151 +chr1 116 112 117 +chr1 238 228 204 +chr1 95 86 96 +chr1 106 60 82 +chr1 74 60 64 +chr1 112 106 115 +chr1 220 199 228 +chr1 94 151 64 +chr1 32 18 27 +chr1 90 87 100 +chr1 75 54 47 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/egglib-alignment.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/egglib-alignment.fa Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,3232 @@\n+>Cc01g01120_ref_1\n+ATGGATTCTGTAGAAACCACCGAAAAACCCCATGCAGTCTTGGTTCCAATTCCAGCTCAAGGCCATGTTAGCCCATTAATGAGACTTGCCAAGCTTTTGCACGCAAAAAGGTTCCATATAACCTTCGTCAACACTGAATTAAATCACAAACGTTTGATCCGATCGAATGGGCCAGACTCAGTTAAAGGGTTCGATGATTTCAGGTTTGAGACTATCCCTGATGGGATGCCACCGTCAGATAAAGATGCCACTCAAGACGTGCCTCAGCTCTGTGATTCTTGCCCCCCAGTTAGTTGTGTGATTTCTGATGGTGGCATGCGCTTTGGCATCAAAGCTGCTGAAGATTTGGGCATCCCTGAAGTTCAATTCTGGACTGCTTCTGCTTGCTCTTTCATTGGATATTTGCACTACAGAGAGCTCATCAGGAGAGGGATTTTTCCATTCAAAAATGACGATTACCTTACAGATGGTACTCTTGATAAGCCTGTTGATTGGATTTGTGGCATGAGCAATGTAAAATTCAGGGACCTTCCAAGCTTTTTAAGAACAACAGATCCCAATGACATTATGTTTGATTTCATGGGAGAGGAAGCACAGAGTTGTCTGAAAGCTTCATCAATAATCTTCAATGCCTTCGATGAATTTGAAACAGAAGCATTGGAGGCAATCATTTCGAAGTTCAATTTCCCAAATATTTATACTATAGGCCCTCTACAGTTATTAGCGAGGCACATTGTTTCCAAAAGCCAAGTCAATTCCCTGAATTCAAGTTTATGGAAGCCTGACTCGAAAGTTTTCGAGTGGCTAGATCAAAGAGCACCAAACTCAATTGTTTATGTTAATTATGGAAGTGTAACAACCATGACTGACCATCATTTCAGAGAATTTGCTTGGGGACTTGCCAACAGCAGGCAACAGTTCTTGTGGATTGTGCGGCCTGATGTAGTGCAGGGAGGAGAATCAGCAATGTTGCCTGAAGATTTCCTGGAAGAGATTCAGGATAGAGGGTTCTTAACAAGCTGGTGTGCACAGGAGAAAGTCTTGGAGCATTCAGCTGTTCGCGCATTTTTGACACACTGTGGATGGAATTCTATGATGGAAACTATTTGTGCTGGTGTGCCTGTCATCTGTTGGCCTTTCTTTGCTGATCAGCAAACTAATTGTCATTACTCTTGTGAGAAATGGGAAATTGGAATGGAAATAAATCATGATGTGAAGCGCGATGAAGTTGCAGAACTTATACGCAAAATGATTGTGGGAGAGGAAGGGGAAAAAATGAGGTTCAAAGCTAAAGAATGGAAGAAGAAAGCTGACGAAGCAACTGAAGTAGGGGGATCATCTTACATTAATTTTGACAAGTTCATCAATGAGGCTCTTCATTACAAGGGATGA\n+>Cc01g01120_ref_2\n+ATGGATTCTGTAGAAACCACCGAAAAACCCCATGCAGTCTTGGTTCCAATTCCAGCTCAAGGCCATGTTAGCCCATTAATGAGACTTGCCAAGCTTTTGCACGCAAAAAGGTTCCATATAACCTTCGTCAACACTGAATTAAATCACAAACGTTTGATCCGATCGAATGGGCCAGACTCAGTTAAAGGGTTCGATGATTTCAGGTTTGAGACTATCCCTGATGGGATGCCACCGTCAGATAAAGATGCCACTCAAGACGTGCCTCAGCTCTGTGATTCTTGCCCCCCAGTTAGTTGTGTGATTTCTGATGGTGGCATGCGCTTTGGCATCAAAGCTGCTGAAGATTTGGGCATCCCTGAAGTTCAATTCTGGACTGCTTCTGCTTGCTCTTTCATTGGATATTTGCACTACAGAGAGCTCATCAGGAGAGGGATTTTTCCATTCAAAAATGACGATTACCTTACAGATGGTACTCTTGATAAGCCTGTTGATTGGATTTGTGGCATGAGCAATGTAAAATTCAGGGACCTTCCAAGCTTTTTAAGAACAACAGATCCCAATGACATTATGTTTGATTTCATGGGAGAGGAAGCACAGAGTTGTCTGAAAGCTTCATCAATAATCTTCAATGCCTTCGATGAATTTGAAACAGAAGCATTGGAGGCAATCATTTCGAAGTTCAATTTCCCAAATATTTATACTATAGGCCCTCTACAGTTATTAGCGAGGCACATTGTTTCCAAAAGCCAAGTCAATTCCCTGAATTCAAGTTTATGGAAGCCTGACTCGAAAGTTTTCGAGTGGCTAGATCAAAGAGCACCAAACTCAATTGTTTATGTTAATTATGGAAGTGTAACAACCATGACTGACCATCATTTCAGAGAATTTGCTTGGGGACTTGCCAACAGCAGGCAACAGTTCTTGTGGATTGTGCGGCCTGATGTAGTGCAGGGAGGAGAATCAGCAATGTTGCCTGAAGATTTCCTGGAAGAGATTCAGGATAGAGGGTTCTTAACAAGCTGGTGTGCACAGGAGAAAGTCTTGGAGCATTCAGCTGTTCGCGCATTTTTGACACACTGTGGATGGAATTCTATGATGGAAACTATTTGTGCTGGTGTGCCTGTCATCTGTTGGCCTTTCTTTGCTGATCAGCAAACTAATTGTCATTACTCTTGTGAGAAATGGGAAATTGGAATGGAAATAAATCATGATGTGAAGCGCGATGAAGTTGCAGAACTTATACGCAAAATGATTGTGGGAGAGGAAGGGGAAAAAATGAGGTTCAAAGCTAAAGAATGGAAGAAGAAAGCTGACGAAGCAACTGAAGTAGGGGGATCATCTTACATTAATTTTGACAAGTTCATCAATGAGGCTCTTCATTACAAGGGATGA\n+>Cc01g01120_BA55_1\n+ATGGATTCTGTAGAAACCACTGAAAAACCCCATGCAGTCTTGGTTCCAATTCCAGCTCAAGGCCATGTTAGCCCATTAATGAGACTTGCCAAGCTTTTGCACGCAAAAAGGTTCCATATAACCTT?GTCAACACTGAATT?AATCACAAACGTTTGATCCGATCGAA?GGGCCAGA?TCAGTTAAAGGGTTCGATGATTTCAGGTTTGAGACTATCCCTGATGGGATGCCACCGTCAGATAAAGATGCCACTCAAGACGTGCCTCAGCTCTGTGATTCTTGCCCCCCAGTTAGTTGTGTGATTTCTGATGGTGGCATGCGCTTTGGCATCAAAGCTGCTGAAGATTTGGGCATCCCTGAAGTTCAATTCTGGACTGCTTCTGCTTGCTCTTTCATTGGATATTTGCACTACAGAGAGCTCATCAGGAGAGGGATTTTTCCATTCAAAAATGACGATTACCTTACAGATGGTACTCTTGATAAGCCTGTTGATTGGATTTGTGGCATGAGCAATGTAAAATTCAGGGACCTTCCAAGCTTTTTAAGAACAACAGATCCCAATGACATTATGTTTGATTTCATGGGAGAGGAAGCACAGAGTTGTCTGAAAGCTTCATCAATAATCTTCAATGCCTTCGATGAATTTGAAACAGAAGCATTGGAGGCAATCATTTCGAAGTTCAATTTCCCAAATATTTATACTATAGGCCCTCTACAGTTATTAGCGAGGCACATTGTTTCCAAAAGCCAAGTCAATTCCCTGAATTCAAGTTTATGGAAGCCTGACTCGAAAGTTTTCGAGTGGCTAGATCAAAGAGCACCAAACTCAATTGTTTATGTTAATTATGGAAGTGTAACAACCATGACTGACCATCATTTCAGAGAATTTGCTTGGGGACTTGCCAACAGCAGGCAACAGTTCTTGTGGATTGTGCGGCCTGATGTAGTGCAGGGAGGAGAATCAGCAATG?TGCCTGAAGATTTCCTGGAAGAGATTCAGGATAGAGGGTTCTTAACAAGCTGGTGTGCACAGGAGAAAGTTTTGGAGCATTCAGCTGTTTGCGCATTTTTGACACACTGTGGATGGAATTCTATGATGGAAACTATTTGTGCTGGTGTGCCTGTCATCTGTTG'..b'GGTTTTCAAAGCCGACAATGTGCTGGACGAGCTCAACTATGAAAATCTTCGTCGGAAGGTGAAGTATCAAAATCAACTCACGAAAAAGAAGGTATTCTTCTGCTTTTCATTCTTTAATAAAATTGGTTTTCGTTGGAGGTTGGGTTCAATGATCAGGGAGATCAACACGAACCTTCAAAGTATCCATCTGGATGCGGAAGCTATGGGACTGGCCTACAAGCCCCTAGTTGAAGAAGCATTCNCTACAATTGCTGCTGGAGCCACAACAAGCCGACAGACCGACTCTAAGATTGTTCGAAGTGATGTCCTAGGAAGAGACGAGGATGAATCANAAATAGTTATGAAGTTGTTGACCGAATCTGAAAGTGATCGTATTTCAGTTATTTCCGTAACTGGCATGGGTGGTTTAGGCAAAACAACTCTGGCTAAAGCCGTTTACAACAATCCACAGTTTAATGATAATCATTTTGACAAAAAAATTTGGGTTTGTGTGGCTAAAGAAGTTGAAACCATGGATCTCTTCAAAATGATTCTAGAATCGTCAACAGGAAACAAGCCTGACGCGGATGTTAGGGACGTAATAGTTCGAGGAATTCAAAATGAAATCAAGGGAAAAAGATGTTTGCTTGTTCTTGACGATTTGTGGAATCATCAACAATTGGATGACTTTTTCACCACATTGAAGGCACTCGAAGCGAAGAAAGGGAGCTGGTGTCTTGTTACCACTCGTCTGCAAGAAGTGGAAACTACTCTGTCCGGTNTTCCGCAGATCAATTTTACTCGCCATGGGCTAGGAAAGCTATGCAATGATGATTGCTGGTCCATCATTAATAAATGGGCAACTGTAGGGGAAGAAGTACCAAAAGAATTGGAAGACATAAGGGAGCGAGTTTTAAGAAGATGTGACGGTCTACCTCTGGCAGCAAAGTTAATTGGAGGTTTGTTATATAAAAAGAGAAAAGAGGAGTGGCAATCTATTTTGGAGGAGAGTCTGTTGAATGGAGACCAAGGTCGGATCGAGCAAATAATTAAGGTGAGTTTTGATCATCTGTCACTTGCACCGGTTAAGAAATGTTTTGCATATTGCTCAATTTTTGATCAAGATGCTGAGTTGGAACAAGATCTACTAGTTGAGCTTTGGATGGCTGAAGGCTTTCTTCAACCGGATTCCCAAAATGAAAGAACGATGGAGAAAATAGGATGT\n+>Cc01g00010_j1_1\n+ATGGCTGATGCTGCTGTTAGTGCTACTATTAAGGTTGCATTGCAGG?GCTGAAGAAACTCGACAAATCTGCTGCAAGGATCCAATGCTTCTTGGCCGGTGCTGACGAGGCAAAATATTGCAATGATGCGAAGCTTCTACGGGTGCAATAATGGCTCAAGGATCTGGAAGAAGAGGTTTTCAAAGCCGACAATGTGCTGGACGAGCTCAACTATGAAAATCTTCGTCGGAAGGTGAAGTATCAAAATCAACTCACGAAAAAGAAGGTATTCTTCTGCTTTTCATTCTTTAATAAAATTGGTTTTCGTTGGAGGTTGGGTTCAATGATCAGGGAGATCAACACGAACCTTCAAAGTATCCATCCGGATGCTGAAGCTATGGGACTGGCCAACAAGCCCCTAGTTGAAGAAGCATTCTCTACAATTGCTGCTGGAGCCACAACAAGCCGACAGACCGACTCTAAGATTGTTCGAAGTGATGTCCTAGGAAGAGACGAGGATGAATCA?AAATAGTTATGAAGTTGTTGACCGAATCTGAAAGTGATCGTATTTCAGTTATTTCCGTAACTGGCATGGGTGGTTTAGGCAAAACAACTCTGGCTAAAGCCGTTTACAACAATCCACAGTTTAATGATAATCATTTTGACAAAAAAATTTGGGTTTGTGTGGCTAAAGAAGTTGAAACCATGGATCTCTTCAAAATGATTCTAGAATCGTCAACAGGAAACAAGCCTGACGCGGATGTTAGGGACGTAATAGTTCGAGGAATTCAAAATGAAATCAAGGGAAAAAGATGTTTGCTTGTTCTTGACGATTTGTGGAATCATCAACAATTGGATGACTTTTTCACCACATTGAAGGCACTCGAAGCGAAGAAAGGGAGCTGGTGTCTTGTTACCACTCGTCTGCAAGAAGTGGAAACTACTCTGTCCGGTGTTCCGCAGATCAATTTTACTCGCCATGGGCTAGGAAAGCTATGCAATGATGATTGCTGGTCCATCATTAATAAATGGGCAACTGTAGGGGAAGAAGTACCAAAAGAATTGGAAGACATAAGGGAGCGAGTTTTAAGAAGATGTGACGGTCTACCTCTGGCAGCAAAGTTAATTGGAGGTTTGTTATATAAAAAGAGAAAAGAGGAGTGGCAATCTATTTTGGAGGAGAGTCTGTTGAATGGAGACCAAGGTCGGATCGAGCAAATAATTAAGGTGAGTTTTGATCATCTGTCACTTGCACCGGTTAAGAAATGTTTTGCATATTGCTCAATTTTTGATCAAGATGCTGAGTTGGAACAAGATCTACTAGTTGAGCTTTGGATGGCTGAAGGCTTTCTTCAACCGGATTCCCAAAATGAAAGAACGATGGAGAAAATAGGATGT\n+>Cc01g00010_j1_2\n+ATGGCTGATGCTGCTGTTAGTGCTACTATTAAGGTTGCATTGCAGGNGCTGAAGAAACTCGACAAATCTGCTGCAAGGATCCAATGCTTCTTGGCCGGTGCTGACGAGGCAAAATATTGCAATGATGCGAAGCTTCTACGGGTGCAATAATGGCTCAAGGATCTGGAAGAAGAGGTTTTCAAAGCCGACAATGTGCTGGACGAGCTCAACTATGAAAATCTTCGTCGGAAGGTGAAGTATCAAAATCAACTCACGAAAAAGAAGGTATTCTTCTGCTTTTCATTCTTTAATAAAATTGGTTTTCGTTGGAGGTTGGGTTCAATGATCAGGGAGATCAACACGAACCTTCAAAGTATCCATCCGGATGCTGAAGCTATGGGACTGGCCAACAAGCCCCTAGTTGAAGAAGCATTCTCTACAATTGCTGCTGGAGCCACAACAAGCCGACAGACCGACTCTAAGATTGTTCGAAGTGATGTCCTAGGAAGAGACGAGGATGAATCANAAATAGTTATGAAGTTGTTGACCGAATCTGAAAGTGATCGTATTTCAGTTATTTCCGTAACTGGCATGGGTGGTTTAGGCAAAACAACTCTGGCTAAAGCCGTTTACAACAATCCACAGTTTAATGATAATCATTTTGACAAAAAAATTTGGGTTTGTGTGGCTAAAGAAGTTGAAACCATGGATCTCTTCAAAATGATTCTAGAATCGTCAACAGGAAACAAGCCTGACGCGGATGTTAGGGACGTAATAGTTCGAGGAATTCAAAATGAAATCAAGGGAAAAAGATGTTTGCTTGTTCTTGACGATTTGTGGAATCATCAACAATTGGATGACTTTTTCACCACATTGAAGGCACTCGAAGCGAAGAAAGGGAGCTGGTGTCTTGTTACCACTCGTCTGCAAGAAGTGGAAACTACTCTGTCCGGTGTTCCGCAGATCAATTTTACTCGCCATGGGCTAGGAAAGCTATGCAATGATGATTGCTGGTCCATCATTAATAAATGGGCAACTGTAGGGGAAGAAGTACCAAAAGAATTGGAAGACATAAGGGAGCGAGTTTTAAGAAGATGTGACGGTCTACCTCTGGCAGCAAAGTTAATTGGAGGTTTGTTATATAAAAAGAGAAAAGAGGAGTGGCAATCTATTTTGGAGGAGAGTCTGTTGAATGGAGACCAAGGTCGGATCGAGCAAATAATTAAGGTGAGTTTTGATCATCTGTCACTTGCACCGGTTAAGAAATGTTTTGCATATTGCTCAATTTTTGATCAAGATGCTGAGTTGGAACAAGATCTACTAGTTGAGCTTTGGATGGCTGAAGGCTTTCTTCAACCGGATTCCCAAAATGAAAGAACGATGGAGAAAATAGGATGT\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/egglib-result.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/egglib-result.txt Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,101 @@ +Cc01g00550;16;2241;2234;20;0.00269799;0.00199194;-1.05268;9;0.766667;4.45;0;1; +Cc01g00100;16;1449;1449;21;0.00436762;0.00538302;0.938842;15;0.991667;7.8;0;1; +Cc01g00150;16;435;435;4;0.00277118;0.00189655;-0.987408;5;0.608333;0.825;0;1; +Cc01g00630;16;477;476;1;0.000633121;0.000262605;-1.16221;2;0.125;0.125;0;1; +Cc01g00640;16;1776;1768;1;0.000170456;0.000296946;1.4737;2;0.525;0.525;0;1; +Cc01g00590;16;1926;1900;0;0;0;0;1;0;0;0;0; +Cc01g00190;16;1002;1002;19;0.00571452;0.00611277;0.279144;15;0.991667;6.125;0;1; +Cc01g00830;16;258;257;2;0.00234526;0.00304799;0.766969;4;0.591667;0.783333;0;1; +Cc01g00900;16;297;294;37;0.037927;0.036763;-0.128356;15;0.991667;10.8083;0;1; +Cc01g00950;16;2205;2181;18;0.0024872;0.00238423;-0.165045;12;0.958333;5.2;0;1; +Cc01g00490;16;372;368;0;0;0;0;1;0;0;0;0; +Cc01g00880;16;453;448;1;0.000672691;0.000520833;-0.448318;2;0.233333;0.233333;0;1; +Cc01g00020;16;513;512;0;0;0;0;1;0;0;0;0; +Cc01g00230;16;2391;2383;2;0.00025293;0.000391663;1.40398;3;0.666667;0.933333;0;1; +Cc01g00720;16;1155;1145;47;0.0123705;0.015313;1.00513;11;0.941667;17.5333;0;1; +Cc01g00890;16;492;482;2;0.00125048;0.000968188;-0.57783;3;0.433333;0.466667;0;1; +Cc01g00480;16;168;166;13;0.0236009;0.0287651;0.843861;11;0.95;4.775;0;1; +Cc01g00980;16;1230;1230;14;0.00343018;0.00278455;-0.731942;5;0.708333;3.425;0;1; +Cc01g00090;16;291;291;5;0.0051781;0.0045819;-0.379442;3;0.433333;1.33333;0;1; +Cc01g00440;16;3468;3437;0;0;0;0;1;0;0;0;0; +Cc01g00050;16;189;189;7;0.0111617;0.0112434;0.0257909;7;0.85;2.125;0;1; +Cc01g00320;16;636;636;15;0.00710768;0.00408805;-1.66425;10;0.9;2.6;0;1; +Cc01g00750;16;240;239;0;0;0;0;1;0;0;0;0; +Cc01g00220;16;1176;1176;8;0.00205011;0.0017432;-0.539708;8;0.833333;2.05;0;1; +Cc01g00460;16;876;874;0;0;0;0;1;0;0;0;0; +Cc01g01040;16;2742;2742;44;0.00483592;0.00457999;-0.223048;14;0.975;12.5583;0;1; +Cc01g00770;16;354;353;12;0.0102447;0.00880548;-0.536657;7;0.841667;3.10833;0;1; +Cc01g00910;16;1482;1466;11;0.00226127;0.00244998;0.315288;10;0.9;3.59167;0;1; +Cc01g00280;16;1155;1155;21;0.00547937;0.00427128;-0.890361;11;0.933333;4.93333;0;1; +Cc01g00710;16;378;377;11;0.00879316;0.00705128;-0.748416;4;0.658333;2.65833;0;1; +Cc01g01050;16;1524;1523;12;0.00237452;0.00327752;1.45271;11;0.941667;4.99167;0;1; +Cc01g00820;16;2988;2987;26;0.0026232;0.00295447;0.517834;9;0.908333;8.825;0;1; +Cc01g00760;16;438;437;0;0;0;0;1;0;0;0;0; +Cc01g00840;16;894;883;2;0.000682595;0.000736127;0.200738;3;0.575;0.65;0;1; +Cc01g00130;16;465;465;5;0.00324049;0.0040681;0.841663;7;0.8;1.89167;0;1; +Cc01g00160;16;2493;2463;58;0.00709671;0.00749763;0.240477;15;0.991667;18.4667;0;1; +Cc01g01120;16;1392;1385;3;0.000652777;0.000854392;0.895369;4;0.691667;1.18333;0;1; +Cc01g00690;16;720;714;0;0;0;0;1;0;0;0;0; +Cc01g00510;16;324;323;0;0;0;0;1;0;0;0;0; +Cc01g01010;16;1806;1806;20;0.00333738;0.00398671;0.782639;10;0.933333;7.2;0;1; +Cc01g00970;16;2469;2469;42;0.00512651;0.00607196;0.775775;13;0.966667;14.9917;0;1; +Cc01g01000;16;1809;1809;22;0.00366503;0.00515018;1.64226;10;0.925;9.31667;0;1; +Cc01g00060;16;654;654;5;0.00230402;0.00271407;0.586507;5;0.608333;1.775;0;1; +Cc01g00040;16;1383;1359;0;0;0;0;1;0;0;0;0; +Cc01g00610;16;1722;1699;21;0.00372494;0.00321267;-0.555361;11;0.875;5.45833;0;1; +Cc01g00500;16;510;507;6;0.00356646;0.00368179;0.110691;6;0.833333;1.86667;0;1; +Cc01g00740;16;1662;1662;3;0.000543981;0.000491376;-0.280343;4;0.591667;0.816667;0;1; +Cc01g00870;16;369;369;4;0.00326684;0.00264228;-0.598115;4;0.525;0.975;0;1; +Cc01g00860;16;1350;1350;8;0.00178587;0.00160494;-0.365251;9;0.883333;2.16667;0;1; +Cc01g00620;16;1497;1480;4;0.000814502;0.000546171;-1.03066;5;0.666667;0.808333;0;1; +Cc01g00990;16;579;579;3;0.00156148;0.0011802;-0.707875;4;0.591667;0.683333;0;1; +Cc01g00520;16;2988;2951;9;0.000919109;0.000739862;-0.716259;9;0.85;2.18333;0;1; +Cc01g00350;16;822;822;11;0.00403287;0.00408556;0.0493619;10;0.916667;3.35833;0;1; +Cc01g01060;16;390;390;10;0.00772732;0.00786325;0.0656036;8;0.875;3.06667;0;1; +Cc01g00410;16;324;320;10;0.00941767;0.00630208;-1.23382;6;0.716667;2.01667;0;1; +Cc01g00330;16;5265;5265;72;0.00412124;0.00378443;-0.350038;15;0.991667;19.925;0;1; 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| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/gwas-hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gwas-hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,3093 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tGG\tGG\tGG\tGG\tGG\tGG\tCC\tCC\tCC\tGG\tGG\tCC\tCC\tNN\tCC\tCC\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tCC\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/gwas-result.hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gwas-result.hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,2953 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/gwas-result.stats --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gwas-result.stats Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,14 @@ +============================================== +Individuals +============================================== +Individuals in hapmap file: 281 +Individuals in trait file: 301 +Individuals found in both files: 279 +============================================== +Markers +============================================== +Discarded markers: +Monomorphic: 140 +Not biallelic: 0 +Modified markers: +Difference in variation: 47 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/gwas-result.trait --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gwas-result.trait Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,280 @@ +<Trait> EarHT dpoll EarDia +CML287 95 75 37.24 +CML311 89.25 -999 -999 +MO24W 101.5 67.5 45.51175 +NC368 64.5 69 42.06567 +IDS69 44 65 24.88225 +CML77 63 68.5 43.716 +CI187-2 62.63 70.5 34.085 +CI7 84.67 68.5 37.889 +WD 48.5 62.5 30.479 +NC314 58 66 36.278 +NC358 41 63 35.785 +IDS28 71.5 63 31.358 +HP301 62 61.5 27.158 +DE3 70 65 44.496 +OH43E 31.5 61 37.124 +NC302 53 67.5 36.349 +CM174 34.5 64 32.9705 +E2558W 59.5 67.5 37.38 +NC342 68 64.5 35.18633 +NC318 72 72 31.811 +CML238 57.5 74 42.477 +H95 55 65.5 38.834 +L317 98 65.5 34.72825 +F44 94 75 36.49875 +CML103 88.5 69 42.029 +A680 68 65.5 41.152 +B75 56 62 38.2075 +4722 81.13 71.5 32.421 +B103 37 57.5 -999 +B14A 57 63.5 38.067 +R229 76 67 43.504 +CO106 34.5 55 -999 +TZI8 89.5 72.5 41.56075 +NC338 71.5 70 33.97 +KY228 58.38 75.5 -999 +IL677A 45.5 64.5 36.276 +TZI25 82 72.5 38.817 +A654 39 64 -999 +U267Y 53.5 75.5 35.491 +H91 60 64.5 39.201 +B109 67 64 38.951 +NC354 67 71.5 32.8105 +KI2021 107 75 40.14633 +CML277 82.5 75 39.036 +TZI16 76.75 74 41.737 +NC306 62.88 68 34.54667 +CML264 60.5 82 -999 +CI21E 64 68 40.991 +NC222 84.5 70.5 37.047 +CML91 64.5 69.5 39.435 +VA17 49 63.5 34.376 +A554 38.5 66 33.41775 +MO1W 62 65 42.972 +CO125 32.13 60 31.788 +OH40B 51.5 67.5 34.962 +B97 53 60.5 37.665 +CI64 64.5 70.5 41.403 +CML38 82.5 75.5 32.36083 +B57 41 65 37.87475 +EP1 37.08 62 -999 +CM7 28 61.5 31.667 +MO45 74.33 65.5 35.389 +NC232 55 68.5 44.877 +KI43 59 76 30.326 +B68 65 71.5 38.889 +A635 37 64 35.3005 +A632 60 61 35.953 +IL14H 46 61 34.999 +K55 43 67.5 39.8425 +NC350 49.5 69.5 32.829 +CML228 74 72.5 31.339 +CML322 66.75 68 40.0235 +CMV3 32.5 59.5 -999 +NC260 52.5 63 35.866 +R109B 45 65 -999 +YU796NS 56.5 64 40.755 +K148 42 65.5 33.984 +4226 65.5 59.5 32.21933 +SC357 55.5 74.5 34.858 +W182B 46 62.5 31.492 +GA209 76.33 74.5 34.958 +NC320 83 71.5 41.711 +AB28A 73.5 78 32.504 +CML108 55.5 71.5 40.739 +CML314 81.5 69 38.929 +VAW6 38 62.5 35.685 +F2834T 40 62 33.28333 +B115 68 65.5 37.05975 +CML157Q 111.5 71.5 40.303 +TX303 102 71 41.5 +OH43 45 61 37.77 +MO46 54.5 65 39.526 +VA22 62.5 66 36.168 +SD40 46.5 60 38.5555 +SG18 88.5 63.5 29.78 +R177 31 61 38.019 +MT42 44.5 59 29.971 +H84 48 64 41.838 +C49A 22.5 57 28.544 +KI14 95.5 78 29.192 +NC264 48 65 38.303 +MS71 47.5 57 35.358 +CML11 97.25 80.5 33.48683 +SC55 128 75 41.88 +B77 50 65 39.028 +HY 56.5 64.5 34.823 +NC258 60.5 70 36.866 +P39 43.5 64 35.394 +A641 54.5 66 33.727 +B37 72.5 65.5 36.4475 +CH701-30 61 60 33.5835 +VA102 47.5 65 -999 +NC298 62 72.5 29.191 +MP339 71.5 71.5 38.333 +N28HT 57 66.5 41.431 +C123 32 62.5 -999 +T232 73.5 70 35.651 +NC360 56 71.5 37.205 +CML92 68 71.5 40.503 +T8 87.75 70.5 35.29 +OS420 66 60.5 39.417 +NC346 62 68 36.276 +NC238 43 78 38.29429 +VA99 56 67.5 40.421 +CML323 63 70.5 39.081 +IA2132 43 67 35.154 +A272 35.63 70 -999 +CML247 68.5 78 37.79683 +A661 51.5 59 39.323 +TZI18 79.38 70 39.82575 +VA26 41 61 37.617 +CI90C 63.5 67.5 33.92475 +SD44 39 61.5 36.73775 +CML333 97.5 69 36.581 +NC310 60.5 65 41.4595 +MO47 36.5 59 35.91767 +TZI11 75.5 71.5 32.988 +NC356 56 66.5 34.34075 +CML328 74.5 65 34.876 +NC366 58 72.5 35.826 +DE1 64.5 69 44.774 +K64 69.25 67.5 42.828 +NC230 57 70 43.833 +A556 28 65 31.929 +NC300 68 70 42.694 +CI3A 66.5 70 44.051 +PA762 50.5 67 37.828 +A682 47 57.5 35.928 +B164 66 58 35.562 +B10 74 69 36.561 +MO18W 65.5 70.5 39.596 +C103 52.5 66.5 34.91575 +WF9 52 64.5 36.61475 +CML10 110 77 33.33867 +KI44 55 71 33.19267 +NC294 74 66.5 38.888 +SA24 60.5 65 29.11575 +KI21 87.5 70.5 40.063 +M162W 63.5 74.5 40.095 +NC296A 59.5 68.5 38.211 +CML341 94.63 73 42.116 +KY226 64 72.5 37.37125 +GT112 136 78.5 -999 +A441-5 53.5 67.5 35.008 +NC324 56.5 68 33.9025 +B104 56.25 64.5 44.773 +N6 45 61 39.82533 +PA875 67 65.5 40.87967 +NC250 37 64 36.44 +KI11 63 74.5 40.465 +F6 101.5 77 -999 +SC213R 67 76 34.337 +NC262 25 59 37.31 +NC290A 34 61.5 40.5525 +D940Y 74 71.5 34.624 +W22 44 63.5 36.041 +I29 54 63 31.407 +NC236 58 72.5 36.2865 +M37W 62.88 70 38.801 +VA35 52 63 40.0005 +CO255 38 61.5 32.06183 +A634 54 59 35.601 +CML218 62 69 35.57 +CML158Q 74 74.5 41.6995 +F7 27.5 58 27.689 +CML220 44 63.5 40.216 +CML14 80 82 30.863 +TX601 87.63 78.5 42.91188 +CML331 59 77 -999 +CM37 24 57.5 25.74375 +MO17 46 59.5 33.672 +R168 57.92 64.5 28.88775 +NC304 8 65 -999 +CML5 94.25 78 -999 +B79 66.5 66.5 41.61 +VA59 36.5 60.5 37.58 +CML52 104.33 81 32.69017 +CML254 70 -999 -999 +M14 35 59.5 35.6355 +B73 83.25 70 41.633 +CH9 41.5 67.5 38.90333 +NC336 50.5 75.5 34.172 +A6 109.5 80.5 31.5175 +NC340 60.5 65.5 38.974 +CI91B 49 66.5 35.53867 +A679 65 66 42.471 +NC328 60 66 37.45 +MOG 87.88 65 42.585 +IDS91 41 62.5 27.553 +VA14 56 66.5 36.955 +B105 67.5 68 39.857 +ND246 32.5 54.5 28.935 +A214N 65 69 32.006 +R4 48 67 37.284 +KY21 76.5 70.5 38.93467 +33-16 64.75 64.5 -999 +W64A 59.5 62.5 35.982 +MS153 55 59 42.406 +CI31A 74 73 -999 +K4 70 69 36.81433 +CI28A 72.5 66.5 37.328 +H99 31 68.5 34.677 +IL101 31.5 65 32.357 +CML69 76 73.5 37.723 +N192 42.5 57.5 40.355 +CML258 133 81 37.02083 +CI66 47 75 32.5045 +OH603 48.5 65.5 -999 +A659 46.5 58.5 38.84617 +B73HTRHM 73 67 42.956 +NC344 63.5 70.5 38.60725 +KI3 57.75 72 34.7015 +38-11 92.25 68.5 37.897 +MO44 46 57.5 38.022 +B46 42 69 40.699 +L578 101.5 72.5 39.627 +A239 47.88 61 36.064 +CML261 104.17 77 37.46267 +A619 36 61 40.63 +NC362 51.5 63 38.849 +MEF156-55-2 62.5 -999 -999 +B52 72.5 70 -999 +N7A 54.5 63.5 41.767 +I205 55 66 -999 +CML332 66.5 70.5 37.182 +B84 72 67.5 37.622 +VA85 66 62.5 37.304 +NC296 68.5 67 38.83125 +CML45 45 82.5 -999 +B76 53 61.5 35.33575 +NC352 53.5 72 35.537 +DE2 57.5 65.5 46.353 +NC348 73 67 31.202 +H49 58 61.5 39.416 +I137TN 56.5 69 -999 +NC326 88 67 41.2355 +OH7B 87 72.5 37.535 +B64 74.5 68.5 37.221 +MS1334 54.5 66 30.83556 +NC364 48.5 64.5 38.6825 +PA91 63 68.5 36.12175 +PA880 69.5 64.5 -999 +W117HT 31 66 23.72333 +IA5125 29.5 64 29.7525 +B2 39.5 70 -999 +T234 63.08 68.5 39.432 +CM105 31.5 65.5 36.218 +DE811 80 72.5 35.45125 +CML321 82 79.5 39.339 +HI27 93.5 71 35.425 +NC33 101 72 36.104 +W153R 27.5 66 -999 +TZI9 79 72 40.403 +A188 27.5 62 31.419 +H105W 44.5 61.5 40.51 +TZI10 81 78 33.84983 +SG1533 82.5 62.5 33.8 +CML281 73.5 81 -999 +CML154Q 61 72.5 42.933 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/gwas-trait --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gwas-trait Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,302 @@ +<Trait> EarHT dpoll EarDia +811 59.5 -999 -999 +33-16 64.75 64.5 -999 +38-11 92.25 68.5 37.897 +4226 65.5 59.5 32.21933 +4722 81.13 71.5 32.421 +A188 27.5 62 31.419 +A214N 65 69 32.006 +A239 47.88 61 36.064 +A272 35.63 70 -999 +A441-5 53.5 67.5 35.008 +A554 38.5 66 33.41775 +A556 28 65 31.929 +A6 109.5 80.5 31.5175 +A619 36 61 40.63 +A632 60 61 35.953 +A634 54 59 35.601 +A635 37 64 35.3005 +A641 54.5 66 33.727 +A654 39 64 -999 +A659 46.5 58.5 38.84617 +A661 51.5 59 39.323 +A679 65 66 42.471 +A680 68 65.5 41.152 +A682 47 57.5 35.928 +AB28A 73.5 78 32.504 +B10 74 69 36.561 +B103 37 57.5 -999 +B104 56.25 64.5 44.773 +B105 67.5 68 39.857 +B109 67 64 38.951 +B115 68 65.5 37.05975 +B14A 57 63.5 38.067 +B164 66 58 35.562 +B2 39.5 70 -999 +B37 72.5 65.5 36.4475 +B46 42 69 40.699 +B52 72.5 70 -999 +B57 41 65 37.87475 +B64 74.5 68.5 37.221 +B68 65 71.5 38.889 +B73 83.25 70 41.633 +B73HTRHM 73 67 42.956 +B75 56 62 38.2075 +B76 53 61.5 35.33575 +B77 50 65 39.028 +B79 66.5 66.5 41.61 +B84 72 67.5 37.622 +B97 53 60.5 37.665 +C103 52.5 66.5 34.91575 +C123 32 62.5 -999 +C49 22 55.5 32.93267 +C49A 22.5 57 28.544 +CH701-30 61 60 33.5835 +CH9 41.5 67.5 38.90333 +CI187-2 62.63 70.5 34.085 +CI21E 64 68 40.991 +CI28A 72.5 66.5 37.328 +CI31A 74 73 -999 +CI3A 66.5 70 44.051 +CI44 57 73 40.172 +CI64 64.5 70.5 41.403 +CI66 47 75 32.5045 +CI7 84.67 68.5 37.889 +CI90C 63.5 67.5 33.92475 +CI91B 49 66.5 35.53867 +CM105 31.5 65.5 36.218 +CM174 34.5 64 32.9705 +CM37 24 57.5 25.74375 +CM7 28 61.5 31.667 +CML10 110 77 33.33867 +CML103 88.5 69 42.029 +CML108 55.5 71.5 40.739 +CML11 97.25 80.5 33.48683 +CML14 80 82 30.863 +CML154Q 61 72.5 42.933 +CML157Q 111.5 71.5 40.303 +CML158Q 74 74.5 41.6995 +CML218 62 69 35.57 +CML220 44 63.5 40.216 +CML228 74 72.5 31.339 +CML238 57.5 74 42.477 +CML247 68.5 78 37.79683 +CML254 70 -999 -999 +CML258 133 81 37.02083 +CML261 104.17 77 37.46267 +CML264 60.5 82 -999 +CML277 82.5 75 39.036 +CML281 73.5 81 -999 +CML287 95 75 37.24 +CML311 89.25 -999 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61.5 27.158 +HY 56.5 64.5 34.823 +I137TN 56.5 69 -999 +I205 55 66 -999 +I29 54 63 31.407 +IA2132 43 67 35.154 +IA5125 29.5 64 29.7525 +IDS28 71.5 63 31.358 +IDS69 44 65 24.88225 +IDS91 41 62.5 27.553 +IL101 31.5 65 32.357 +IL14H 46 61 34.999 +IL677A 45.5 64.5 36.276 +K148 42 65.5 33.984 +K4 70 69 36.81433 +K55 43 67.5 39.8425 +K64 69.25 67.5 42.828 +KI11 63 74.5 40.465 +KI14 95.5 78 29.192 +KI2021 107 75 40.14633 +KI21 87.5 70.5 40.063 +KI3 57.75 72 34.7015 +KI43 59 76 30.326 +KI44 55 71 33.19267 +KI2007 61 67.5 37.622 +KY21 76.5 70.5 38.93467 +KY226 64 72.5 37.37125 +KY228 58.38 75.5 -999 +L317 98 65.5 34.72825 +L578 101.5 72.5 39.627 +M14 35 59.5 35.6355 +M162W 63.5 74.5 40.095 +M37W 62.88 70 38.801 +MEF15655 -999 65 -999 +MEF156-55-2 62.5 -999 -999 +MO17 46 59.5 33.672 +MO18W 65.5 70.5 39.596 +MO1W 62 65 42.972 +MO24W 101.5 67.5 45.51175 +MO44 46 57.5 38.022 +MO45 74.33 65.5 35.389 +MO46 54.5 65 39.526 +MO47 36.5 59 35.91767 +MOG 87.88 65 42.585 +MP339 71.5 71.5 38.333 +MS1334 54.5 66 30.83556 +MS153 55 59 42.406 +MS71 47.5 57 35.358 +MT42 44.5 59 29.971 +N192 42.5 57.5 40.355 +N28HT 57 66.5 41.431 +N6 45 61 39.82533 +N7A 54.5 63.5 41.767 +NC222 84.5 70.5 37.047 +NC230 57 70 43.833 +NC232 55 68.5 44.877 +NC236 58 72.5 36.2865 +NC238 43 78 38.29429 +NC250 37 64 36.44 +NC258 60.5 70 36.866 +NC260 52.5 63 35.866 +NC262 25 59 37.31 +NC264 48 65 38.303 +NC268 74.38 69.5 32.867 +NC290A 34 61.5 40.5525 +NC292 55.5 65.5 42.8125 +NC294 74 66.5 38.888 +NC296 68.5 67 38.83125 +NC296A 59.5 68.5 38.211 +NC298 62 72.5 29.191 +NC300 68 70 42.694 +NC302 53 67.5 36.349 +NC304 8 65 -999 +NC306 62.88 68 34.54667 +NC308 59.63 66 39.408 +NC310 60.5 65 41.4595 +NC312 67.5 69.5 38.0875 +NC314 58 66 36.278 +NC316 85.38 69 42.321 +NC318 72 72 31.811 +NC320 83 71.5 41.711 +NC322 77.5 71.5 33.15975 +NC324 56.5 68 33.9025 +NC326 88 67 41.2355 +NC328 60 66 37.45 +NC33 101 72 36.104 +NC330 70 70 42.79525 +NC332 76.5 71 34.923 +NC334 80.5 70.5 33.938 +NC336 50.5 75.5 34.172 +NC338 71.5 70 33.97 +NC340 60.5 65.5 38.974 +NC342 68 64.5 35.18633 +NC344 63.5 70.5 38.60725 +NC346 62 68 36.276 +NC348 73 67 31.202 +NC350 49.5 69.5 32.829 +NC352 53.5 72 35.537 +NC354 67 71.5 32.8105 +NC356 56 66.5 34.34075 +NC358 41 63 35.785 +NC360 56 71.5 37.205 +NC362 51.5 63 38.849 +NC364 48.5 64.5 38.6825 +NC366 58 72.5 35.826 +NC368 64.5 69 42.06567 +NC370 70.63 72.5 42.082 +NC372 69 68 42.281 +ND246 32.5 54.5 28.935 +OH40B 51.5 67.5 34.962 +OH43 45 61 37.77 +OH43E 31.5 61 37.124 +OH603 48.5 65.5 -999 +OH7B 87 72.5 37.535 +OS420 66 60.5 39.417 +P39 43.5 64 35.394 +PA762 50.5 67 37.828 +PA875 67 65.5 40.87967 +PA880 69.5 64.5 -999 +PA91 63 68.5 36.12175 +Q6199 -999 85 -999 +R109B 45 65 -999 +R168 57.92 64.5 28.88775 +R177 31 61 38.019 +R229 76 67 43.504 +R4 48 67 37.284 +SA24 60.5 65 29.11575 +SC213R 67 76 34.337 +SC357 55.5 74.5 34.858 +SC55 128 75 41.88 +SD40 46.5 60 38.5555 +SD44 39 61.5 36.73775 +SG1533 82.5 62.5 33.8 +SG18 88.5 63.5 29.78 +T232 73.5 70 35.651 +T234 63.08 68.5 39.432 +T8 87.75 70.5 35.29 +TX303 102 71 41.5 +TX601 87.63 78.5 42.91188 +TZI10 81 78 33.84983 +TZI11 75.5 71.5 32.988 +TZI16 76.75 74 41.737 +TZI18 79.38 70 39.82575 +TZI25 82 72.5 38.817 +TZI8 89.5 72.5 41.56075 +TZI9 79 72 40.403 +U267Y 53.5 75.5 35.491 +VA102 47.5 65 -999 +VA14 56 66.5 36.955 +VA17 49 63.5 34.376 +VA22 62.5 66 36.168 +VA26 41 61 37.617 +VA35 52 63 40.0005 +VA59 36.5 60.5 37.58 +VA85 66 62.5 37.304 +VA99 56 67.5 40.421 +VAW6 38 62.5 35.685 +W117HT 31 66 23.72333 +W153R 27.5 66 -999 +W182B 46 62.5 31.492 +W22 44 63.5 36.041 +W401 35.5 58.5 35.40125 +W64A 59.5 62.5 35.982 +WD 48.5 62.5 30.479 +WF9 52 64.5 36.61475 +YU796NS 56.5 64 40.755 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/hapmap2mlmm-hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hapmap2mlmm-hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,3093 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tGG\tGG\tGG\tGG\tGG\tGG\tCC\tCC\tCC\tGG\tGG\tCC\tCC\tNN\tCC\tCC\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tCC\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tNN\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\tGG\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/hapmap2mlmm-result_genot --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hapmap2mlmm-result_genot Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,282 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\t0\t0\t0\t0\t0\t2\t0\t0\t0\t2\t0\t0\tNA\t0\tNA\t0\t0\t0\t2\t2\t0\t0\t2\t2\tNA\t0\t2\t2\t0\t2\t0\t0\t2\t2\t2\t2\t2\t0\t0\t2\t2\t0\t0\t2\t0\t0\t0\t2\t0\t1\t2\t2\t0\t2\tNA\t0\t0\tNA\t2\t2\tNA\t0\t0\t2\t2\t2\t2\t0\t2\tNA\t1\t2\t0\t2\t2\t0\t2\t2\t2\t0\t0\t0\t0\t0\t2\tNA\t0\t0\t0\t2\t2\t0\t2\t2\t0\t2\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/hapmap2mlmm-result_snp.hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hapmap2mlmm-result_snp.hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,3093 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2bed-input.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2bed-input.map Tue Dec 15 05:18:02 2015 -0500 |
| b |
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1208561\n+Chr1 Chr1:1229816 0 1229816\n+Chr1 Chr1:1250047 0 1250047\n+Chr1 Chr1:1286631 0 1286631\n+Chr1 Chr1:1303497 0 1303497\n+Chr1 Chr1:1306055 0 1306055\n+Chr1 Chr1:1306058 0 1306058\n+Chr1 Chr1:1306085 0 1306085\n+Chr1 Chr1:1318689 0 1318689\n+Chr1 Chr1:1358972 0 1358972\n+Chr1 Chr1:1359766 0 1359766\n+Chr1 Chr1:1359769 0 1359769\n+Chr1 Chr1:1365854 0 1365854\n+Chr1 Chr1:1404921 0 1404921\n+Chr1 Chr1:1407386 0 1407386\n+Chr1 Chr1:1443131 0 1443131\n+Chr1 Chr1:1446645 0 1446645\n+Chr1 Chr1:1486728 0 1486728\n+Chr1 Chr1:1492913 0 1492913\n+Chr1 Chr1:1496524 0 1496524\n+Chr1 Chr1:1509728 0 1509728\n+Chr1 Chr1:1515087 0 1515087\n+Chr1 Chr1:1546579 0 1546579\n+Chr1 Chr1:1551208 0 1551208\n+Chr1 Chr1:1563026 0 1563026\n+Chr1 Chr1:1563029 0 1563029\n+Chr1 Chr1:1565548 0 1565548\n+Chr1 Chr1:1598133 0 1598133\n+Chr1 Chr1:1627278 0 1627278\n+Chr1 Chr1:1627327 0 1627327\n+Chr1 Chr1:1632085 0 1632085\n+Chr1 Chr1:1655772 0 1655772\n+Chr1 Chr1:1655775 0 1655775\n+Chr1 Chr1:1671697 0 1671697\n+Chr1 Chr1:1685316 0 1685316\n+Chr1 Chr1:1687456 0 1687456\n+Chr1 Chr1:1703238 0 1703238\n+Chr1 Chr1:1703264 0 1703264\n+Chr1 Chr1:1722207 0 1722207\n+Chr1 Chr'..b'+Chr1 Chr1:41945638 0 41945638\n+Chr1 Chr1:41954934 0 41954934\n+Chr1 Chr1:41958052 0 41958052\n+Chr1 Chr1:41961218 0 41961218\n+Chr1 Chr1:41961221 0 41961221\n+Chr1 Chr1:41965592 0 41965592\n+Chr1 Chr1:41965659 0 41965659\n+Chr1 Chr1:41968928 0 41968928\n+Chr1 Chr1:41968936 0 41968936\n+Chr1 Chr1:41970211 0 41970211\n+Chr1 Chr1:41998459 0 41998459\n+Chr1 Chr1:42001355 0 42001355\n+Chr1 Chr1:42047135 0 42047135\n+Chr1 Chr1:42047157 0 42047157\n+Chr1 Chr1:42061862 0 42061862\n+Chr1 Chr1:42063149 0 42063149\n+Chr1 Chr1:42081350 0 42081350\n+Chr1 Chr1:42081405 0 42081405\n+Chr1 Chr1:42088625 0 42088625\n+Chr1 Chr1:42089983 0 42089983\n+Chr1 Chr1:42097607 0 42097607\n+Chr1 Chr1:42106144 0 42106144\n+Chr1 Chr1:42138453 0 42138453\n+Chr1 Chr1:42150639 0 42150639\n+Chr1 Chr1:42155417 0 42155417\n+Chr1 Chr1:42156013 0 42156013\n+Chr1 Chr1:42164107 0 42164107\n+Chr1 Chr1:42165734 0 42165734\n+Chr1 Chr1:42169797 0 42169797\n+Chr1 Chr1:42169819 0 42169819\n+Chr1 Chr1:42187340 0 42187340\n+Chr1 Chr1:42192288 0 42192288\n+Chr1 Chr1:42196386 0 42196386\n+Chr1 Chr1:42227135 0 42227135\n+Chr1 Chr1:42229251 0 42229251\n+Chr1 Chr1:42231379 0 42231379\n+Chr1 Chr1:42242069 0 42242069\n+Chr1 Chr1:42244104 0 42244104\n+Chr1 Chr1:42276315 0 42276315\n+Chr1 Chr1:42301791 0 42301791\n+Chr1 Chr1:42302347 0 42302347\n+Chr1 Chr1:42324275 0 42324275\n+Chr1 Chr1:42332621 0 42332621\n+Chr1 Chr1:42352040 0 42352040\n+Chr1 Chr1:42352085 0 42352085\n+Chr1 Chr1:42352093 0 42352093\n+Chr1 Chr1:42352397 0 42352397\n+Chr1 Chr1:42354188 0 42354188\n+Chr1 Chr1:42354191 0 42354191\n+Chr1 Chr1:42357534 0 42357534\n+Chr1 Chr1:42357591 0 42357591\n+Chr1 Chr1:42367404 0 42367404\n+Chr1 Chr1:42367442 0 42367442\n+Chr1 Chr1:42419046 0 42419046\n+Chr1 Chr1:42419769 0 42419769\n+Chr1 Chr1:42421769 0 42421769\n+Chr1 Chr1:42423110 0 42423110\n+Chr1 Chr1:42427556 0 42427556\n+Chr1 Chr1:42460597 0 42460597\n+Chr1 Chr1:42460615 0 42460615\n+Chr1 Chr1:42469025 0 42469025\n+Chr1 Chr1:42471750 0 42471750\n+Chr1 Chr1:42479925 0 42479925\n+Chr1 Chr1:42487487 0 42487487\n+Chr1 Chr1:42487514 0 42487514\n+Chr1 Chr1:42548763 0 42548763\n+Chr1 Chr1:42583428 0 42583428\n+Chr1 Chr1:42586452 0 42586452\n+Chr1 Chr1:42594255 0 42594255\n+Chr1 Chr1:42596478 0 42596478\n+Chr1 Chr1:42602822 0 42602822\n+Chr1 Chr1:42602885 0 42602885\n+Chr1 Chr1:42610308 0 42610308\n+Chr1 Chr1:42612885 0 42612885\n+Chr1 Chr1:42616231 0 42616231\n+Chr1 Chr1:42620187 0 42620187\n+Chr1 Chr1:42620190 0 42620190\n+Chr1 Chr1:42620878 0 42620878\n+Chr1 Chr1:42620881 0 42620881\n+Chr1 Chr1:42631741 0 42631741\n+Chr1 Chr1:42634538 0 42634538\n+Chr1 Chr1:42664013 0 42664013\n+Chr1 Chr1:42665624 0 42665624\n+Chr1 Chr1:42666354 0 42666354\n+Chr1 Chr1:42669650 0 42669650\n+Chr1 Chr1:42669653 0 42669653\n+Chr1 Chr1:42673304 0 42673304\n+Chr1 Chr1:42674707 0 42674707\n+Chr1 Chr1:42682058 0 42682058\n+Chr1 Chr1:42682061 0 42682061\n+Chr1 Chr1:42690508 0 42690508\n+Chr1 Chr1:42706257 0 42706257\n+Chr1 Chr1:42711112 0 42711112\n+Chr1 Chr1:42762398 0 42762398\n+Chr1 Chr1:42763941 0 42763941\n+Chr1 Chr1:42763944 0 42763944\n+Chr1 Chr1:42766241 0 42766241\n+Chr1 Chr1:42777810 0 42777810\n+Chr1 Chr1:42780446 0 42780446\n+Chr1 Chr1:42825046 0 42825046\n+Chr1 Chr1:42826857 0 42826857\n+Chr1 Chr1:42880271 0 42880271\n+Chr1 Chr1:42916070 0 42916070\n+Chr1 Chr1:42916090 0 42916090\n+Chr1 Chr1:42920553 0 42920553\n+Chr1 Chr1:42928342 0 42928342\n+Chr1 Chr1:42959997 0 42959997\n+Chr1 Chr1:42968423 0 42968423\n+Chr1 Chr1:43046967 0 43046967\n+Chr1 Chr1:43048104 0 43048104\n+Chr1 Chr1:43065469 0 43065469\n+Chr1 Chr1:43068624 0 43068624\n+Chr1 Chr1:43072051 0 43072051\n+Chr1 Chr1:43073361 0 43073361\n+Chr1 Chr1:43079457 0 43079457\n+Chr1 Chr1:43079480 0 43079480\n+Chr1 Chr1:43093204 0 43093204\n+Chr1 Chr1:43100601 0 43100601\n+Chr1 Chr1:43123958 0 43123958\n+Chr1 Chr1:43132577 0 43132577\n+Chr1 Chr1:43141118 0 43141118\n+Chr1 Chr1:43141179 0 43141179\n+Chr1 Chr1:43154143 0 43154143\n+Chr1 Chr1:43158899 0 43158899\n+Chr1 Chr1:43179527 0 43179527\n+Chr1 Chr1:43214669 0 43214669\n+Chr1 Chr1:43229591 0 43229591\n+Chr1 Chr1:43249859 0 43249859\n+Chr1 Chr1:43269458 0 43269458\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2bed-input.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2bed-input.ped Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,93 @@\n+IRAT112\t1\t0\t0\t1\t1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t1 1\t2 2\t1 1\t4 4\t1 1\t1 1\t4 4\t2 2\t4 4\t1 1\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t3 3\t4 4\t4 4\t2 2\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t2 2\t4 4\t2 2\t1 1\t1 1\t3 3\t3 3\t4 4\t4 4\t3 3\t3 3\t2 2\t1 1\t2 2\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t3 3\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t4 4\t4 4\t3 3\t4 4\t1 1\t3 3\t3 3\t3 3\t1 1\t2 2\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t3 3\t2 2\t3 3\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t2 2\t4 4\t4 4\t1 1\t4 4\t2 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4\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t3 3\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t2 2\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t3 3\t1 1\t2 2\t1 1\t1 1\t4 4\t4 4\t2 2\t1 1\t1 1\t2 2\t4 4\t1 1\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t3 3\t2 2\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t3 3\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t2 2\t4 4\t1 1\t3 3\t3 3\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t3 3\t1 1\t3 3\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3'..b' 1\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t3 3\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t3 3\t2 2\t4 4\t1 1\t4 4\t1 1\t4 4\t2 2\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t1 1\t1 1\t3 3\t2 2\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t4 4\t1 1\t2 2\t4 4\t1 1\t3 3\t1 1\t1 1\t3 3\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t3 3\t3 3\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t3 3\t4 4\t3 3\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t4 4\t2 2\t2 2\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t4 4\t3 3\t1 1\t3 3\t3 3\t3 3\t4 4\t4 4\t2 2\t1 1\t2 2\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t2 2\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t2 2\t3 3\t4 4\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t2 2\t1 1\t3 3\t3 3\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t2 2\t4 4\t1 1\t2 2\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t3 3\t1 1\t4 4\t4 4\t3 3\t3 3\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t3 3\t3 3\t2 2\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t4 4\t4 4\t1 1\t3 3\t2 2\t2 2\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t3 3\t3 3\t1 1\t2 2\t2 2\t4 4\t2 2\t3 3\t1 1\t1 1\t3 3\t3 3\t1 1\t4 4\t1 1\t1 1\t3 3\t4 4\t2 2\t4 4\t4 4\t3 3\t2 2\t3 3\t3 3\t4 4\t4 4\t2 2\t2 2\t4 4\t2 2\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t3 3\t1 1\t1 1\t3 3\t1 1\t4 4\t3 3\t3 3\t1 1\t4 4\t1 1\t3 3\t3 3\t3 3\t1 1\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t3 3\t4 4\t1 1\t1 1\t2 2\t4 4\t3 3\t2 2\t3 3\t1 1\t1 1\t4 4\t4 4\t4 4\t3 3\t2 2\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t1 1\t1 1\t4 4\t1 1\t3 3\t1 1\t3 3\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t3 3\t3 3\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t2 2\t4 4\t2 2\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t2 2\t4 4\t1 1\t1 1\t1 1\t3 3\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t3 3\t4 4\t1 1\t4 4\t3 3\t3 3\t3 3\t1 1\t4 4\t3 3\t3 3\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t2 2\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t3 3\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t1 1\t2 2\t4 4\t1 1\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t2 2\t4 4\t4 4\t3 3\t1 1\t1 1\t4 4\t2 2\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t2 2\t3 3\t4 4\t2 2\t4 4\t4 4\t2 2\t1 1\t2 2\t1 1\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t3 3\t4 4\t2 2\t1 1\t2 2\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t2 2\t3 3\t1 1\t1 1\t4 4\t4 4\t1 1\t2 2\t4 4\t1 1\t1 1\t2 2\t1 1\t4 4\t4 4\t4 4\t4 4\t3 3\t3 3\t4 4\t4 4\t2 2\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t3 3\t4 4\t3 3\t4 4\t4 4\t1 1\t3 3\t4 4\t1 1\t4 4\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t3 3\t2 2\t4 4\t4 4\t4 4\t4 4\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t1 1\t4 4\t1 1\t2 2\t3 3\t2 2\t4 4\t1 1\t1 1\t4 4\t3 3\t2 2\t4 4\t2 2\t1 1\t3 3\t4 4\t1 1\t1 1\t1 1\t3 3\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t3 3\t4 4\t2 2\t4 4\t1 1\t1 1\t4 4\t2 2\t4 4\t4 4\t4 4\t3 3\t1 1\t1 1\t3 3\t1 1\t2 2\t1 1\t3 3\t2 2\t1 1\t2 2\t1 1\t1 1\t1 1\t2 2\t1 1\t4 4\t3 3\t1 1\t3 3\t1 1\t1 1\t3 3\t4 4\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t1 1\t2 2\t3 3\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t4 4\t2 2\t1 1\t4 4\t2 2\t2 2\t4 4\t4 4\t1 1\t2 2\t4 4\t3 3\t4 4\t4 4\t4 4\t1 1\t3 3\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t2 2\t4 4\t4 4\t4 4\t1 1\t4 4\t3 3\t4 4\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t1 1\t1 1\t1 1\t3 3\t4 4\t1 1\t1 1\t4 4\t1 1\t4 4\t3 3\t1 1\t1 1\t4 4\t3 3\t1 1\t4 4\t2 2\t4 4\t1 1\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t1 1\t2 2\t4 4\t3 3\t1 1\t2 2\t1 1\t1 1\t1 1\t4 4\t4 4\t4 4\t1 1\t4 4\t1 1\t3 3\t1 1\t2 2\t3 3\t2 2\t3 3\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t3 3\t4 4\t2 2\t1 1\t1 1\t4 4\t4 4\t4 4\t2 2\t4 4\t4 4\t4 4\t4 4\t2 2\t1 1\t3 3\t4 4\t4 4\t4 4\t1 1\t1 1\t3 3\t1 1\t3 3\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t3 3\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t1 1\t4 4\t1 1\t1 1\t1 1\t4 4\t1 1\t4 4\t4 4\t4 4\t2 2\t3 3\t3 3\t1 1\t1 1\t2 2\t4 4\t1 1\t1 1\t2 2\t4 4\t3 3\t2 2\t4 4\t4 4\t1 1\t4 4\t4 4\t4 4\t1 1\t1 1\t4 4\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2bed-result.bed |
| b |
| Binary file test-data/ped2bed-result.bed has changed |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2bed-result.bim --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2bed-result.bim Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,2013 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2bed-result.fam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2bed-result.fam Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,93 @@ +IRAT112 1 0 0 1 1 +IAC25 1 0 0 1 1 +IAC165 1 0 0 1 1 +KARASUKARASURANKASU 1 0 0 1 1 +DOURADOPRECOCE 1 0 0 1 1 +CUIABANA 1 0 0 1 1 +BICOBRANCO 1 0 0 1 1 +CAAWA/FORTUNA6 1 0 0 1 1 +CANELADEFERRO 1 0 0 1 1 +CIRAD358 1 0 0 1 1 +COLOMBIA1 1 0 0 1 1 +CIRAD409 1 0 0 1 1 +BAGANANASALAO 1 0 0 1 1 +BAKUNGH 1 0 0 1 1 +FOHISOMOTRA 1 0 0 1 1 +KAKANI2 1 0 0 1 1 +GUARANI 1 0 0 1 1 +DOURADOAGULHA 1 0 0 1 1 +IRAT13 1 0 0 1 1 +DAWASANRED 1 0 0 1 1 +GRAZI 1 0 0 1 1 +IRAT144 1 0 0 1 1 +IAC47 1 0 0 1 1 +MOROBEREKAN 1 0 0 1 1 +IRAT362 1 0 0 1 1 +GIZA171 1 0 0 1 1 +IDSA77 1 0 0 1 1 +IRAT216 1 0 0 1 1 +IRAT177 1 0 0 1 1 +CHAPHUMA 1 0 0 1 1 +CIRAD392 1 0 0 1 1 +ARROZCEBADA 1 0 0 1 1 +INDANE 1 0 0 1 1 +DINORADO 1 0 0 1 1 +63-104 1 0 0 1 1 +IR63380-16 1 0 0 1 1 +CANAROXA 1 0 0 1 1 +CICIHBETON 1 0 0 1 1 +IR68704-145-1-1-B 1 0 0 1 1 +HAWMOM 1 0 0 1 1 +IRAT364 1 0 0 1 1 +IRAT212 1 0 0 1 1 +KHAODAM 1 0 0 1 1 +62667 1 0 0 1 1 +IRAT234 1 0 0 1 1 +NIPPONBARE_D 1 0 0 1 1 +JUMULA2 1 0 0 1 1 +CUBA65 1 0 0 1 1 +BABER 1 0 0 1 1 +CIRAD488 1 0 0 1 1 +BENGALYVAKARINA 1 0 0 1 1 +ESPERANZA 1 0 0 1 1 +BULUPANDAK 1 0 0 1 1 +ARIAS 1 0 0 1 1 +GOMPA2 1 0 0 1 1 +CT13582-15-5-M 1 0 0 1 1 +IRAT335 1 0 0 1 1 +M202 1 0 0 1 1 +IR65907-188-1-B 1 0 0 1 1 +IR71525-19-1-1 1 0 0 1 1 +CNA-7_BO_1_1_33-13-6-1 1 0 0 1 1 +IRAT257 1 0 0 1 1 +IRAT109 1 0 0 1 1 +KANIRANGA 1 0 0 1 1 +IR66421-096-2-1-1 1 0 0 1 1 +GOGO 1 0 0 1 1 +GEMJYAJYANAM 1 0 0 1 1 +DANGREY 1 0 0 1 1 +BINULAWAN 1 0 0 1 1 +CAIAPO 1 0 0 1 1 +IGUAPECATETO 1 0 0 1 1 +IRAT170 1 0 0 1 1 +IRAT380 1 0 0 1 1 +ARAGUAIA 1 0 0 1 1 +GOGOLEMPAK 1 0 0 1 1 +JAOHAW 1 0 0 1 1 +CHALOYOE 1 0 0 1 1 +GANIGI 1 0 0 1 1 +GUNDILKUNING 1 0 0 1 1 +IRAT2 1 0 0 1 1 +IRAT366 1 0 0 1 1 +IRAT104 1 0 0 1 1 +DAVAO 1 0 0 1 1 +HD1-4 1 0 0 1 1 +CURINCA 1 0 0 1 1 +DAM 1 0 0 1 1 +CIRAD403 1 0 0 1 1 +JUMALI 1 0 0 1 1 +JIMBRUKJOLOWORO 1 0 0 1 1 +GOGOLEMPUK 1 0 0 1 1 +CIRAD394 1 0 0 1 1 +IR63372-08 1 0 0 1 1 +IR60080-46A 1 0 0 1 1 |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2fasta-result.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2fasta-result.fa Tue Dec 15 05:18:02 2015 -0500 |
| b |
|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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/ped2fasta-sample.ped --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ped2fasta-sample.ped Tue Dec 15 05:18:02 2015 -0500 |
| b |
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| diff -r 345f88a8f483 -r 10627af23f10 test-data/rooting-newick --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rooting-newick Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,2 @@ +(((((((((((((((((((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.004740):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):0.000858,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.027110,GRAZI:0.022678):0.000763):0.009870,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:-0.000887,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):0.000971):0.009442):0.002985,(((((((((JUMALI:0.077650,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607,ref:0.722923):0.015245,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.043699,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.032650):0.012575,VIETNAM1:0.049323):0.003110,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.014450):0.010970):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.006240,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.020665,CUIABANA:0.066182):0.018877,((GANIGI:0.040448,PULULAPA:0.039840):0.020258,GOGO:0.060904):0.005609):0.001416,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.021620,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.059430,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.008281):0.005079,RT1031-69:0.043520):0.002593,MANDRIRAVI:0.049833):0.005647,IRAT234:0.037316):0.007912,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.011250,(((IAC47:0.007321,(IAC165:0.000500,VARYLAVA90:0.001650):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.001457,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.144370):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.043160,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.014180,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.057970):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.003440,(((((KUROKA:0.096901,IRAT144:0.032372):0.040630,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.034180):0.011060,CAIAPO:0.072220):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.004673,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.006303,((OS4:0.021016,OS6:0.015670):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.001209,TRESMESES:0.028972):0.002988,PACHOLINHA:0.042509):0.002897,CANELADEFE:0.050931):0.011439,CAAWA/FORT:0.055630):0.006838,((LUDAN:0.054230,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):0.000088):0.004898,DINORADO:0.065206):0.004869,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004581,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.031721,PALAWAN:0.032789,KENDINGA5H:0.028863); + |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/rooting-out_tree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rooting-out_tree Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,1 @@ +(ref:0.575788,(((((((((((((((((((((((PALAWAN:0.032789,KENDINGA5H:0.028863):0.031721,((SPEAKER:0.057882,(KEDAYAN:0.065817,ARIAS:0.074161):0.019154):0.012584,(TANDUI:0.078177,KETANMENAH:0.079797):0.013169):0.003598):0.004581,(BAGANANASA:0.049455,BAKUNGH:0.048193):0.021502):0.004869,DINORADO:0.065206):0.004898,((LUDAN:0.05423,((CUBA65:0.037658,(IR53236-27:0.026784,AZUCENA:0.025318):0.020859):0.017556,DAVAO:0.045931):0.005774):0.010335,(BINULAWAN:0.059589,MALAGKITPI:0.062856):0.004216):8.8E-5):0.006838,CAAWA/FORT:0.05563):0.011439,CANELADEFE:0.050931):0.002897,PACHOLINHA:0.042509):0.002988,TRESMESES:0.028972):0.001209,((OS4:0.021016,OS6:0.01567):0.010953,(CANAROXA:0.018385,KINANDANGP:0.047364):0.022379):0.007502):0.006303,((IR47686-09:0.045565,IRAT104:0.041351):0.019777,IR71524-44:0.058741):0.008141):0.004673,((((((((IR60080-46:0.102166,IR71525-19:0.037083):0.071364,IR68704-14:0.14437):0.009188,((IR66421-10:0.104309,IR66421-09:0.112363):0.044923,CNA-7_BO_1:0.097756):0.030658):0.04316,(((((((CIRAD403:0.043568,MARAVILHA:0.105095):0.009135,CURINCA:0.140813):0.023139,CIRAD409:0.038172):0.045565,PCT4_SA_4_:0.177389):0.024197,(PCT11_0_0_:0.075858,P5589-1-1-:0.044714):0.022844):0.006949,ESPERANZA:0.077139):0.022033,((CT13582-15:0.086985,((((((IRAT216:0.017956,IR47684-05:0.006483):0.01418,((IR63372-08:0.008257,IR65907-18:0.049347):0.060968,IR65907-20:0.025334):0.004085):0.028888,COLOMBIA1:0.106747):0.009488,WAB56-50:0.048646):0.019308,IDSA77:0.026889):0.022776,WAB56-125:0.05797):0.025793):0.017149,IRAT362:0.030612):0.021338):0.005273):0.007474,((IR65261-19:0.088569,IR63380-16:0.060828):0.017377,ORYZICASAB:0.059793):0.020771):0.010205,((((IRAT2:0.006656,(62667:0.002564,(IRAT177:0.003065,IRAT13:0.006564):0.001422):0.001435):0.014034,IRAT109:0.079089):0.006041,IRAT170:0.013368):0.020262,63-104:0.022825):0.010789):0.00344,(((((KUROKA:0.096901,IRAT144:0.032372):0.04063,CIRAD488:0.062971):0.026055,(IRAT212:0.041268,PRIMAVERA:0.059109):0.012806):0.027141,((CIRAD392:0.025487,IRAT380:0.024721):0.028822,CIRAD394:0.055046):0.03418):0.01106,CAIAPO:0.07222):0.009469):0.006119,((ARAGUAIA:0.084755,(IRAT335:0.077784,IRAT112:0.027346):0.006445):0.007072,IRAT257:0.036873):0.020075):0.002575):0.001457,((((EARLYMUTAN:0.015218,(IAC25:0.007986,(DOURADOAGU:0.001563,DOURADOPRE:0.001763):0.010062):0.002688):0.01125,(((IAC47:0.007321,(IAC165:5.0E-4,VARYLAVA90:0.00165):0.006263):0.003063,HD1-4:0.015932):0.006876,GUARANI:0.013831):0.005817):0.007843,IGUAPECATE:0.036421):0.002898,BICOBRANCO:0.031026):0.008082):0.007912,IRAT234:0.037316):0.005647,MANDRIRAVI:0.049833):0.002593,RT1031-69:0.04352):0.005079,((((((((GOGOLEMPUK:0.001198,GOGOLEMPAK:0.002128):0.030378,TREMBESE:0.013258):0.055246,(((JIMBRUKJOL:0.045219,KETANKONIR:0.035298):0.006267,KANIRANGA:0.042518):0.020121,(VARYMADINI:0.039903,BENGALYVAK:0.032305):0.012408):0.00474):0.001841,(((YANCAOUSSA:0.006364,PATEBLANCM:0.008832):8.58E-4,MOROBEREKA:0.004615):0.013114,VARYMALADY:0.026086):0.024153):0.015663,WAB706-3-4:0.050598):0.004174,(MAINTIMOLO:0.044761,(FOHISOMOTR:0.005656,VARYSOMOTR:0.006949):0.030574):0.009217):0.006248,IRAT364:0.047033):0.003654,((IRAT366:0.033773,CIRAD358:0.093382):0.015822,(((MANANELATR:0.040437,(ARROZCEBAD:0.02711,GRAZI:0.022678):7.63E-4):0.00987,KOMOJAMANI:0.049216):0.006713,((TSIPALA89:0.0,VARYLAVADE:0.037778):0.044182,MITSANGANA:0.082664):0.068968):9.71E-4):0.009442):0.002985):0.008281,(((((GUNDILKUNI:0.019719,(CICIHBETON:0.02162,BULUPANDAK:0.016924):0.008554):0.028704,PADIBOENAR:0.052396):0.002882,(REKETMAUN:0.05943,((POENOETHIT:0.042637,KETANLUMBU:0.035696):0.016617,MOLOK:0.055674):0.015506):0.001164):0.024179,PADIKASALL:0.093595):0.063014,RATHAL:0.090729):0.015609):0.001416,((GANIGI:0.040448,PULULAPA:0.03984):0.020258,GOGO:0.060904):0.005609):0.018877,CUIABANA:0.066182):0.020665,((((((((DAM:0.054359,((((VIETNAM3:0.030951,SENG:0.038876):0.007914,(NABESHI:0.010252,KARASUKARA:0.010553):0.03265):0.012575,VIETNAM1:0.049323):0.00311,(PEHPINUO:0.070737,(CHUAN3:0.020631,CHUAN4:0.024135):0.01445):0.01097):0.020849):0.002227,(((((JAOHAW:0.044517,KHAODAM:0.031174):0.017389,MAHAE:0.041633):0.006695,(KHAOKAPXAN:0.005767,HAWMOM:0.009429):0.031367):0.015885,CHAPHUMA:0.071266):0.005503,KU115:0.043819):0.007631):0.009768,NHTA10:0.061745):0.006241,INDANE:0.079646):0.007679,(((GEMJYAJYAN:0.012403,YANGKUMRED:0.014267):0.008479,DANGREY:0.024493):0.020552,DAWASANRED:0.030369):0.065249):0.00624,CHALOYOE:0.058075):0.012844,NHTA5:0.138764):0.005686,YUNLU7:0.079119):0.012627):0.043699,((((NPE826:0.019317,NPE253:0.017161):0.033863,((GIZA171:0.023894,NIPPONBARE:0.027998):0.013954,M202:0.053155):0.016691):0.020398,NEPHOAVANG:0.097913):0.011042,BABER:0.155657):0.024483):0.015245,(((JUMALI:0.07765,LAMBAYQUE1:0.170057):0.027742,(GOMPA2:0.049418,KAKANI2:0.052752):0.024526):0.081123,JUMULA2:0.075284):0.027607):0.14713500000000007); |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-reference.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-reference.fa Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,636558 @@\n+>chr1\n+CAGTAAAGTTTGCAAAGAGATTCTGGCAAAGTTGTAATCATCGAATGTGAAATGTCAAGT\n+AAGTGTAAATGGATTAGTTTGCCAATGGAGGTCGGCAACTCTTTCACATCTGCTCCAAAC\n+AATTTTAGGACATGCAAGTATTTGAACTTTGATAACATATCATCAGCTATGCCACCCTCC\n+AGAAATAATGTGCGAAGTGATGCTGATTTTTTTTCATTGATGATTTCCACCATTCTTTCG\n+GATGAGTATACTGCAAGGTAGCGGTCCTCATTGCTGCTGCTACGATTCAAAATTGATTTT\n+GCAAAATCGTGCACAAGGTCATGCATTTTATACCTATTTTCTTTTACTTCTTCCAATAAG\n+GAAGTTTGCAGCAAAATTCTCAAATACTCACATCCTATTTTCTCCATCGTTCTTTCATTT\n+TGGGAATCCGGTTGAAGAAAGCCTTCAGCCATCCAAAGCTCAACTAGTAGATCTTGTTCC\n+AACTCAGCATCTTGATCAAAAATTGAGCAATATGCAAAACATTTCTTAACCGGTGCAAGT\n+GACAGATGATCAAAACTCACCTTAATTATTTGCTCGATCCGACCTTGGTCTCCATTCAAC\n+AGACTCTCCTCCAAAATAGATTGCCACTCCTCTTTTCTCTTTTTATATAACAAACCTCCA\n+ATTAACTTTGCTGCCAGAGGTAGACCGTCACATCTTCTTAAAACTCGCTCCCTTATGTCT\n+TCCAATTCTTTTGGTACTTCTTCCCCTACAGTTGCCCATTTATTAATGATGGACCAGCAA\n+TCATCATTGCATAGCTTTCCTAGCCCATGGCGAGTAAAATTGATCTGCGGAAGACCGGAC\n+AGAGTAGTTTCCACTTCTTGCAGACGAGTGGTAACAAGACACCAGCTCCCTTTCTTCGCT\n+TCGAGTGCCTTCAATGTGGTGAAAAAGTCATCCAATTGTTGATGATTCCACAAATCGTCA\n+AGAACAAGCAAACATCTTTTTCCCTTGATTTCATTTTGAATTCCTCGAACTATTACGTCC\n+CTAACATCCGCGTCAGGCTTGTTTCCTGTTGACGATTCTAGAATCATTTTGAAGAGATCC\n+ATGGTTTCAACTTCTTTAGCCACACAAACCCAAATTTTTTTGTCAAAATGATTATCATTA\n+AACTGTGGATTGTTGTAAACGGCTTTAGCCAGAGTTGTTTTGCCTAAACCACCCATGCCA\n+GTTACGGAAATAACTGAAATACGATCACTTTCAGATTCGGTCAACAACTTCTTAACTATT\n+TCTGATTCATCCTCGTCTCTTCCTAGGACATCACTTCGAACAATCTTAGAGTCGGTCTGT\n+CGGCTTGTTGTGGCTCCAGCAGCAATTGTAGTGAATGCTTCTTCAACTAGGGGCTTGTAG\n+GCCAGTCCCAAACGTTCTGCATCCCGATGGATACTTTGAAGGTTCGTGTTGATCTCCCTG\n+ATCATTGAACCCAACCTCCAACGAAAACCAATTTTATTAAAGAATGAAAAGCAGAAGAAT\n+ACCTTCTTTTTCGTGAGTTGATTTTGATACTTCACCTTCCGACGAAGATTTTCATAGTTG\n+AGCTCGTCCAGCACATTGTCGGCTTTGAAAACCTCTTCTTCCAGATCCTTGAGCCATTTT\n+TGCACCCCAAGAAGCTTCGGATCATTGCAATATTTTGCCTCGTCAGCACCGGCCAAGAAG\n+CATTGGATCCTTGCAGCAGATTTGTCGAGTTTCTTCAGCTCCGTTGGGAATTCACGAACC\n+AGATTAACATGATCAGCAGCAAGGGAAGCAACCGCCTGCAATGCAACCTTAATAGTAGCA\n+CTAACAGCAGCATCAGCCATTTTTTCTCGCTTGGGATTGGAATTAGGATGAAAGTGTTCT\n+GCAATGGTGATGGGGGGATGCTTTCTGCTATGAGACAAGGAAGGATATGGTTCAACTTTG\n+GCAACTAAGGGCAGCAAAATCTGTGGAGGCTAAAACTTGAGGGAATGAAATTTTTCCACA\n+CAATTTTTGCACTTCCAAAATTTTCCACTTTGTGCAATTTGCCACCCGGCTTCACTCTGC\n+AAAGCTACACTCCAAAGACGTCACCAACGAACTTTTCTTTTACCGCGTTACCCTGGACTT\n+CCTGGAAGTTGCCGACAATTCGTAGCCACACCTTCTTGCCGACAAGTCGTCGCATCTGCA\n+GCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTGACTGGCTTAAC\n+GATATTGTAAGATGACTCAGAGGCCCACTTTTTTTTTAAAAATCAGCCTGTCCCCAGCCG\n+TGCTGACTGGGCACGGCTGGGACAGGCGGCAAAAAAAAGGGCCAGCAAATGGGATGTATT\n+TGGGGACATAAATTTTGTAGCAAAAGTGAAACGAAAGGCCATACAAATTCACCGCACTAG\n+CTGCCCTTTTACTTTCTTTCACTCTTTCCTATGCTCTTTATTTTTTGGAAGAGATACCTA\n+AACGATTTTATTGCCCTAATCCTAATCAAAGATTTTGATTTTATAACTTAAAGATTTTGC\n+TGTGGAGTCTTATAACACTTAAGTTAGGAAGATCAAAATTTTAAAGTGGAAATGGAAGAT\n+TATTATATTTTTCAAACTGCAAATTAGTATAATTCTATGTACAATAAAAATTCAATGCTT\n+GCTCAAATTTTTTGACGAACAACATGTGTAAGCTAATATATGAATATTTATATGTAAATT\n+AAATGCAGTTTATACGCAACAAAATTCATGAATAAGAATCCATATATGTAAAATTAATAT\n+ACATTTTTAAAATTTTTTCTTGTAATTAGATACATTTGTGACTAACTGGTTTTCAAAGAT\n+AATTTTTAAATTGTAATATTATAAGACGCTAAATTTTAAATTGTATTAAAATTTAGTTTT\n+GAAAACCAGTTAGTCATAAATGTATCTAATTACAAGCAAAAATTAAAAAAATATATATAT\n+ATATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGTTGCGTATAAACTGCAT\n+TTAATTTACATATAAATATTCATATATTAGCTTACACATGTTGTTCGTCAAAAAATTTGA\n+GCAAGCATTGAATTTTTATTGTACATAGAATTATACTAATTTGCAGTTTGAAAAATATAA\n+TAATCTTCCATTTCCACTTTAAAATTTTGATCTTCCTAACTTAAGTGTTATAAGACTCCA\n+CAGCAAAATCTTTAAGTTATAAAATCAAAATCTTTGATTAGGATTAGGGCAATAAAATCG\n+TTTAGGTATCTCTTCCAAAAAATAAAGAGCATAGGAAAGAGTGAAAGAAAGTAAAAGGGC\n+AGCTAGTGCGGTGAATTTGTATGGCCTTTCGTTTCACTTTTGCTACAAAATTCATGTTCC\n+CAAATACAACCCATTTGCTGGCCCCTTTTTTTTTTGCCACCTGTCCCCAGCCGTATTTTT\n+TTTTTCTTCTTAAGGAATCATCAATTTTGTACTTACATAACCTTGTAGTACCGTTTATAT\n+AACACTTTCTCCTGTAACATAATTTCCTATGTTTATGTAATATTAGCATCAATTAGGATC\n+ACAAATTAAGATATTATCTGGTATTATTAGTATCAATTAGAATCATCAATTGAGATCCTG\n+ATTATCATCCCAATTGATGATTCTAATTGATACTAATAATACCAGATAATATCTTAATTT\n+GTGATCCTAATTGATGCTAATATTACATAAACATAGGAAATTATGTTACAGGAGAAAGTG\n+TTATATAAACGGTACTACAAGGTTATGTAAGTACAAAATTGATGATTCCTTAAGAAGAAA\n+AAAAAAAATCTGGGCTTTGTTCTAACATTGTCATAGAGAGTCAACAAGAAGAAGAAGATG\n+GT'..b'CTCAAAGAATTGTCACCTAAAGGCGGACCTTTGACTTCCAAATTCTTAAT\n+AAATTGGTAATTTTGTTCTAAATTCACGTCATAATATCAGAATTGTAAATCACCAGCAAT\n+TCTTCACCATAACCGATCCTATCATCTTTCCACATCATTGGATATTGGTTTTGGTGCACG\n+GTGGACTGGACCAATGATATGATGACTCGGGAACAGTAGTATTGCACATCATCCATTCCC\n+CTATTCGATAGATGGGTAATAACTTAAGCAAAAACACTTAATTCATCCGGGCAACGAGAT\n+GAACTCTTTATATTATTATTATTATTATTTTTTTATAACGGCATATCGAGTCTAACTTAC\n+TCCTACTCTTGCTCTAACCTCTAATTTTTTTGTTTGTCATGTTTCTATATTTAGTTTTAC\n+ATTAGACTCTAATCATGGAATCAAAGAAGGATAATGTATGACACAAATATGGTAAGATGC\n+GCCTAAACATTCTTGATTTGACGGGTTAACTTGTACCCTTAATTGTCGAAGGAATAATAA\n+TAGGTTATGATACTTGGATATCAACCTTGTATTCCTTAAAAAAAAAAATTCAACCTTGTA\n+CCAGGAGAAGCGCAAGTTTTTATTCTAAAATTTTGCAAGGTTTGTCTGTGGGCAAATTGC\n+AGTCTGCGGACAAAGTGGGGAAGATATCACCAGTTGGGATCTTCTATACCATTATTCGGT\n+GTCAAATTCAGTGTCAATCTCACTTATCATATGGTGATAGAAAAAATTTAAATAACTAGC\n+ACGTGACAAATGAAAAAAACAGGACACTTGGCATAAATATAGAAGTGACACTGAATTATC\n+AGAGTGTCACGACTAGTTGACCATGCACCTACTAGTACTAATTTTTTAATTATTATTATT\n+AAGCGGGATCTCACGAAACCGTTTGTACGTGGAAGAAAATTTCCGAGCATTAGTACTGAT\n+TGACTTTTCATTAACTAAACCAACCCAAGATGAAGACAAAAGAAAGAGGTTAGTAGCAGT\n+AGATCACATACTGTTTTTGGTTTTTTTTTTTTGGCAATGATGGATGATTAGTCGCTGCAG\n+GTAATTTAATGTGATGCCCACAGGCTCCTGTGTAGAAAATGAATGATCGATTGACATAAC\n+ATATGGATAAAAAGTAATGCGACAGTATTAATTAATTAACAACAATTACTAAGCGGTAGT\n+TTATTTAGTACTACCTACTTGAATTAAATTAAATTAAAAGGAGTTTCAACTGCCAACCAA\n+CGTAACTAACTACCCGTACCCACCAACCACTCAGGTCAGAAGTCTGGACGCTCATCTCAT\n+GTTAATTTGCGGCTTTCATGTTCTGACTCGTTTCTTGCTGGGTCTTTAGTCTTTACCAGT\n+TACCGCCGCCGCCCTATTTACCCCTTTCTTTTTCTTTTTGGTGCGCCTAGAGCTGTAAAC\n+GAACCGAATCGAACCGAGTATCTCATGTTTGAGCTCTGTTCGTTAAGCAGTTCGAACAAC\n+GTTCGTGTTCGTTCGTTAATTTTCGAACTCCAAACCTGTGTTCGTGTTCGANNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAGTACTAAGTGACTAAATTCTATTATT\n+CATTAACTATATAACTAACATTAACATAAAAACAACAAATAAAACAAAGAAATTTGCCCT\n+CCAAATATAAAAGTCCAGCCATAAAATTAACCCTAAATTTGTTAAATGATAATTATGTCT\n+ATGTTCGCGAACGTTCGTTAAAACTCGCGAACATGTTCGTGTTCGCGAACGTTCGTTTAG\n+CATGTTCGCGAACGTTCGTTAAAACTCGTGAACATGCTCGTGTTCGCTCGATTATTAATC\n+GAACAAAAAAATTCGTTCGAACTCGGTTCGTTTAAAATTTCGAACGAGCCTTTCACGAAC\n+ACGAACGAGCCGAAACGAACCGAGCTACCGAACAGCTACTGAACACAGGGCATGTTATCG\n+AAGCATAATGCTACCACAAAACAAAACAAGCAGAAAATACCCAAAAGTAGGAAGCTAAAT\n+AGGTTGGGACGGACGCTAGTGGACAGCTAATTACGAATATACTTCCATCCTCTTTGGACT\n+CAGCAGCTTCTTATTCTATTGCAGTCTTCTTATCCTCATTCCTGCCTTGCCACTGTGTTA\n+CATATAAACACGGGAGCATGTCCATCTCGTCTTGCTTAATTTAGTAGTATCATTTTTCGG\n+GTCTCCACGAAGCCACACAAGTGCAGGAACAGCAACAGTTTGACCGCCGGTCATCACCCA\n+AGTTTCTCTCACAAACGCAAGCCCGTCAAAGTCCCCTTTTCTTTAACAGCTTCCACGAAC\n+CTACTAGTGCCAATTTATTATCAGTTTCCAACCTCACAACTCAGTTTTGTGACCATTTAG\n+AGGCACACAGACTGATCAACCATGCCATGCTCTTCAGGATCAGAGGTCATGTTTTAAGCG\n+CCTTAAGTAGATATTTACAATTTAACAGATTGTGGTTCAAAACTAGCACCCAACTTGACA\n+TGCATACTTTTGACCCCTTTAATCCGACCCAAATATTTGTCAATTTTAGACTTCGACAGT\n+CCAATCATCATAACATTGTAGTCTAACTCTTATATTTTTATAATTAAAACTTGACCCCAC\n+TCTTTTAGTATAATTACTTTTGACCCTATATTTTTGTCAAATTAAAATAAACCACTATAT\n+TTTTATATATTAAAAATTTGAGCCTACTTTTTTTAGATAATTCCTTTTTTATAGGTTAAT\n+TTATAGCCAATTGGTAATTTACTAAAATATCGGGGTCTAGTTATAAATTACTAAAATATT\n+GGGGTAAGTATTTAATTTAATAAAAGTATAGAGGTCACCTTACAATTTCACTAAAATATT\n+AGGGTCAAAACATAATTTTACACAGACTAAGGGATGAAACTATAATTTTCTATAAATTTA\n+GGGTTTAGGGTTTAGGGTTTAGGGTTTAGGGTTAGGGTTTAGGGTTTAGGGTTTAGGGTT\n+TAGGGTTTAGGGTTTAGGGTTTAGGGTAGTTTAGGGTAGG\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-reference.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-reference.gff Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,76375 @@\n+##gff-version 3\n+chr1\tmanual_curation\tgene\t390\t1820\t.\t-\t.\tID=GSCOCG00012439001;Name=Cc01_g00010\n+chr1\tmanual_curation\tmRNA\t390\t1820\t.\t-\t.\tID=GSCOCT00012439001;Parent=GSCOCG00012439001;Name=Cc01_g00010\n+chr1\tmanual_curation\tpolypeptide\t390\t1820\t.\t-\t.\tID=GSCOCP00012439001;Dbxref=InterPro:IPR000767,InterPro:IPR002182,PFAM:PF00931,PRINTS:PR00364,SwissProt:Q7XA40,SwissProt:Q7XBQ9,SwissProt:Q9LRR4,TAIR:AT1G50180.1,TAIR:AT3G14460.1,TAIR:AT3G14470.1,TrEMBL:B9GZ62,TrEMBL:B9IBB8,TrEMBL:B9NBB7;Derives_from=GSCOCT00012439001;Name=Cc01_g00010;Ontology_term=CC_evidence_code:ISS,GO:0005524,GO:0006915,GO:0006952,CC_EC_number:missing_EC_number,PRODUCT:Putative disease resistance protein RGA3,CC_functional_completeness:fragment,CC_gene:RGA3,CC_gene:RPPL1,CC_gene:RGA2;alternative_location=no_alternative_location;annotator_comment=missing_annotator_comment;date=Tue Jul 31 10:05:06 CEST 2012;inference={gaze};note=GSCOCT00012439001~ Putative disease resistance protein RGA3~ RGA3~ fragment;original_location=join(390862..390909%2C390964..392292);owner=coffea\n+chr1\tmanual_curation\texon\t1773\t1820\t.\t-\t.\tParent=GSCOCT00012439001\n+chr1\tmanual_curation\texon\t390\t1718\t.\t-\t.\tParent=GSCOCT00012439001\n+chr1\tmanual_curation\tCDS\t1773\t1820\t.\t-\t0\tParent=GSCOCT00012439001\n+chr1\tmanual_curation\tCDS\t390\t1718\t.\t-\t0\tParent=GSCOCT00012439001\n+chr1\tmanual_curation\tgene\t4545\t12431\t.\t-\t.\tID=GSCOCG00012438001;Name=Cc01_g00020\n+chr1\tmanual_curation\tmRNA\t4545\t12431\t.\t-\t.\tID=GSCOCT00012438001;Parent=GSCOCG00012438001;Name=Cc01_g00020\n+chr1\tmanual_curation\tpolypeptide\t5023\t10877\t.\t-\t.\tID=GSCOCP00012438001;Dbxref=GENE3D:G3DSA:2.30.30.30,GENE3D:G3DSA:2.40.50.140,InterPro:IPR001059,InterPro:IPR008991,InterPro:IPR012340,InterPro:IPR013185,InterPro:IPR013852,InterPro:IPR014722,InterPro:IPR015365,InterPro:IPR016027,InterPro:IPR020599,PFAM:PF01132,PFAM:PF08207,PFAM:PF09285,PIR:PIRSF005901,PROSITE:PS01275,SMART:SM00841,SUPERFAMILY:SSF50104,SUPERFAMILY:SSF50249,SwissProt:A9H6E1,SwissProt:Q0BT69,SwissProt:Q5FUC7,TAIR:AT3G08740.1,TAIR:AT4G26310.2,TrEMBL:D7SLK8,TrEMBL:I1PGI0,TrEMBL:Q84M44;Derives_from=GSCOCT00012438001;Name=Cc01_g00020;Ontology_term=CC_evidence_code:ISS,GO:0003746,GO:0006414,CC_EC_number:missing_EC_number,PRODUCT:Putative Elongation factor P,CC_functional_completeness:complete,CC_gene:efp;alternative_location=no_alternative_location;annotator_comment=missing_annotator_comment;date=Tue Jul 31 10:05:06 CEST 2012;inference={gaze};note=GSCOCT00012438001~ Putative Elongation factor P~ efp~ complete;original_location=join(381805..381822%2C382048..382098%2C383122..383191%2C384170..384236%2C384325..384392%2C384571..384694%2C385829..385868%2C387202..387269%2C387653..387659);owner=coffea\n+chr1\tmanual_curation\texon\t12138\t12431\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t10860\t10890\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t10584\t10634\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t9491\t9560\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t8446\t8512\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t8290\t8357\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t7988\t8111\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t6814\t6853\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t5413\t5480\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\texon\t4545\t5029\t.\t-\t.\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t10860\t10877\t.\t-\t0\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t10584\t10634\t.\t-\t0\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t9491\t9560\t.\t-\t0\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t8446\t8512\t.\t-\t1\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t8290\t8357\t.\t-\t2\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t7988\t8111\t.\t-\t1\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t6814\t6853\t.\t-\t2\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t5413\t5480\t.\t-\t0\tParent=GSCOCT00012438001\n+chr1\tmanual_curation\tCDS\t5023\t5029\t.\t-\t2\tParent=GSCOCT00012438001\n+chr1\t'..b'8278\t.\t+\t0\tParent=GSCOCT00038323001\n+chr11\tmanual_curation\tCDS\t33508499\t33508549\t.\t+\t2\tParent=GSCOCT00038323001\n+chr11\tmanual_curation\tCDS\t33508691\t33508817\t.\t+\t2\tParent=GSCOCT00038323001\n+chr11\tmanual_curation\tgene\t33526867\t33528402\t.\t+\t.\tID=GSCOCG00038325001;Name=Cc11_g17510\n+chr11\tmanual_curation\tmRNA\t33526867\t33528402\t.\t+\t.\tID=GSCOCT00038325001;Parent=GSCOCG00038325001;Name=Cc11_g17510\n+chr11\tmanual_curation\tpolypeptide\t33526930\t33528073\t.\t+\t.\tID=GSCOCP00038325001;Dbxref=HAMAP:MF_01217,InterPro:IPR003231,InterPro:IPR006162,InterPro:IPR006163,InterPro:IPR009081,InterPro:IPR020806,PFAM:PF00550,PROFILE:PS50075,PROSITE:PS00012,SMART:SM00823,SUPERFAMILY:SSF47336,SwissProt:P52411,SwissProt:P52413,SwissProt:P93092,TAIR:AT1G54580.1,TAIR:AT1G54630.1,TAIR:AT4G25050.2,TIGRFAMs:TIGR00517,TrEMBL:B9I3Y4,TrEMBL:D7TYT3,TrEMBL:I1KP35;Derives_from=GSCOCT00038325001;Name=Cc11_g17510;Ontology_term=CC_evidence_code:ISS,GO:0000036,GO:0006633,GO:0031177,GO:0048037,CC_EC_number:missing_EC_number,PRODUCT:Acyl carrier protein 1%2C chloroplastic,CC_functional_completeness:complete,CC_gene:ACP1,CC_gene:ACL1.1,CC_gene:ACL1.3;alternative_location=no_alternative_location;annotator_comment=missing_annotator_comment;date=Tue Jul 31 10:05:06 CEST 2012;inference={gaze};note=GSCOCT00038325001~ Acyl carrier protein 1%2C chloroplastic~ ACP1~ complete;original_location=join(1801624..1801698%2C1802129..1802230%2C1802344..1802466%2C1802630..1802767);owner=coffea\n+chr11\tmanual_curation\texon\t33526867\t33527004\t.\t+\t.\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\texon\t33527435\t33527536\t.\t+\t.\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\texon\t33527650\t33527772\t.\t+\t.\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\texon\t33527936\t33528402\t.\t+\t.\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\tCDS\t33526930\t33527004\t.\t+\t0\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\tCDS\t33527435\t33527536\t.\t+\t0\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\tCDS\t33527650\t33527772\t.\t+\t0\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\tCDS\t33527936\t33528073\t.\t+\t0\tParent=GSCOCT00038325001\n+chr11\tmanual_curation\tgene\t33534437\t33534898\t.\t+\t.\tID=GSCOCG00038326001;Name=Cc11_g17520\n+chr11\tmanual_curation\tmRNA\t33534437\t33534898\t.\t+\t.\tID=GSCOCT00038326001;Parent=GSCOCG00038326001;Name=Cc11_g17520\n+chr11\tmanual_curation\tpolypeptide\t33534505\t33534774\t.\t+\t.\tID=GSCOCP00038326001;Dbxref=InterPro:IPR022251,PFAM:PF12609;Derives_from=GSCOCT00038326001;Name=Cc11_g17520;Ontology_term=CC_evidence_code:ISS,CC_EC_number:missing_EC_number,PRODUCT:Putative Protein of unknown function wound-induced,CC_functional_completeness:complete,CC_gene:unknown_gene;alternative_location=no_alternative_location;annotator_comment=missing_annotator_comment;date=Tue Jul 31 10:05:06 CEST 2012;inference={gaze};note=GSCOCT00038326001~ Putative Protein of unknown function wound-induced~ unknown_gene~ complete;original_location=1809199..1809468;owner=coffea\n+chr11\tmanual_curation\texon\t33534437\t33534898\t.\t+\t.\tParent=GSCOCT00038326001\n+chr11\tmanual_curation\tCDS\t33534505\t33534774\t.\t+\t0\tParent=GSCOCT00038326001\n+chr11\tmanual_curation\tgene\t33536746\t33538065\t.\t+\t.\tID=GSCOCG00038328001;Name=Cc11_g17530\n+chr11\tmanual_curation\tmRNA\t33536746\t33538065\t.\t+\t.\tID=GSCOCT00038328001;Parent=GSCOCG00038328001;Name=Cc11_g17530\n+chr11\tmanual_curation\tpolypeptide\t33536746\t33536928\t.\t+\t.\tID=GSCOCP00038328001;Derives_from=GSCOCT00038328001;Name=Cc11_g17530;Ontology_term=CC_evidence_code:ISS,CC_EC_number:missing_EC_number,PRODUCT:Hypothetical protein,CC_functional_completeness:missing_functional_completeness,CC_gene:unknown_gene;alternative_location=no_alternative_location;annotator_comment=missing_annotator_comment;date=Tue Jul 31 10:05:06 CEST 2012;inference={gaze};note=GSCOCT00038328001~ Hypothetical protein~ unknown_gene~ missing_functional_completeness;original_location=1811440..1811622;owner=coffea\n+chr11\tmanual_curation\texon\t33536746\t33538065\t.\t+\t.\tParent=GSCOCT00038328001\n+chr11\tmanual_curation\tCDS\t33536746\t33536928\t.\t+\t0\tParent=GSCOCT00038328001\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result1.hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result1.hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,4956 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result2.flanking.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result2.flanking.txt Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| b'@@ -0,0 +1,4955 @@\n+chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2264,TTTCTKACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAAT[C/T]AGCCTGTCCCCAGCCGTGCTGACTGGGCACGGCTGGGACAGGCGGCAAAAAAAAGGGCCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2353,ACGGCTGGGACAGGCGGCAAAAAAAAGGGCCAGCAAATGGGATGTATTTGGGGACATAAA[T/A]TTTGTAGCAAAAGTGAAACGAAAGGCCATACAAATTCACCGCACTAGCTGCCCTTTTACT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2482,CTCTTTCCTATGCTCTTTATTTTTTGGAAGAGATACCTAAACGATTTTATTGCCCTAATC[C/T]TAATCAAAGATTTTGATTTTATAACTTAAAGATTTTGCTGTGGAGTCTTATAACACTTAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2558,ATTTTATAACTTAAAGATTTTGCTGTGGAGTCTTATAACACTTAAGTTAGGAAGATCAAA[A/T]TTTTAAAGTGGAAATGGAAGATTATTATATTTTTCAAACTGCAAATTAGTATAATTCTAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2925,ATTAAAATTTAGTTTTGAAAACCAGTTAGTCATAAATGTATCTAATTACAAGCAAAAATT[A/T]AAAAAATATATATATRTATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGTY,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2941,GAAAACCAGTTAGTCATAAATGTATCTAATTACAAGCAAAAATTWAAAAAATATATATAT[A/G]TATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGTYGCGTATAAACTGCATT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2985,WAAAAAATATATATATRTATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGT[T/C]GCGTATAAACTGCATTTAATTTACATATAAATATTCATATATTAGCTTACACATGTTGTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3705,GATAATATCTTAATTTGTGATCCTAATTGATGCTAATATTACATAAACATAGGAAATTAT[G/T]TTACAGGAGAAAGTGTTATATAAACGGTACTACAAGGTTWTGTAAGTACAAAATTGATGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3745,ACATAAACATAGGAAATTATKTTACAGGAGAAAGTGTTATATAAACGGTACTACAAGGTT[A/T]TGTAAGTACAAAATTGATGATTCCTTAAGAAGAAAAAAAAAAATCTGGGCTTTGTTCTAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3864,AACATTGTCATAGAGAGTCAACAAGAAGAAGAAGATGGTGTCATGCTTATGCTTTCCATG[C/T]TGTCCATTCATGCGGCGAAAGASCAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGAC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3887,AGAAGAAGAAGATGGTGTCATGCTTATGCTTTCCATGYTGTCCATTCATGCGGCGAAAGA[G/C]CAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGACAAAGCCGGTGGTGGTGGCTKCTG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3944,AGASCAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGACAAAGCCGGTGGTGGTGGCT[G/T]CTGTGGACAGGGATGTGATTGGATTTGTGATTGCCATAGTTGATCCCATTATACATTAGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4109,TCAATTTTGAGAGGGAAGATCATGAGAAATTCGAGCCTCTCTTCCCGGACGCTCTTCCTA[C/T]GTGCTTCGCCCTACATCTTGAGTTCAAAAACTTTGATGACACAGAATACGAGTACCAGCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4438,ACCATGGTAGCTTTAGATTAGTCCAACTGGTAATTATTTTGTCCTGCTTTGTAAGGAAGT[T/C]AAATCAAAAGCTGAACAATTCCACCCAGTAAACTAAAACTTGCTAGATTGGCATCATGCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4555,TGCATGGTGATTCACGTTGATTCTTTATTGAAAAAAGATAAACGTTTTATGTACAAGATT[G/A]GGTAAGAAGCACAAATCAATTGAAGAGATCAATAATACCCGTGATAATAAAACACTAATG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4733,GCTGATCCAAATATGAATACCTGTGTCAAAAATCCATTCTAATGGTCCATCTCCATCCAT[C/G]AGTTCTTTTCCAAAACCACTGGACAAAGCTGTAGCCTCATCACCTCCCTCCCACTGGGGG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4879,GTGGGATTCTCATAAATATGCAAAATGTAAAACATTCTCATTTGAAAGAAATACTGCATA[T/C]GCAATAACCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4945,AACCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTG[G/A]ASTAATCCTATATAAYGAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4947,CCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTGRA[C/G]TAATCCTATATAAYGAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGCAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4961,CTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTGRASTAATCCTATATAA[C/T]GAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGCATTCAAAAGGGCCCAG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4967,TCTCATCAA'..b'-187522,ACAACAATTTCAAARAAGCAATATATAATAGCAWATTTAAAAATACAGCAGAAAATTCAT[A/T]AAAAAAAATATCATTTTTTATGCAWTTTGATTTTTTGCATTTGTTAAATTTTGTATATTA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187574,AAATTCATAAAAAAAAATATCATTTTTTATGCAWTTTGATTTTTTGCATTTGTTAAATTT[T/A]GTATATTATTCARTTAATAGTTATTGGATCTTAAGAAAATAAAAAAAAAACTAAAACATG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187614,TTTTTGCATTTGTTAAATTTTGTATATTATTCARTTAATAGTTATTGGATCTTAAGAAAA[A/G]AAAAAAAAAACTAAAACATGGTGTTTATGTAGGAGAAATGACAATATAATAAAAAAATGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187714,GACAATATAATAAAAAAATGAGACAGAGAATGGSACAGAGTGTGGGACAGAAGATCCGTT[G/C]CGTTTTTAATCYTCCTCCTTTTTCCTCTTTTCCTTTAAAAGGATTGGAGTCYCCTTTGGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187753,GTGTGGGACAGAAGATCCGTTGCGTTTTTAATCYTCCTCCTTTTTCCTCTTTTCCTTTAA[T/C]AGGATTGGAGTCYCCTTTGGATTAAAAAAAATGTATCATTTTGAATTAATCATTGATTAC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187793,TTTTTCCTCTTTTCCTTTAAAAGGATTGGAGTCYCCTTTGGATTAAAAAAAATGTATCAT[T/C]TTGAATTAATCATTGATTACTAAYTTTTTTGGAAATTATGCTTTGAGTCTATTTTGTCTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187844,ATGTATCATTTTGAATTAATCATTGATTACTAAYTTTTTTGGAAATTATGCTTTGAGTCT[T/C]TTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAACTTCAAAATTTA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187894,CTTTGAGTCTATTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAAC[G/A]TCAAAATTTAAAGCTTAATGTGCAGAAACAAAGCTCCTAAAACACATCGTGTTTGATACA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187903,TATTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAACTTCAAAATT[C/T]AAAGCTTAATGTGCAGAAACAAAGCTCCTAAAACACATCGTGTTTGATACAATAAAGTCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188013,CAATAAAGTCAATAGTGAGAATAATTTTATCCTWGCAAAATATGAAGAAAAAAAAATGCA[T/A]TACGGACTTTGCATGGCCTATAGTCAATTAGATAGGAAAAGTCGAGAAGTTGGAAAAGTC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188103,AGATAGGAAAAGTCGAGAAGTTGGAAAAGTCGGRAGCAAGAGAGAATGGAAAAGTCGGAA[G/A]CACGAAAGAAACCAAGAAGGCACGGCACGGGCACGGGCACGGRCACAGACTGTGTATGCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188173,AACCAAGAAGGCACGGCACGGGCACGGGCACGGRCACAGACTGTGTATGCTTTTAAGGTA[G/A]AGAGCAACAACAGACTGATTGTTTAGTTGATTCGTTAACTGCAGTTGATGCTACAAAAGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188266,CGTTAACTGCAGTTGATGCTACAAAAGCAACTGRAAARCTGGTTCACGCCTGCTGGAACA[A/G]ACTCAGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGGCGGCAATAGATATATT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188270,AACTGCAGTTGATGCTACAAAAGCAACTGRAAARCTGGTTCACGCCTGCTGGAACAAACT[A/G]AGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGGCGGCAATAGATATATTCGGY,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188311,ACGCCTGCTGGAACAAACTCAGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGG[T/G]GGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188357,TTATTAAATGATGGCGGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCT[C/T]CTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188364,ATGATGGCGGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCTTCTGGTT[G/C]CYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAGTCGGGTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188393,CTTTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGC[T/C]AGAATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188395,TTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCA[C/G]AATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGGCC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188416,TTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGC[T/C]GTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGGCCGATTCTCGGGGAAACACTGGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188438,CCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCC[C/A]GGGAGCTTTGGGTGGCCGATTCTCGGGGAAACACTGGAGTTTCTTCAGAGCGGATGGGAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188621,GACTTCATTGACCGGTGAGCCTATGGCCGTCTTRTCCGGCCCTGCAGCTCATAAGTTCTT[G/A]TTTGGCAACGAAAACAAGCTGGTCCAGGTCTGGTGGCCTCCCTCAGCAAAGAAGCTGCTG,0,0,0,Project_name,0,diploid,Other,Forward\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result2.hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result2.hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,4956 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result3.flanking.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result3.flanking.txt Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| b'@@ -0,0 +1,4955 @@\n+chr1-2209,GTCGCATCTGCAGCATATAGCCAACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCT[G/T]ACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2232,ACCTTCAACTTGCAGCTAAAACTCATCATCTCTTTCTKACTGGCTTAACGATATTGTAAG[A/C]TGACTCAGAGGCCCACTTTTTTTTTAAAAATYAGCCTGTCCCCAGCCGTGCTGACTGGGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2264,TTTCTKACTGGCTTAACGATATTGTAAGMTGACTCAGAGGCCCACTTTTTTTTTAAAAAT[C/T]AGCCTGTCCCCAGCCGTGCTGACTGGGCACGGCTGGGACAGGCGGCAAAAAAAAGGGCCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2353,ACGGCTGGGACAGGCGGCAAAAAAAAGGGCCAGCAAATGGGATGTATTTGGGGACATAAA[T/A]TTTGTAGCAAAAGTGAAACGAAAGGCCATACAAATTCACCGCACTAGCTGCCCTTTTACT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2482,CTCTTTCCTATGCTCTTTATTTTTTGGAAGAGATACCTAAACGATTTTATTGCCCTAATC[C/T]TAATCAAAGATTTTGATTTTATAACTTAAAGATTTTGCTGTGGAGTCTTATAACACTTAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2558,ATTTTATAACTTAAAGATTTTGCTGTGGAGTCTTATAACACTTAAGTTAGGAAGATCAAA[A/T]TTTTAAAGTGGAAATGGAAGATTATTATATTTTTCAAACTGCAAATTAGTATAATTCTAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2925,ATTAAAATTTAGTTTTGAAAACCAGTTAGTCATAAATGTATCTAATTACAAGCAAAAATT[A/T]AAAAAATATATATATRTATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGTY,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2941,GAAAACCAGTTAGTCATAAATGTATCTAATTACAAGCAAAAATTWAAAAAATATATATAT[A/G]TATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGTYGCGTATAAACTGCATT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-2985,WAAAAAATATATATATRTATATTAATTTTACATATATGGATTCTTATTCATGAATTTTGT[T/C]GCGTATAAACTGCATTTAATTTACATATAAATATTCATATATTAGCTTACACATGTTGTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3705,GATAATATCTTAATTTGTGATCCTAATTGATGCTAATATTACATAAACATAGGAAATTAT[G/T]TTACAGGAGAAAGTGTTATATAAACGGTACTACAAGGTTWTGTAAGTACAAAATTGATGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3745,ACATAAACATAGGAAATTATKTTACAGGAGAAAGTGTTATATAAACGGTACTACAAGGTT[A/T]TGTAAGTACAAAATTGATGATTCCTTAAGAAGAAAAAAAAAAATCTGGGCTTTGTTCTAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3864,AACATTGTCATAGAGAGTCAACAAGAAGAAGAAGATGGTGTCATGCTTATGCTTTCCATG[C/T]TGTCCATTCATGCGGCGAAAGASCAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGAC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3887,AGAAGAAGAAGATGGTGTCATGCTTATGCTTTCCATGYTGTCCATTCATGCGGCGAAAGA[G/C]CAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGACAAAGCCGGTGGTGGTGGCTKCTG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-3944,AGASCAAGAACAAGAAGCAGCAGCAGCAGCAGGAAACTGACAAAGCCGGTGGTGGTGGCT[G/T]CTGTGGACAGGGATGTGATTGGATTTGTGATTGCCATAGTTGATCCCATTATACATTAGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4109,TCAATTTTGAGAGGGAAGATCATGAGAAATTCGAGCCTCTCTTCCCGGACGCTCTTCCTA[C/T]GTGCTTCGCCCTACATCTTGAGTTCAAAAACTTTGATGACACAGAATACGAGTACCAGCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4438,ACCATGGTAGCTTTAGATTAGTCCAACTGGTAATTATTTTGTCCTGCTTTGTAAGGAAGT[T/C]AAATCAAAAGCTGAACAATTCCACCCAGTAAACTAAAACTTGCTAGATTGGCATCATGCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4555,TGCATGGTGATTCACGTTGATTCTTTATTGAAAAAAGATAAACGTTTTATGTACAAGATT[G/A]GGTAAGAAGCACAAATCAATTGAAGAGATCAATAATACCCGTGATAATAAAACACTAATG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4733,GCTGATCCAAATATGAATACCTGTGTCAAAAATCCATTCTAATGGTCCATCTCCATCCAT[C/G]AGTTCTTTTCCAAAACCACTGGACAAAGCTGTAGCCTCATCACCTCCCTCCCACTGGGGG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4879,GTGGGATTCTCATAAATATGCAAAATGTAAAACATTCTCATTTGAAAGAAATACTGCATA[T/C]GCAATAACCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4945,AACCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTG[G/A]ASTAATCCTATATAAYGAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4947,CCCCGAAATGAACACTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTGRA[C/G]TAATCCTATATAAYGAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGCAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4961,CTTGTTTCTCATCAACCCATCATTACCTACAGTGACAAAATTTGRASTAATCCTATATAA[C/T]GAGTGYCTGCAGAAAAGGTMCATCCKGAACGATAACTCCAGAGCATTCAAAAGGGCCCAG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-4967,TCTCATCAA'..b'-187522,ACAACAATTTCAAARAAGCAATATATAATAGCAWATTTAAAAATACAGCAGAAAATTCAT[A/T]AAAAAAAATATCATTTTTTATGCAWTTTGATTTTTTGCATTTGTTAAATTTTGTATATTA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187574,AAATTCATAAAAAAAAATATCATTTTTTATGCAWTTTGATTTTTTGCATTTGTTAAATTT[T/A]GTATATTATTCARTTAATAGTTATTGGATCTTAAGAAAATAAAAAAAAAACTAAAACATG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187614,TTTTTGCATTTGTTAAATTTTGTATATTATTCARTTAATAGTTATTGGATCTTAAGAAAA[A/G]AAAAAAAAAACTAAAACATGGTGTTTATGTAGGAGAAATGACAATATAATAAAAAAATGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187714,GACAATATAATAAAAAAATGAGACAGAGAATGGSACAGAGTGTGGGACAGAAGATCCGTT[G/C]CGTTTTTAATCYTCCTCCTTTTTCCTCTTTTCCTTTAAAAGGATTGGAGTCYCCTTTGGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187753,GTGTGGGACAGAAGATCCGTTGCGTTTTTAATCYTCCTCCTTTTTCCTCTTTTCCTTTAA[T/C]AGGATTGGAGTCYCCTTTGGATTAAAAAAAATGTATCATTTTGAATTAATCATTGATTAC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187793,TTTTTCCTCTTTTCCTTTAAAAGGATTGGAGTCYCCTTTGGATTAAAAAAAATGTATCAT[T/C]TTGAATTAATCATTGATTACTAAYTTTTTTGGAAATTATGCTTTGAGTCTATTTTGTCTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187844,ATGTATCATTTTGAATTAATCATTGATTACTAAYTTTTTTGGAAATTATGCTTTGAGTCT[T/C]TTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAACTTCAAAATTTA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187894,CTTTGAGTCTATTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAAC[G/A]TCAAAATTTAAAGCTTAATGTGCAGAAACAAAGCTCCTAAAACACATCGTGTTTGATACA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-187903,TATTTTGTCTTTGACCCAAATAAARATAACTTTYAGGTGGGAACTTGAAACTTCAAAATT[C/T]AAAGCTTAATGTGCAGAAACAAAGCTCCTAAAACACATCGTGTTTGATACAATAAAGTCA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188013,CAATAAAGTCAATAGTGAGAATAATTTTATCCTWGCAAAATATGAAGAAAAAAAAATGCA[T/A]TACGGACTTTGCATGGCCTATAGTCAATTAGATAGGAAAAGTCGAGAAGTTGGAAAAGTC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188103,AGATAGGAAAAGTCGAGAAGTTGGAAAAGTCGGRAGCAAGAGAGAATGGAAAAGTCGGAA[G/A]CACGAAAGAAACCAAGAAGGCACGGCACGGGCACGGGCACGGRCACAGACTGTGTATGCT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188173,AACCAAGAAGGCACGGCACGGGCACGGGCACGGRCACAGACTGTGTATGCTTTTAAGGTA[G/A]AGAGCAACAACAGACTGATTGTTTAGTTGATTCGTTAACTGCAGTTGATGCTACAAAAGC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188266,CGTTAACTGCAGTTGATGCTACAAAAGCAACTGRAAARCTGGTTCACGCCTGCTGGAACA[A/G]ACTCAGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGGCGGCAATAGATATATT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188270,AACTGCAGTTGATGCTACAAAAGCAACTGRAAARCTGGTTCACGCCTGCTGGAACAAACT[A/G]AGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGGCGGCAATAGATATATTCGGY,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188311,ACGCCTGCTGGAACAAACTCAGCTGCAGGCAGTKGTATTGCAGTGATTATTAAATGATGG[T/G]GGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188357,TTATTAAATGATGGCGGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCT[C/T]CTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188364,ATGATGGCGGCAATAGATATATTCGGYGTCTTTSTTAATATTATTGCACCTCTTCTGGTT[G/C]CYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAGTCGGGTT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188393,CTTTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGC[T/C]AGAATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGG,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188395,TTSTTAATATTATTGCACCTCTTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCA[C/G]AATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGGCC,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188416,TTCTGGTTACYGSTGTTTTCCTCCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGC[T/C]GTCGGGTTTGCGTCTTCCTCCGGGGAGCTTTGGGTGGCCGATTCTCGGGGAAACACTGGA,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188438,CCGATATTTGAYCGCCAGAATAAGAAACAAGAAMAAGCAGTCGGGTTTGCGTCTTCCTCC[C/A]GGGAGCTTTGGGTGGCCGATTCTCGGGGAAACACTGGAGTTTCTTCAGAGCGGATGGGAT,0,0,0,Project_name,0,diploid,Other,Forward\n+chr1-188621,GACTTCATTGACCGGTGAGCCTATGGCCGTCTTRTCCGGCCCTGCAGCTCATAAGTTCTT[G/A]TTTGGCAACGAAAACAAGCTGGTCCAGGTCTGGTGGCCTCCCTCAGCAAAGAAGCTGCTG,0,0,0,Project_name,0,diploid,Other,Forward\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result3.gene_alignment.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result3.gene_alignment.fas Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -0,0 +1,72 @@ +>Cc01g00080_CATB1_1 +T +>Cc01g00080_CATB1_2 +T +>Cc01g00090_CATB1_1 +T +>Cc01g00090_CATB1_2 +T +>Cc01g00050_CATB1_1 +C +>Cc01g00050_CATB1_2 +A +>Cc01g00140_CATB1_1 +G +>Cc01g00140_CATB1_2 +A +>Cc01g00150_CATB1_1 +G +>Cc01g00150_CATB1_2 +A +>Cc01g00100_CATB1_1 +G +>Cc01g00100_CATB1_2 +C +>intergenic_CATB1_1 +T +>intergenic_CATB1_2 +A +>Cc01g00180_CATB1_1 +G +>Cc01g00180_CATB1_2 +A +>Cc01g00110_CATB1_1 +T +>Cc01g00110_CATB1_2 +A +>Cc01g00130_CATB1_1 +C +>Cc01g00130_CATB1_2 +T +>Cc01g00160_CATB1_1 +C +>Cc01g00160_CATB1_2 +T +>Cc01g00030_CATB1_1 +T +>Cc01g00030_CATB1_2 +C +>Cc01g00020_CATB1_1 +G +>Cc01g00020_CATB1_2 +C +>Cc01g00070_CATB1_1 +A +>Cc01g00070_CATB1_2 +A +>Cc01g00060_CATB1_1 +T +>Cc01g00060_CATB1_2 +A +>Cc01g00170_CATB1_1 +A +>Cc01g00170_CATB1_2 +G +>Cc01g00120_CATB1_1 +C +>Cc01g00120_CATB1_2 +C +>Cc01g00040_CATB1_1 +G +>Cc01g00040_CATB1_2 +G |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-result3.hapmap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-result3.hapmap Tue Dec 15 05:18:02 2015 -0500 |
| b |
| b'@@ -0,0 +1,4956 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|
| b |
| diff -r 345f88a8f483 -r 10627af23f10 test-data/vcf2fastaAndHapmap-sample.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcf2fastaAndHapmap-sample.vcf Tue Dec 15 05:18:02 2015 -0500 |
| [ |
| b'@@ -0,0 +1,5000 @@\n+##fileformat=VCFv4.1\n+##FILTER=<ID=LowQual,Description="Low quality">\n+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">\n+##GATKCommandLine=<ID=UnifiedGenotyper,Version=2.7-4-g6f46d11,Date="Fri Nov 01 16:17:42 CET 2013",Epoch=1383319062999,CommandLineOptions="analysis_type=UnifiedGenotyper input_file=[/scratch/hueber-35211/CATB1.RG.sorted.indelrealigned.bam] read_buffer_size=null phone_home=AWS gatk_key=null tag=NA read_filter=[BadCigar] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/projects/coffee_snp/donnees_genomiques/pseudomolecules.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 allow_bqsr_on_reduced_bams_despite_repeated_warnings=false validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=null disable_auto_index_creation_and_locking_when_reading_rods=false num_threads=4 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false version=false genotype_likelihoods_model=SNP pcr_error_rate=1.0E-4 computeSLOD=false annotateNDA=false pair_hmm_implementation=LOGLESS_CACHING min_base_quality_score=17 max_deletion_fraction=0.05 allSitePLs=false min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false output_mode=EMIT_VARIANTS_ONLY heterozygosity=0.001 indel_heterozygosity=1.25E-4 genotyping_mode=DISCOVERY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=6 input_prior=[] contamination_fraction_to_filter=0.0 contamination_fraction_per_sample_file=null p_nonref_model=EXACT_INDEPENDENT exactcallslog=null dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub onlyEmitSamples=[] debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">\n+##INFO=<ID=AF,Number=A,Type'..b'm=1.599;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:20,22:42:99:726,0,669\n+chr1\t188266\t.\tA\tG\t878.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.261;DP=56;Dels=0.00;FS=2.268;HaplotypeScore=3.8663;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-1.827;QD=15.69;ReadPosRankSum=0.412;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:28,27:56:99:907,0,965\n+chr1\t188270\t.\tA\tG\t850.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=1.747;DP=54;Dels=0.00;FS=3.828;HaplotypeScore=4.8662;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.692;QD=15.75;ReadPosRankSum=0.709;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,27:54:99:879,0,898\n+chr1\t188311\t.\tT\tG\t901.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.508;DP=53;Dels=0.00;FS=2.345;HaplotypeScore=0.7340;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.454;QD=17.01;ReadPosRankSum=0.223;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,28:53:99:930,0,831\n+chr1\t188357\t.\tC\tT\t1327.77\t.\tAC=2;AF=1.00;AN=2;DP=36;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=2;MLEAF=1.00;MQ=60.00;MQ0=0;QD=24.46;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t1/1:0,36:36:99:1356,105,0\n+chr1\t188364\t.\tG\tC\t578.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.285;DP=40;Dels=0.00;FS=0.000;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.585;QD=14.47;ReadPosRankSum=-0.612;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:22,18:40:99:607,0,770\n+chr1\t188393\t.\tT\tC\t515.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.106;DP=42;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.191;QD=12.28;ReadPosRankSum=-1.385;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:24,18:42:99:544,0,828\n+chr1\t188395\t.\tC\tG\t543.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-1.484;DP=41;Dels=0.00;FS=0.000;HaplotypeScore=2.5781;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.775;QD=13.26;ReadPosRankSum=-1.773;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:23,18:41:99:572,0,791\n+chr1\t188416\t.\tT\tC\t397.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=-0.717;DP=39;Dels=0.00;FS=1.302;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=-0.893;QD=10.20;ReadPosRankSum=0.571;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:25,14:39:99:426,0,821\n+chr1\t188438\t.\tC\tA\t930.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=2.123;DP=50;Dels=0.00;FS=5.900;HaplotypeScore=0.0000;MLEAC=1;MLEAF=0.500;MQ=59.41;MQ0=0;MQRankSum=0.020;QD=18.62;ReadPosRankSum=-0.472;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),UTR_5_PRIME(MODIFIER||||Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:21,29:50:99:959,0,659\n+chr1\t188621\t.\tG\tA\t704.77\t.\tAC=1;AF=0.500;AN=2;BaseQRankSum=0.090;DP=49;Dels=0.00;FS=5.986;HaplotypeScore=0.9996;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=0.090;QD=14.38;ReadPosRankSum=-0.774;EFF=DOWNSTREAM(MODIFIER||||Cc01g00190|mRNA||GSCOCT00012415001|),SYNONYMOUS_CODING(LOW|SILENT|ttG/ttA|L4|Cc01g00180|mRNA||GSCOCT00012416001|Exon_chr1_188034_188856)\tGT:AD:DP:GQ:PL\t0/1:27,22:49:99:733,0,926\n' |
| b |
| diff -r 345f88a8f483 -r 10627af23f10 tool_dependencies.xml --- a/tool_dependencies.xml Fri Jul 10 10:38:43 2015 -0400 +++ b/tool_dependencies.xml Tue Dec 15 05:18:02 2015 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> <package name="plink" version="1.07"> - <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="65400c333b88" name="package_plink_1_07" owner="dereeper" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |