| Previous changeset 6:626b714f72bb (2012-04-10) Next changeset 8:30771a097f14 (2012-06-20) |
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Commit message:
change wsf -> snp; wpf -> sap |
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modified:
add_fst_column.xml average_fst.xml coverage_distributions.xml datatypes_conf.xml dpmix.xml extract_flanking_dna.xml extract_primers.xml find_intervals.xml lib/galaxy/datatypes/wsf.py modify_snp_table.xml pathway_image.xml phylogenetic_tree.xml prepare_population_structure.xml rank_pathways.xml select_individuals.xml select_snps.xml specify_restriction_enzymes.xml |
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added:
test-data/test_in/sample.sap test-data/test_in/sample.snp test-data/test_out/add_fst_column/add_fst_column.snp test-data/test_out/modify_snp_table/modify.snp test-data/test_out/select_snps/select_snps.snp test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp |
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removed:
test-data/test_in/sample.wpf test-data/test_in/sample.wsf test-data/test_out/add_fst_column/add_fst_column.wsf test-data/test_out/modify_snp_table/modify.wsf test-data/test_out/select_snps/select_snps.wsf test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.wsf |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 add_fst_column.xml --- a/add_fst_column.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/add_fst_column.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -10,7 +10,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <param name="p1_input" type="data" format="ind" label="Population 1 individuals" /> <param name="p2_input" type="data" format="ind" label="Population 2 individuals" /> @@ -40,12 +40,12 @@ </inputs> <outputs> - <data name="output" format="wsf" metadata_source="input" /> + <data name="output" format="snp" metadata_source="input" /> </outputs> <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="p1_input" value="test_in/a.ind" ftype="ind" /> <param name="p2_input" value="test_in/b.ind" ftype="ind" /> <param name="data_source" value="0" /> @@ -54,7 +54,7 @@ <param name="retain" value="0" /> <param name="discard_fixed" value="1" /> <param name="biased" value="0" /> - <output name="output" file="test_out/add_fst_column/add_fst_column.wsf" /> + <output name="output" file="test_out/add_fst_column/add_fst_column.snp" /> </test> </tests> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 average_fst.xml --- a/average_fst.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/average_fst.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -15,7 +15,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <param name="p1_input" type="data" format="ind" label="Population 1 individuals" /> <param name="p2_input" type="data" format="ind" label="Population 2 individuals" /> @@ -61,7 +61,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="p1_input" value="test_in/a.ind" ftype="ind" /> <param name="p2_input" value="test_in/b.ind" ftype="ind" /> <param name="ds_choice" value="0" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 coverage_distributions.xml --- a/coverage_distributions.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/coverage_distributions.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -21,7 +21,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <conditional name="individuals"> <param name="choice" type="select" label="Individuals"> @@ -54,7 +54,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="choice" value="0" /> <output name="output" file="test_out/coverage_distributions/coverage.html" ftype="html" compare="diff" lines_diff="2"> <extra_files type="file" name="coverage.pdf" value="test_out/coverage_distributions/coverage.pdf" compare="sim_size" delta = "1000"/> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 datatypes_conf.xml --- a/datatypes_conf.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/datatypes_conf.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -6,8 +6,8 @@ <registration> <datatype extension="ind" type="galaxy.datatypes.wsf:Individuals" display_in_upload="true"/> <datatype extension="wped" type="galaxy.datatypes.wsf:Wped" display_in_upload="true"/> - <datatype extension="wsf" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> - <datatype extension="wpf" type="galaxy.datatypes.wsf:SapFile" display_in_upload="true"/> + <datatype extension="snp" type="galaxy.datatypes.wsf:SnpFile" display_in_upload="true"/> + <datatype extension="sap" type="galaxy.datatypes.wsf:SapFile" display_in_upload="true"/> </registration> - <sniffers/> + <sniffers/> </datatypes> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 dpmix.xml --- a/dpmix.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/dpmix.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -10,7 +10,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="Dataset"> + <param name="input" type="data" format="snp" label="Dataset"> <validator type="unspecified_build" message="This dataset does not have a reference species and cannot be used with this tool" /> </param> <param name="ap1_input" type="data" format="ind" label="Ancestral population 1 individuals" /> @@ -32,7 +32,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="ap1_input" value="test_in/a.ind" ftype="ind" /> <param name="ap2_input" value="test_in/b.ind" ftype="ind" /> <param name="p_input" value="test_in/c.ind" ftype="ind" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 extract_flanking_dna.xml --- a/extract_flanking_dna.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/extract_flanking_dna.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -43,7 +43,7 @@ <!-- Need snpcalls files from Webb before uncommenting <tests> <test> - <param name="input" value="test_out/select_snps/select_snps.wsf" ftype="wsf" /> + <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" /> <param name="output_format" value="primer3" /> <param name="choice" value="0" /> <output name="output" file="test_out/extract_flanking_dna/extract_flanking_dna.txt" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 extract_primers.xml --- a/extract_primers.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/extract_primers.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -37,7 +37,7 @@ <tests> <test> - <param name="input" value="test_out/select_snps/select_snps.wsf" ftype="wsf" /> + <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" /> <param name="choice" value="0"/> <output name="output" file="test_out/extract_primers/extract_primers.txt" /> </test> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 find_intervals.xml --- a/find_intervals.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/find_intervals.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -71,7 +71,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="score_col" value="5" /> <param name="type" value="value" /> <param name="cutoff_val" value="700.0" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 lib/galaxy/datatypes/wsf.py --- a/lib/galaxy/datatypes/wsf.py Tue Apr 10 13:51:19 2012 -0400 +++ b/lib/galaxy/datatypes/wsf.py Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -141,7 +141,7 @@ class SnpFile( Fake ): """ Webb's SNP file format """ - file_ext = 'wsf' + file_ext = 'snp' MetadataElement( name="individual_names", desc="individual names", visible=False, readonly=True ) MetadataElement( name="individual_columns", desc="individual columns", visible=False, readonly=True ) @@ -178,7 +178,7 @@ class SapFile( Fake ): """ Webb's SAP file format """ - file_ext = 'wpf' + file_ext = 'sap' MetadataElement( name="kegg_gene", desc="KEGG gene code column", param=metadata.ColumnParameter, default=0 ) MetadataElement( name="kegg_path", desc="KEGG pathway code/name column", param=metadata.ColumnParameter, default=0 ) |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 modify_snp_table.xml --- a/modify_snp_table.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/modify_snp_table.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -15,7 +15,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <param name="p1_input" type="data" format="ind" label="Population individuals" /> <conditional name="limit_coverage"> <param name="choice" type="select" format="integer" label="Option"> @@ -33,19 +33,19 @@ </inputs> <outputs> - <data name="output" format="wsf" metadata_source="input" /> + <data name="output" format="snp" metadata_source="input" /> </outputs> <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="p1_input" value="test_in/a.ind" ftype="ind" /> <param name="choice" value="1" /> <param name="lo_coverage" value="0" /> <param name="hi_coverage" value="1000" /> <param name="low_ind_cov" value="3" /> <param name="lo_quality" value="30" /> - <output name="output" file="test_out/modify_snp_table/modify.wsf" /> + <output name="output" file="test_out/modify_snp_table/modify.snp" /> </test> </tests> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 pathway_image.xml --- a/pathway_image.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/pathway_image.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -11,7 +11,7 @@ </command> <inputs> - <param name="input" type="data" format="wpf" label="Table"> + <param name="input" type="data" format="sap" label="Table"> <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" /> </param> <param name="pathway" type="select"> @@ -29,7 +29,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wpf" ftype="wpf" /> + <param name="input" value="test_in/sample.sap" ftype="sap" /> <param name="pathway" value="cfa05214" /> <output name="output" file="test_out/pathway_image/pathway_image.png" compare="sim_size" delta = "10000" /> </test> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 phylogenetic_tree.xml --- a/phylogenetic_tree.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/phylogenetic_tree.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -28,7 +28,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <conditional name="individuals"> <param name="choice" type="select" label="Individuals"> @@ -86,7 +86,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="choice" value="0" /> <param name="minimum_coverage" value="3" /> <param name="minimum_quality" value="30" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 prepare_population_structure.xml --- a/prepare_population_structure.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/prepare_population_structure.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -18,7 +18,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf" label="SNP table" /> + <param name="input" type="data" format="snp" label="SNP table" /> <param name="min_reads" type="integer" min="0" value="0" label="Minimum reads covering a SNP, per individual" /> <param name="min_qual" type="integer" min="0" value="0" label="Minimum quality value, per individual" /> <param name="min_spacing" type="integer" min="0" value="0" label="Minimum spacing between SNPs on the same scaffold" /> @@ -46,7 +46,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="min_reads" value="3" /> <param name="min_qual" value="30" /> <param name="min_spacing" value="0" /> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 rank_pathways.xml --- a/rank_pathways.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/rank_pathways.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -16,7 +16,7 @@ </command> <inputs> - <param name="input" type="data" format="wpf" label="Table"> + <param name="input" type="data" format="sap" label="Table"> <validator type="metadata" check="kegg_gene,kegg_path" message="Missing KEGG gene code column and/or KEGG pathway code/name column metadata. Click the pencil icon in the history item to edit/save the metadata attributes" /> </param> <param name="output_format" type="select" label="Output format"> @@ -31,7 +31,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wpf" ftype="wpf" /> + <param name="input" value="test_in/sample.sap" ftype="sap" /> <param name="output_format" value="a" /> <output name="output" file="test_out/rank_pathways/rank_pathways.tabular" /> </test> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 select_individuals.xml --- a/select_individuals.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/select_individuals.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -12,7 +12,7 @@ </command> <inputs> - <param name="input" type="data" format="wsf"/> + <param name="input" type="data" format="snp"/> <param name="individuals" type="select" display="checkboxes" multiple="true" label="Individuals to include"> <options> <filter type="data_meta" ref="input" key="individual_names" /> @@ -27,7 +27,7 @@ <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf" /> + <param name="input" value="test_in/sample.snp" ftype="snp" /> <param name="individuals" value="PB1,PB2" /> <output name="output" file="test_in/a.ind" /> </test> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 select_snps.xml --- a/select_snps.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/select_snps.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -35,15 +35,15 @@ </inputs> <outputs> - <data format="wsf" name="output" metadata_source="input"/> + <data format="snp" name="output" metadata_source="input"/> </outputs> <tests> <test> - <param name="input" value="test_in/sample.wsf" ftype="wsf"/> + <param name="input" value="test_in/sample.snp" ftype="snp"/> <param name="num_snps" value="100"/> <param name="choice" value="0"/> - <output name="output" file="test_out/select_snps/select_snps.wsf" /> + <output name="output" file="test_out/select_snps/select_snps.snp" /> </test> </tests> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 specify_restriction_enzymes.xml --- a/specify_restriction_enzymes.xml Tue Apr 10 13:51:19 2012 -0400 +++ b/specify_restriction_enzymes.xml Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -40,15 +40,15 @@ </inputs> <outputs> - <data format="wsf" name="output" metadata_source="input"/> + <data format="snp" name="output" metadata_source="input"/> </outputs> <tests> <test> - <param name="input" value="test_out/select_snps/select_snps.wsf" ftype="wsf" /> + <param name="input" value="test_out/select_snps/select_snps.snp" ftype="snp" /> <param name="choice" value="0" /> <param name="enzymes" value="Bsp1286I,HaeII,RsaI" /> - <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.wsf" /> + <output name="output" file="test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp" /> </test> </tests> |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_in/sample.sap --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_in/sample.sap Wed Apr 18 11:12:21 2012 -0400 |
| [ |
| b'@@ -0,0 +1,401 @@\n+#{"column_names":["contig","pos","ref","rPos","trns","pep","AA1","loc","AA2","KEGG","pred","path"],"pos":2,"rPos":4,"ref":3,"dbkey":"canFam2","scaffold":1,"species":"bear","kegg_gene":10,"kegg_path":12}\n+Contig39_chr1_3261104_3261850\t414\tchr1\t3261546\tENSCAFT00000000001\tENSCAFP00000000001\tS\t667\tF\t476153\tprobably damaging\tcfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways\n+Contig62_chr1_19011969_19012646\t265\tchr1\t19012240\tENSCAFT00000000144\tENSCAFP00000000125\t*\t161\tR\t483960\tprobably damaging\tN\n+Contig36_chr1_20102654_20103213\t365\tchr1\t20103029\tENSCAFT00000000160\tENSCAFP00000000140\tR\t407\tQ\t610160\tpossibly damaging\tN\n+Contig136_chr10_3710404_3714591\t3079\tchr10\t3713499\tENSCAFT00000000215\tENSCAFP00000000194\tT\t103\tP\tU\tbenign\tN\n+Contig36_chr1_23682012_23682647\t374\tchr1\t23682388\tENSCAFT00000000233\tENSCAFP00000000210\tN\t234\tS\t483973\tbenign\tN\n+Contig163_chr10_4573526_4574494\t487\tchr10\t4574010\tENSCAFT00000000365\tENSCAFP00000000332\tR\t186\tK\t474414\tbenign\tcfa00450=Selenocompound metabolism.cfa00970=Aminoacyl-tRNA biosynthesis\n+Contig55_chr1_40056604_40059808\t2081\tchr1\t40058686\tENSCAFT00000000507\tENSCAFP00000000458\tI\t247\tK\t484023\tpossibly damaging\tN\n+Contig17_chr1_40203628_40205630\t1417\tchr1\t40205044\tENSCAFT00000000517\tENSCAFP00000000468\tN\t109\tS\t476233\tbenign\tN\n+Contig97_chr1_44847984_44848380\t285\tchr1\t44848272\tENSCAFT00000000674\tENSCAFP00000000618\tQ\t27\tR\t611986\tbenign\tN\n+Contig214_chr10_16106753_16106969\t121\tchr10\t16106873\tENSCAFT00000000724\tENSCAFP00000000668\tA\t301\tT\t609478\tbenign\tN\n+Contig75_chr1_45731970_45732932\t436\tchr1\t45732397\tENSCAFT00000000760\tENSCAFP00000000701\tI\t490\tV\tU\tbenign\tN\n+Contig33_chr1_45614845_45617413\t1835\tchr1\t45616685\tENSCAFT00000000760\tENSCAFP00000000701\tA\t4390\tV\tU\tbenign\tN\n+Contig95_chr10_18829724_18831056\t914\tchr10\t18830645\tENSCAFT00000000762\tENSCAFP00000000703\tA\t512\tV\tU\tpossibly damaging\tN\n+Contig197_chr13_8622062_8623071\t606\tchr13\t8622665\tENSCAFT00000001047\tENSCAFP00000000959\tT\t406\tI\t475067\tpossibly damaging\tcfa00240=Pyrimidine metabolism.cfa00410=beta-Alanine metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa00983=Drug metabolism - other enzymes.cfa01100=Metabolic pathways\n+Contig243_chr10_19959210_19960069\t701\tchr10\t19959858\tENSCAFT00000001052\tENSCAFP00000000964\tE\t1345\tK\tU\tbenign\tN\n+Contig137_chr13_10622950_10624043\t1039\tchr13\t10623979\tENSCAFT00000001063\tENSCAFP00000000975\tE\t10\tK\t481999\tbenign\tN\n+Contig137_chr13_10622950_10624043\t1006\tchr13\t10623946\tENSCAFT00000001063\tENSCAFP00000000975\tR\t21\tC\t481999\tprobably damaging\tN\n+Contig115_chr12_4411478_4412322\t124\tchr12\t4411614\tENSCAFT00000001076\tENSCAFP00000000986\tR\t177\tH\tU\tbenign\tN\n+Contig150_chr12_4438230_4439944\t385\tchr12\t4438614\tENSCAFT00000001104\tENSCAFP00000001014\tY\t277\tD\t607591\tbenign\tN\n+Contig84_chr1_52076858_52077103\t80\tchr1\t52076943\tENSCAFT00000001141\tENSCAFP00000001046\tC\t147\tY\t484064\tbenign\tN\n+Contig29_chr13_13215547_13217183\t793\tchr13\t13216352\tENSCAFT00000001146\tENSCAFP00000001050\tP\t1\tR\t475076\tprobably damaging\tN\n+Contig251_chr10_22876556_22877097\t152\tchr10\t22876714\tENSCAFT00000001204\tENSCAFP00000001103\tE\t1162\tD\t481203\tbenign\tN\n+Contig21_chr10_22964856_22965302\t202\tchr10\t22965058\tENSCAFT00000001219\tENSCAFP00000001115\tP\t6\tQ\t474465\tbenign\tN\n+Contig199_chr12_5083018_5084534\t453\tchr12\t5083472\tENSCAFT00000001250\tENSCAFP00000001144\tI\t185\tT\t481729.481731\tbenign\tN.cfa04145=Phagosome.cfa04514=Cell adhesion molecules (CAMs).cfa04612=Antigen processing and presentation.cfa04672=Intestinal immune network for IgA production.cfa04940=Type I diabetes mellitus.cfa05140=Leishmaniasis.cfa05145=Toxoplasmosis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05164=Influenza A.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft re'..b'1\t701\tchr6\t25357665\tENSCAFT00000035750\tENSCAFP00000031044\tP\t479\tS\t608555\tbenign\tcfa04142=Lysosome\n+Contig18_chr9_58576258_58576773\t215\tchr9\t58576474\tENSCAFT00000035914\tENSCAFP00000031224\tK\t118\tE\t480706\tbenign\tN\n+Contig8_chr15_38734005_38734403\t242\tchr15\t38734244\tENSCAFT00000035916\tENSCAFP00000031226\tA\t237\tV\t611996\tpossibly damaging\tN\n+Contig76_chr3_30625909_30626247\t159\tchr3\t30626069\tENSCAFT00000036198\tENSCAFP00000031549\tT\t135\tS\t479171\tbenign\tcfa00260=Glycine, serine and threonine metabolism.cfa00270=Cysteine and methionine metabolism.cfa01100=Metabolic pathways\n+Contig86_chr37_14528768_14530343\t873\tchr37\t14529628\tENSCAFT00000036570\tENSCAFP00000031969\tV\t738\tD\t478875.609202\tpossibly damaging\tcfa04060=Cytokine-cytokine receptor interaction.cfa04350=TGF-beta signaling pathway\n+Contig9_chr5_54124181_54125739\t1134\tchr5\t54125291\tENSCAFT00000036640\tENSCAFP00000032043\tA\t187\tT\t610286\tbenign\tN\n+Contig107_chr9_8990420_8991676\t1178\tchr9\t8991591\tENSCAFT00000036774\tENSCAFP00000032186\tT\t55\tM\t483288\tbenign\tN\n+Contig47_chr12_20319418_20320775\t1212\tchr12\t20320622\tENSCAFT00000036825\tENSCAFP00000032241\tK\t606\tT\t474930\tbenign\tcfa00280=Valine, leucine and isoleucine degradation.cfa00630=Glyoxylate and dicarboxylate metabolism.cfa00640=Propanoate metabolism.cfa01100=Metabolic pathways\n+Contig4_chr2_45195542_45196115\t233\tchr2\t45195785\tENSCAFT00000037022\tENSCAFP00000032463\tD\t833\tN\t478055\tpossibly damaging\tN\n+Contig8_chr8_77227029_77227651\t339\tchr8\t77227366\tENSCAFT00000037096\tENSCAFP00000032544\tT\t61\tA\t490895.612602\tbenign\tcfa04020=Calcium signaling pathway.cfa04145=Phagosome.cfa04640=Hematopoietic cell lineage.cfa04650=Natural killer cell mediated cytotoxicity.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04666=Fc gamma R-mediated phagocytosis.cfa04672=Intestinal immune network for IgA production.cfa05140=Leishmaniasis.cfa05143=African trypanosomiasis.cfa05146=Amoebiasis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05162=Measles.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05340=Primary immunodeficiency.cfa05414=Dilated cardiomyopathy.cfa05416=Viral myocarditis\n+Contig2_chr7_60049092_60051693\t266\tchr7\t60049361\tENSCAFT00000038176\tENSCAFP00000033857\tT\t195\tM\tU\tprobably damaging\tN\n+Contig31_chr30_24179816_24187402\t4867\tchr30\t24184686\tENSCAFT00000038211\tENSCAFP00000033897\tG\t103\tS\tU\tbenign\tN\n+Contig9_chr27_48250956_48251793\t192\tchr27\t48251161\tENSCAFT00000038256\tENSCAFP00000033944\tT\t166\tM\t477739\tprobably damaging\tN\n+Contig45_chr27_43537046_43537944\t568\tchr27\t43537599\tENSCAFT00000038301\tENSCAFP00000033996\tM\t69\tI\t611773\tbenign\tcfa04010=MAPK signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa05200=Pathways in cancer.cfa05218=Melanoma\n+Contig133_chr18_28371600_28372547\t83\tchr18\t28371695\tENSCAFT00000038383\tENSCAFP00000034090\tL\t102\tQ\t475933\tprobably damaging\tN\n+Contig11_chr28_8532951_8533892\t511\tchr28\t8533462\tENSCAFT00000038937\tENSCAFP00000034728\tR\t19\tC\t477763\tprobably damaging\tcfa03008=Ribosome biogenesis in eukaryotes.cfa03013=RNA transport\n+Contig1_chr14_5733966_5735336\t783\tchr14\t5734754\tENSCAFT00000039094\tENSCAFP00000034905\tA\t166\tT\tU\tbenign\tN\n+Contig48_chr27_6001075_6001818\t392\tchr27\t6001478\tENSCAFT00000039109\tENSCAFP00000034919\tR\t103\tH\tU\tprobably damaging\tN\n+Contig40_chr11_43589173_43590288\t973\tchr11\t43590138\tENSCAFT00000039148\tENSCAFP00000034962\tR\t1617\tP\t481557\tbenign\tN\n+Contig1_chr14_30424688_30425258\t179\tchr14\t30424861\tENSCAFT00000039390\tENSCAFP00000035239\tT\t648\tI\t475245\tbenign\tcfa04666=Fc gamma R-mediated phagocytosis.cfa04810=Regulation of actin cytoskeleton\n+Contig58_chr8_7461111_7462065\t323\tchr8\t7461423\tENSCAFT00000039451\tENSCAFP00000035309\tL\t112\tF\tU\tbenign\tN\n+Contig1_chr25_43094809_43095852\t908\tchr25\t43095708\tENSCAFT00000039609\tENSCAFP00000035483\tW\t18\tG\tU\tunknown\tN\n+Contig114_chr25_43076436_43076800\t141\tchr25\t43076581\tENSCAFT00000039609\tENSCAFP00000035483\tS\t45\tC\tU\tunknown\tN\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_in/sample.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_in/sample.snp Wed Apr 18 11:12:21 2012 -0400 |
| [ |
| b'@@ -0,0 +1,402 @@\n+#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",\n+#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}\n+Contig161_chr1_4641264_4641879\t115\tC\tT\t73.5\tchr1\t4641382\tC\t6\t0\t2\t45\t8\t0\t2\t51\t15\t0\t2\t72\t5\t0\t2\t42\t6\t0\t2\t45\t10\t0\t2\t57\tY\t54\t0.323\t0\n+Contig48_chr1_10150253_10151311\t11\tA\tG\t94.3\tchr1\t10150264\tA\t1\t0\t2\t30\t1\t0\t2\t30\t1\t0\t2\t30\t3\t0\t2\t36\t1\t0\t2\t30\t1\t0\t2\t30\tY\t22\t+99.\t0\n+Contig20_chr1_21313469_21313570\t66\tC\tT\t54.0\tchr1\t21313534\tC\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\tN\t1\t+99.\t0\n+Contig86_chr1_30984450_30985684\t670\tC\tT\t365.0\tchr1\t30985133\tC\t9\t0\t2\t54\t10\t0\t2\t57\t13\t0\t2\t66\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\tY\t145\t0.031\t0\n+Contig5_chr1_32562160_32563940\t1215\tG\tT\t163.0\tchr1\t32563356\tG\t17\t0\t2\t78\t19\t0\t2\t84\t20\t0\t2\t87\t14\t0\t2\t69\t12\t0\t2\t63\t10\t0\t2\t57\tY\t17\t0.251\t0\n+Contig110_chr1_33385093_33386888\t510\tC\tT\t270.0\tchr1\t33385587\tA\t14\t0\t2\t69\t11\t0\t2\t60\t19\t0\t2\t84\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\tY\t13\t0.126\t0\n+Contig100_chr1_33562920_33564288\t743\tC\tT\t178.0\tchr1\t33563655\tC\t6\t0\t2\t45\t10\t0\t2\t57\t8\t0\t2\t51\t5\t0\t2\t42\t13\t0\t2\t66\t7\t0\t2\t48\tY\t13\t0.090\t3\n+Contig7_chr1_37302355_37302489\t97\tA\tG\t59.2\tchr1\t37302452\tG\t3\t0\t2\t36\t8\t0\t2\t51\t5\t0\t2\t42\t8\t0\t2\t51\t7\t0\t2\t48\t6\t0\t2\t45\tN\t56\t2.812\t0\n+Contig62_chr1_41880715_41882180\t1078\tT\tG\t57.6\tchr1\t41881785\tT\t14\t0\t2\t69\t15\t0\t2\t72\t16\t0\t2\t75\t13\t0\t2\t66\t8\t0\t2\t51\t10\t0\t2\t57\tY\t21\t0.477\t0\n+Contig47_chr1_48409178_48409384\t37\tC\tT\t134.0\tchr1\t48409215\tT\t5\t0\t2\t42\t6\t0\t2\t45\t8\t0\t2\t51\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\tN\t66\t+99.\t0\n+Contig119_chr1_49647683_49650077\t1618\tC\tA\t99.7\tchr1\t49649276\tA\t8\t0\t2\t51\t11\t0\t2\t60\t10\t0\t2\t57\t9\t0\t2\t54\t10\t0\t2\t57\t14\t0\t2\t69\tY\t16\t0.166\t0\n+Contig21_chr1_60697952_60699446\t307\tG\tA\t51.9\tchr1\t60698265\tG\t12\t0\t2\t63\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\t9\t0\t2\t54\t4\t0\t2\t39\tY\t98\t0.507\t0\n+Contig131_chr1_62319542_62320564\t169\tC\tG\t103.0\tchr1\t62319709\tC\t12\t0\t2\t63\t12\t0\t2\t66\t14\t0\t2\t69\t12\t0\t2\t63\t9\t0\t2\t54\t9\t0\t2\t54\tY\t73\t0.307\t1\n+Contig14_chr1_63450425_63450680\t101\tT\tA\t102.0\tchr1\t63450530\tT\t8\t0\t2\t51\t10\t0\t2\t57\t18\t0\t2\t81\t8\t0\t2\t51\t8\t0\t2\t34\t8\t0\t2\t51\tN\t99\t1.085\t0\n+Contig83_chr1_63869778_63869942\t40\tT\tC\t23.7\tchr1\t63869819\tC\t5\t0\t2\t42\t7\t0\t2\t48\t2\t0\t2\t33\t4\t0\t2\t39\t6\t0\t2\t48\t4\t0\t2\t39\tN\t654\t1.364\t0\n+Contig30_chr1_64702572_64703138\t178\tA\tT\t117.0\tchr1\t64702750\tT\t10\t0\t2\t57\t10\t0\t2\t57\t20\t0\t2\t87\t21\t0\t2\t90\t6\t0\t2\t45\t12\t0\t2\t63\tY\t50\t3.872\t0\n+Contig101_chr1_69868406_69868872\t287\tG\tA\t14.6\tchr1\t69868689\tG\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t8\t0\t2\t51\t7\t0\t2\t48\t8\t0\t2\t51\tN\t137\t0.305\t0\n+Contig35_chr1_74482577_74482791\t170\tG\tA\t45.4\tchr1\t74482751\tA\t3\t0\t2\t36\t4\t0\t2\t39\t13\t0\t2\t66\t2\t0\t2\t33\t5\t0\t2\t42\t2\t0\t2\t33\tN\t20\t+99.\t3\n+Contig49_chr1_83865731_83865944\t85\tG\tA\t34.1\tchr1\t-1\tN\t4\t0\t2\t39\t4\t0\t2\t39\t8\t0\t2\t51\t2\t0\t2\t33\t5\t0\t2\t42\t4\t0\t2\t39\tN\t-1\t1.485\t0\n+Contig64_chr1_87343284_87345672\t163\tT\tA\t3.76\tchr1\t87343443\tC\t0\t2\t2\t1\t0\t0\t-1\t0\t5\t0\t2\t42\t2\t0\t2\t33\t0\t1\t2\t14\t0\t0\t-1\t0\tN\t3\t0.039\t2\n+Contig20_chr1_110679280_110679687\t181\tC\tT\t87.4\tchr1\t110679454\t-\t1\t0\t2\t30\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\t2\t0\t2\t33\t0\t0\t-1\t0\tN\t31\t0.660\t2\n+Contig129_chr1_117547123_117548666\t926\tG\tA\t126.0\tchr1\t117548059\tG\t19\t0\t2\t84\t9\t0\t2\t54\t11\t0\t2\t60\t10\t0\t2\t57\t12\t0\t2\t63\t11\t0\t2\t60\tY\t64\t0.049\t0\n+Contig7_chr1_125154638_125154844\t190\tG\tT\t130.0\tchr1\t125154818\tA\t5\t0\t2\t42\t4\t0\t2\t39\t7\t0\t2\t48\t2\t0\t2\t33\t7\t0\t2\t48\t4\t0\t2\t39\tN\t33\t+99.\t0\n+Contig222_chr2_9817738_9818143\t220\tC\tT\t888.0\tchr2\t9817960\tC\t17\t0\t2\t78\t12\t0\t2\t63\t20\t0\t2\t87\t8\t0\t2\t51\t11\t0\t2\t60\t12\t0\t2\t63\tY\t76\t0.093\t1\n+Contig47_chr2_25470778_25471576\t126\tG\tA\t888.0\tchr2\t25470896\tG\t12\t0\t2\t63\t14\t0\t2\t69\t14\t0\t2\t69\t10\t0\t2\t57\t18\t0\t2\t81\t13\t0\t2\t66\tN\t11\t0.289\t1\n+Contig10_chr2_40859744_40860534\t637\tG\tA\t888.0\tchr2\t40860397\tA\t3\t0\t2\t36\t3\t0\t2\t36\t2\t0\t2\t33\t7\t0\t2\t48\t6\t0\t2\t45\t8\t0\t2\t51\tY\t42\t1.435\t0\n+Contig52_chr2_41421981_41422725\t604\tC\tA\t888.0\tchr2\t41422583\tA\t17\t0\t2\t78\t18\t0\t2\t81\t14\t0\t2\t69\t17\t0\t2\t78\t12\t0\t2\t63\t14\t0\t2\t69\tY\t44\t0.882\t0\n+Contig94_chr2_43869105_43870358\t220\tG\tA\t888.0\tchr2'..b'\t0\n+Contig5_chr36_4562983_4563634\t343\tC\tT\t151.0\tchr36\t4563324\tT\t20\t0\t2\t87\t20\t0\t2\t87\t23\t0\t2\t96\t24\t0\t2\t99\t9\t0\t2\t54\t8\t0\t2\t51\tY\t40\t1.169\t0\n+Contig75_chr36_7885319_7885588\t53\tG\tA\t25.7\tchr36\t7885372\tG\t10\t0\t2\t57\t8\t0\t2\t51\t13\t0\t2\t66\t7\t0\t2\t48\t4\t0\t2\t39\t7\t0\t2\t48\tN\t7\t2.653\t0\n+Contig184_chr36_18956191_18958552\t187\tA\tG\t11.5\tchr36\t18956371\tG\t10\t0\t2\t57\t11\t0\t2\t60\t21\t0\t2\t90\t14\t0\t2\t69\t7\t0\t2\t48\t4\t0\t2\t39\tN\t278\t1.434\t2\n+Contig12_chr36_21557176_21557828\t513\tT\tA\t159.0\tchr36\t21557695\tA\t11\t0\t2\t60\t14\t0\t2\t69\t21\t0\t2\t90\t12\t0\t2\t63\t15\t0\t2\t72\t11\t0\t2\t60\tY\t55\t0.222\t0\n+Contig2_chr36_22436067_22436794\t653\tC\tT\t73.0\tchr36\t22436730\tC\t11\t0\t2\t60\t16\t0\t2\t75\t13\t0\t2\t66\t11\t0\t2\t60\t21\t0\t2\t90\t21\t0\t2\t90\tY\t9\t0.534\t0\n+Contig133_chr36_32954045_32955409\t136\tA\tG\t116.0\tchr36\t32954182\tA\t16\t0\t2\t75\t15\t0\t2\t72\t20\t0\t2\t87\t11\t0\t2\t60\t18\t0\t2\t81\t13\t0\t2\t66\tY\t74\t3.772\t1\n+Contig53_chr37_6665763_6665919\t116\tC\tT\t111.0\tchr37\t6665875\tC\t9\t0\t2\t54\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t8\t0\t2\t51\t10\t0\t2\t57\tN\t15\t10.875\t1\n+Contig42_chr37_9589176_9591269\t252\tG\tA\t25.1\tchr37\t9589430\tG\t10\t0\t2\t40\t13\t0\t2\t66\t18\t0\t2\t81\t21\t0\t2\t90\t9\t0\t2\t54\t17\t0\t2\t78\tN\t67\t1.170\t2\n+Contig2_chr37_17134963_17136513\t1140\tA\tC\t158.0\tchr37\t17136092\tA\t14\t0\t2\t69\t24\t0\t2\t99\t17\t0\t2\t78\t16\t0\t2\t75\t15\t0\t2\t75\t13\t0\t2\t66\tY\t12\t0.053\t1\n+Contig18_chr37_17147806_17149851\t291\tT\tG\t112.0\tchr37\t17148084\tT\t4\t6\t1\t45\t16\t0\t2\t75\t17\t0\t2\t78\t14\t0\t2\t69\t22\t0\t2\t93\t13\t0\t2\t66\tY\t41\t4.442\t0\n+Contig64_chr37_17606895_17607534\t565\tC\tT\t30.2\tchr37\t17607439\tA\t9\t0\t2\t54\t16\t0\t2\t75\t20\t0\t2\t87\t14\t0\t2\t69\t16\t0\t2\t75\t10\t0\t2\t57\tN\t20\t1.622\t0\n+Contig126_chr37_21587881_21590621\t373\tG\tT\t132.0\tchr37\t21588256\tG\t11\t0\t2\t60\t11\t0\t2\t60\t23\t0\t2\t96\t12\t0\t2\t63\t8\t0\t2\t51\t18\t0\t2\t81\tY\t12\t0.549\t0\n+Contig2_chr37_31197993_31198256\t182\tC\tT\t39.6\tchr37\t31198171\tT\t6\t0\t2\t45\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t12\t0\t2\t63\tN\t2\t0.595\t0\n+Contig46_chr37_31852376_31853555\t825\tA\tG\t111.0\tchr37\t31853191\tG\t19\t0\t2\t84\t14\t0\t2\t69\t15\t0\t2\t72\t7\t0\t2\t48\t8\t0\t2\t51\t16\t0\t2\t75\tY\t17\t0.128\t1\n+Contig7_chr38_12217200_12218387\t1163\tA\tT\t44.4\tchr38\t12218353\tA\t11\t0\t2\t60\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t11\t0\t2\t60\t11\t0\t2\t60\tY\t67\t+99.\t0\n+Contig15_chr38_12282020_12282253\t150\tC\tT\t156.0\tchr38\t12282164\tA\t17\t0\t2\t78\t11\t0\t2\t60\t19\t0\t2\t84\t14\t0\t2\t69\t5\t0\t2\t42\t14\t0\t2\t69\tY\t26\t2.952\t1\n+Contig4_chr38_14807432_14807747\t275\tA\tG\t36.5\tchr38\t14807715\tG\t1\t0\t2\t30\t2\t0\t2\t33\t2\t0\t2\t33\t4\t0\t2\t39\t1\t0\t2\t30\t0\t0\t-1\t0\tY\t28\t+99.\t1\n+Contig6_chr38_16185744_16186110\t325\tA\tG\t74.9\tchr38\t16186061\tA\t5\t0\t2\t42\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\t1\t0\t2\t30\t12\t0\t2\t63\tY\t40\t+99.\t0\n+Contig265_chrX_2689247_2689484\t114\tC\tG\t103.0\tchrX\t2689356\tC\t11\t0\t2\t60\t9\t0\t2\t54\t13\t0\t2\t66\t16\t0\t2\t75\t14\t0\t2\t69\t10\t0\t2\t57\tN\t2\t9.232\t1\n+Contig122_chrX_6026976_6027327\t330\tC\tT\t79.4\tchrX\t6027303\tC\t3\t0\t2\t36\t3\t0\t2\t36\t3\t0\t2\t36\t4\t0\t2\t39\t3\t0\t2\t36\t6\t0\t2\t45\tY\t30\t+99.\t0\n+Contig15_chrX_15659909_15660340\t15\tA\tC\t14.9\tchrX\t15659924\tC\t1\t0\t2\t30\t1\t0\t2\t30\t3\t0\t2\t36\t6\t0\t2\t45\t2\t0\t2\t33\t0\t0\t-1\t0\tY\t216\t+99.\t1\n+Contig12_chrX_23243561_23244412\t479\tC\tG\t67.7\tchrX\t23244037\tC\t2\t0\t2\t33\t4\t2\t2\t8\t2\t6\t1\t43\t7\t0\t2\t48\t6\t0\t2\t45\t4\t0\t2\t39\tY\t208\t1.620\t0\n+Contig113_chrX_26287829_26288398\t385\tC\tT\t59.6\tchrX\t26288213\tC\t9\t0\t2\t54\t9\t0\t2\t54\t17\t0\t2\t78\t11\t0\t2\t60\t3\t8\t1\t44\t4\t0\t2\t39\tN\t13\t0.077\t0\n+Contig186_chrX_29118735_29118939\t192\tG\tA\t7.01\tchrX\t29118931\tG\t1\t0\t2\t30\t7\t0\t2\t48\t4\t0\t2\t39\t5\t0\t2\t42\t8\t0\t2\t51\t4\t0\t2\t39\tN\t50\t+99.\t0\n+Contig237_chrX_31256648_31257654\t165\tT\tA\t246.0\tchrX\t31256814\tT\t7\t0\t2\t48\t23\t0\t2\t96\t19\t0\t2\t84\t17\t0\t2\t78\t14\t0\t2\t69\t8\t0\t2\t51\tY\t37\t1.481\t0\n+Contig25_chrX_40729418_40730089\t332\tC\tT\t31.2\tchrX\t40729745\tC\t0\t0\t-1\t0\t2\t0\t2\t33\t4\t0\t2\t39\t5\t0\t2\t42\t3\t0\t2\t36\t3\t0\t2\t36\tY\t34\t0.212\t0\n+Contig90_chrX_57430715_57431566\t548\tC\tT\t116.0\tchrX\t57431266\tT\t9\t0\t2\t54\t18\t0\t2\t81\t13\t0\t2\t66\t14\t0\t2\t69\t8\t0\t2\t54\t7\t0\t2\t48\tY\t261\t0.154\t1\n+Contig133_chrX_84833782_84834125\t182\tG\tA\t69.7\tchrX\t84833962\tG\t5\t0\t2\t42\t18\t0\t2\t81\t12\t0\t2\t63\t19\t0\t2\t84\t6\t3\t1\t27\t7\t0\t2\t48\tN\t619\t0.278\t0\n+Contig129_chrX_90586053_90586467\t135\tA\tT\t120.0\tchrX\t90586195\tA\t1\t0\t2\t30\t6\t0\t2\t45\t8\t0\t2\t51\t5\t0\t2\t42\t1\t0\t2\t30\t2\t0\t2\t33\tN\t637\t0.245\t0\n+Contig125_chrX_93319363_93320877\t349\tA\tC\t145.0\tchrX\t93319721\tA\t4\t0\t2\t39\t6\t0\t2\t45\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\t6\t0\t2\t45\tY\t59\t1.686\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_in/sample.wpf --- a/test-data/test_in/sample.wpf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,401 +0,0 @@\n-#{"column_names":["contig","pos","ref","rPos","trns","pep","AA1","loc","AA2","KEGG","pred","path"],"pos":2,"rPos":4,"ref":3,"dbkey":"canFam2","scaffold":1,"species":"bear","kegg_gene":10,"kegg_path":12}\n-Contig39_chr1_3261104_3261850\t414\tchr1\t3261546\tENSCAFT00000000001\tENSCAFP00000000001\tS\t667\tF\t476153\tprobably damaging\tcfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways\n-Contig62_chr1_19011969_19012646\t265\tchr1\t19012240\tENSCAFT00000000144\tENSCAFP00000000125\t*\t161\tR\t483960\tprobably damaging\tN\n-Contig36_chr1_20102654_20103213\t365\tchr1\t20103029\tENSCAFT00000000160\tENSCAFP00000000140\tR\t407\tQ\t610160\tpossibly damaging\tN\n-Contig136_chr10_3710404_3714591\t3079\tchr10\t3713499\tENSCAFT00000000215\tENSCAFP00000000194\tT\t103\tP\tU\tbenign\tN\n-Contig36_chr1_23682012_23682647\t374\tchr1\t23682388\tENSCAFT00000000233\tENSCAFP00000000210\tN\t234\tS\t483973\tbenign\tN\n-Contig163_chr10_4573526_4574494\t487\tchr10\t4574010\tENSCAFT00000000365\tENSCAFP00000000332\tR\t186\tK\t474414\tbenign\tcfa00450=Selenocompound metabolism.cfa00970=Aminoacyl-tRNA biosynthesis\n-Contig55_chr1_40056604_40059808\t2081\tchr1\t40058686\tENSCAFT00000000507\tENSCAFP00000000458\tI\t247\tK\t484023\tpossibly damaging\tN\n-Contig17_chr1_40203628_40205630\t1417\tchr1\t40205044\tENSCAFT00000000517\tENSCAFP00000000468\tN\t109\tS\t476233\tbenign\tN\n-Contig97_chr1_44847984_44848380\t285\tchr1\t44848272\tENSCAFT00000000674\tENSCAFP00000000618\tQ\t27\tR\t611986\tbenign\tN\n-Contig214_chr10_16106753_16106969\t121\tchr10\t16106873\tENSCAFT00000000724\tENSCAFP00000000668\tA\t301\tT\t609478\tbenign\tN\n-Contig75_chr1_45731970_45732932\t436\tchr1\t45732397\tENSCAFT00000000760\tENSCAFP00000000701\tI\t490\tV\tU\tbenign\tN\n-Contig33_chr1_45614845_45617413\t1835\tchr1\t45616685\tENSCAFT00000000760\tENSCAFP00000000701\tA\t4390\tV\tU\tbenign\tN\n-Contig95_chr10_18829724_18831056\t914\tchr10\t18830645\tENSCAFT00000000762\tENSCAFP00000000703\tA\t512\tV\tU\tpossibly damaging\tN\n-Contig197_chr13_8622062_8623071\t606\tchr13\t8622665\tENSCAFT00000001047\tENSCAFP00000000959\tT\t406\tI\t475067\tpossibly damaging\tcfa00240=Pyrimidine metabolism.cfa00410=beta-Alanine metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa00983=Drug metabolism - other enzymes.cfa01100=Metabolic pathways\n-Contig243_chr10_19959210_19960069\t701\tchr10\t19959858\tENSCAFT00000001052\tENSCAFP00000000964\tE\t1345\tK\tU\tbenign\tN\n-Contig137_chr13_10622950_10624043\t1039\tchr13\t10623979\tENSCAFT00000001063\tENSCAFP00000000975\tE\t10\tK\t481999\tbenign\tN\n-Contig137_chr13_10622950_10624043\t1006\tchr13\t10623946\tENSCAFT00000001063\tENSCAFP00000000975\tR\t21\tC\t481999\tprobably damaging\tN\n-Contig115_chr12_4411478_4412322\t124\tchr12\t4411614\tENSCAFT00000001076\tENSCAFP00000000986\tR\t177\tH\tU\tbenign\tN\n-Contig150_chr12_4438230_4439944\t385\tchr12\t4438614\tENSCAFT00000001104\tENSCAFP00000001014\tY\t277\tD\t607591\tbenign\tN\n-Contig84_chr1_52076858_52077103\t80\tchr1\t52076943\tENSCAFT00000001141\tENSCAFP00000001046\tC\t147\tY\t484064\tbenign\tN\n-Contig29_chr13_13215547_13217183\t793\tchr13\t13216352\tENSCAFT00000001146\tENSCAFP00000001050\tP\t1\tR\t475076\tprobably damaging\tN\n-Contig251_chr10_22876556_22877097\t152\tchr10\t22876714\tENSCAFT00000001204\tENSCAFP00000001103\tE\t1162\tD\t481203\tbenign\tN\n-Contig21_chr10_22964856_22965302\t202\tchr10\t22965058\tENSCAFT00000001219\tENSCAFP00000001115\tP\t6\tQ\t474465\tbenign\tN\n-Contig199_chr12_5083018_5084534\t453\tchr12\t5083472\tENSCAFT00000001250\tENSCAFP00000001144\tI\t185\tT\t481729.481731\tbenign\tN.cfa04145=Phagosome.cfa04514=Cell adhesion molecules (CAMs).cfa04612=Antigen processing and presentation.cfa04672=Intestinal immune network for IgA production.cfa04940=Type I diabetes mellitus.cfa05140=Leishmaniasis.cfa05145=Toxoplasmosis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05164=Influenza A.cfa05166=HTLV-I infection.cfa05168=Herpes simplex infection.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft re'..b'1\t701\tchr6\t25357665\tENSCAFT00000035750\tENSCAFP00000031044\tP\t479\tS\t608555\tbenign\tcfa04142=Lysosome\n-Contig18_chr9_58576258_58576773\t215\tchr9\t58576474\tENSCAFT00000035914\tENSCAFP00000031224\tK\t118\tE\t480706\tbenign\tN\n-Contig8_chr15_38734005_38734403\t242\tchr15\t38734244\tENSCAFT00000035916\tENSCAFP00000031226\tA\t237\tV\t611996\tpossibly damaging\tN\n-Contig76_chr3_30625909_30626247\t159\tchr3\t30626069\tENSCAFT00000036198\tENSCAFP00000031549\tT\t135\tS\t479171\tbenign\tcfa00260=Glycine, serine and threonine metabolism.cfa00270=Cysteine and methionine metabolism.cfa01100=Metabolic pathways\n-Contig86_chr37_14528768_14530343\t873\tchr37\t14529628\tENSCAFT00000036570\tENSCAFP00000031969\tV\t738\tD\t478875.609202\tpossibly damaging\tcfa04060=Cytokine-cytokine receptor interaction.cfa04350=TGF-beta signaling pathway\n-Contig9_chr5_54124181_54125739\t1134\tchr5\t54125291\tENSCAFT00000036640\tENSCAFP00000032043\tA\t187\tT\t610286\tbenign\tN\n-Contig107_chr9_8990420_8991676\t1178\tchr9\t8991591\tENSCAFT00000036774\tENSCAFP00000032186\tT\t55\tM\t483288\tbenign\tN\n-Contig47_chr12_20319418_20320775\t1212\tchr12\t20320622\tENSCAFT00000036825\tENSCAFP00000032241\tK\t606\tT\t474930\tbenign\tcfa00280=Valine, leucine and isoleucine degradation.cfa00630=Glyoxylate and dicarboxylate metabolism.cfa00640=Propanoate metabolism.cfa01100=Metabolic pathways\n-Contig4_chr2_45195542_45196115\t233\tchr2\t45195785\tENSCAFT00000037022\tENSCAFP00000032463\tD\t833\tN\t478055\tpossibly damaging\tN\n-Contig8_chr8_77227029_77227651\t339\tchr8\t77227366\tENSCAFT00000037096\tENSCAFP00000032544\tT\t61\tA\t490895.612602\tbenign\tcfa04020=Calcium signaling pathway.cfa04145=Phagosome.cfa04640=Hematopoietic cell lineage.cfa04650=Natural killer cell mediated cytotoxicity.cfa04662=B cell receptor signaling pathway.cfa04664=Fc epsilon RI signaling pathway.cfa04666=Fc gamma R-mediated phagocytosis.cfa04672=Intestinal immune network for IgA production.cfa05140=Leishmaniasis.cfa05143=African trypanosomiasis.cfa05146=Amoebiasis.cfa05150=Staphylococcus aureus infection.cfa05152=Tuberculosis.cfa05162=Measles.cfa05310=Asthma.cfa05320=Autoimmune thyroid disease.cfa05322=Systemic lupus erythematosus.cfa05323=Rheumatoid arthritis.cfa05330=Allograft rejection.cfa05340=Primary immunodeficiency.cfa05414=Dilated cardiomyopathy.cfa05416=Viral myocarditis\n-Contig2_chr7_60049092_60051693\t266\tchr7\t60049361\tENSCAFT00000038176\tENSCAFP00000033857\tT\t195\tM\tU\tprobably damaging\tN\n-Contig31_chr30_24179816_24187402\t4867\tchr30\t24184686\tENSCAFT00000038211\tENSCAFP00000033897\tG\t103\tS\tU\tbenign\tN\n-Contig9_chr27_48250956_48251793\t192\tchr27\t48251161\tENSCAFT00000038256\tENSCAFP00000033944\tT\t166\tM\t477739\tprobably damaging\tN\n-Contig45_chr27_43537046_43537944\t568\tchr27\t43537599\tENSCAFT00000038301\tENSCAFP00000033996\tM\t69\tI\t611773\tbenign\tcfa04010=MAPK signaling pathway.cfa04810=Regulation of actin cytoskeleton.cfa05200=Pathways in cancer.cfa05218=Melanoma\n-Contig133_chr18_28371600_28372547\t83\tchr18\t28371695\tENSCAFT00000038383\tENSCAFP00000034090\tL\t102\tQ\t475933\tprobably damaging\tN\n-Contig11_chr28_8532951_8533892\t511\tchr28\t8533462\tENSCAFT00000038937\tENSCAFP00000034728\tR\t19\tC\t477763\tprobably damaging\tcfa03008=Ribosome biogenesis in eukaryotes.cfa03013=RNA transport\n-Contig1_chr14_5733966_5735336\t783\tchr14\t5734754\tENSCAFT00000039094\tENSCAFP00000034905\tA\t166\tT\tU\tbenign\tN\n-Contig48_chr27_6001075_6001818\t392\tchr27\t6001478\tENSCAFT00000039109\tENSCAFP00000034919\tR\t103\tH\tU\tprobably damaging\tN\n-Contig40_chr11_43589173_43590288\t973\tchr11\t43590138\tENSCAFT00000039148\tENSCAFP00000034962\tR\t1617\tP\t481557\tbenign\tN\n-Contig1_chr14_30424688_30425258\t179\tchr14\t30424861\tENSCAFT00000039390\tENSCAFP00000035239\tT\t648\tI\t475245\tbenign\tcfa04666=Fc gamma R-mediated phagocytosis.cfa04810=Regulation of actin cytoskeleton\n-Contig58_chr8_7461111_7462065\t323\tchr8\t7461423\tENSCAFT00000039451\tENSCAFP00000035309\tL\t112\tF\tU\tbenign\tN\n-Contig1_chr25_43094809_43095852\t908\tchr25\t43095708\tENSCAFT00000039609\tENSCAFP00000035483\tW\t18\tG\tU\tunknown\tN\n-Contig114_chr25_43076436_43076800\t141\tchr25\t43076581\tENSCAFT00000039609\tENSCAFP00000035483\tS\t45\tC\tU\tunknown\tN\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_in/sample.wsf --- a/test-data/test_in/sample.wsf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,402 +0,0 @@\n-#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",\n-#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}\n-Contig161_chr1_4641264_4641879\t115\tC\tT\t73.5\tchr1\t4641382\tC\t6\t0\t2\t45\t8\t0\t2\t51\t15\t0\t2\t72\t5\t0\t2\t42\t6\t0\t2\t45\t10\t0\t2\t57\tY\t54\t0.323\t0\n-Contig48_chr1_10150253_10151311\t11\tA\tG\t94.3\tchr1\t10150264\tA\t1\t0\t2\t30\t1\t0\t2\t30\t1\t0\t2\t30\t3\t0\t2\t36\t1\t0\t2\t30\t1\t0\t2\t30\tY\t22\t+99.\t0\n-Contig20_chr1_21313469_21313570\t66\tC\tT\t54.0\tchr1\t21313534\tC\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\tN\t1\t+99.\t0\n-Contig86_chr1_30984450_30985684\t670\tC\tT\t365.0\tchr1\t30985133\tC\t9\t0\t2\t54\t10\t0\t2\t57\t13\t0\t2\t66\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\tY\t145\t0.031\t0\n-Contig5_chr1_32562160_32563940\t1215\tG\tT\t163.0\tchr1\t32563356\tG\t17\t0\t2\t78\t19\t0\t2\t84\t20\t0\t2\t87\t14\t0\t2\t69\t12\t0\t2\t63\t10\t0\t2\t57\tY\t17\t0.251\t0\n-Contig110_chr1_33385093_33386888\t510\tC\tT\t270.0\tchr1\t33385587\tA\t14\t0\t2\t69\t11\t0\t2\t60\t19\t0\t2\t84\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\tY\t13\t0.126\t0\n-Contig100_chr1_33562920_33564288\t743\tC\tT\t178.0\tchr1\t33563655\tC\t6\t0\t2\t45\t10\t0\t2\t57\t8\t0\t2\t51\t5\t0\t2\t42\t13\t0\t2\t66\t7\t0\t2\t48\tY\t13\t0.090\t3\n-Contig7_chr1_37302355_37302489\t97\tA\tG\t59.2\tchr1\t37302452\tG\t3\t0\t2\t36\t8\t0\t2\t51\t5\t0\t2\t42\t8\t0\t2\t51\t7\t0\t2\t48\t6\t0\t2\t45\tN\t56\t2.812\t0\n-Contig62_chr1_41880715_41882180\t1078\tT\tG\t57.6\tchr1\t41881785\tT\t14\t0\t2\t69\t15\t0\t2\t72\t16\t0\t2\t75\t13\t0\t2\t66\t8\t0\t2\t51\t10\t0\t2\t57\tY\t21\t0.477\t0\n-Contig47_chr1_48409178_48409384\t37\tC\tT\t134.0\tchr1\t48409215\tT\t5\t0\t2\t42\t6\t0\t2\t45\t8\t0\t2\t51\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\tN\t66\t+99.\t0\n-Contig119_chr1_49647683_49650077\t1618\tC\tA\t99.7\tchr1\t49649276\tA\t8\t0\t2\t51\t11\t0\t2\t60\t10\t0\t2\t57\t9\t0\t2\t54\t10\t0\t2\t57\t14\t0\t2\t69\tY\t16\t0.166\t0\n-Contig21_chr1_60697952_60699446\t307\tG\tA\t51.9\tchr1\t60698265\tG\t12\t0\t2\t63\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\t9\t0\t2\t54\t4\t0\t2\t39\tY\t98\t0.507\t0\n-Contig131_chr1_62319542_62320564\t169\tC\tG\t103.0\tchr1\t62319709\tC\t12\t0\t2\t63\t12\t0\t2\t66\t14\t0\t2\t69\t12\t0\t2\t63\t9\t0\t2\t54\t9\t0\t2\t54\tY\t73\t0.307\t1\n-Contig14_chr1_63450425_63450680\t101\tT\tA\t102.0\tchr1\t63450530\tT\t8\t0\t2\t51\t10\t0\t2\t57\t18\t0\t2\t81\t8\t0\t2\t51\t8\t0\t2\t34\t8\t0\t2\t51\tN\t99\t1.085\t0\n-Contig83_chr1_63869778_63869942\t40\tT\tC\t23.7\tchr1\t63869819\tC\t5\t0\t2\t42\t7\t0\t2\t48\t2\t0\t2\t33\t4\t0\t2\t39\t6\t0\t2\t48\t4\t0\t2\t39\tN\t654\t1.364\t0\n-Contig30_chr1_64702572_64703138\t178\tA\tT\t117.0\tchr1\t64702750\tT\t10\t0\t2\t57\t10\t0\t2\t57\t20\t0\t2\t87\t21\t0\t2\t90\t6\t0\t2\t45\t12\t0\t2\t63\tY\t50\t3.872\t0\n-Contig101_chr1_69868406_69868872\t287\tG\tA\t14.6\tchr1\t69868689\tG\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t8\t0\t2\t51\t7\t0\t2\t48\t8\t0\t2\t51\tN\t137\t0.305\t0\n-Contig35_chr1_74482577_74482791\t170\tG\tA\t45.4\tchr1\t74482751\tA\t3\t0\t2\t36\t4\t0\t2\t39\t13\t0\t2\t66\t2\t0\t2\t33\t5\t0\t2\t42\t2\t0\t2\t33\tN\t20\t+99.\t3\n-Contig49_chr1_83865731_83865944\t85\tG\tA\t34.1\tchr1\t-1\tN\t4\t0\t2\t39\t4\t0\t2\t39\t8\t0\t2\t51\t2\t0\t2\t33\t5\t0\t2\t42\t4\t0\t2\t39\tN\t-1\t1.485\t0\n-Contig64_chr1_87343284_87345672\t163\tT\tA\t3.76\tchr1\t87343443\tC\t0\t2\t2\t1\t0\t0\t-1\t0\t5\t0\t2\t42\t2\t0\t2\t33\t0\t1\t2\t14\t0\t0\t-1\t0\tN\t3\t0.039\t2\n-Contig20_chr1_110679280_110679687\t181\tC\tT\t87.4\tchr1\t110679454\t-\t1\t0\t2\t30\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\t2\t0\t2\t33\t0\t0\t-1\t0\tN\t31\t0.660\t2\n-Contig129_chr1_117547123_117548666\t926\tG\tA\t126.0\tchr1\t117548059\tG\t19\t0\t2\t84\t9\t0\t2\t54\t11\t0\t2\t60\t10\t0\t2\t57\t12\t0\t2\t63\t11\t0\t2\t60\tY\t64\t0.049\t0\n-Contig7_chr1_125154638_125154844\t190\tG\tT\t130.0\tchr1\t125154818\tA\t5\t0\t2\t42\t4\t0\t2\t39\t7\t0\t2\t48\t2\t0\t2\t33\t7\t0\t2\t48\t4\t0\t2\t39\tN\t33\t+99.\t0\n-Contig222_chr2_9817738_9818143\t220\tC\tT\t888.0\tchr2\t9817960\tC\t17\t0\t2\t78\t12\t0\t2\t63\t20\t0\t2\t87\t8\t0\t2\t51\t11\t0\t2\t60\t12\t0\t2\t63\tY\t76\t0.093\t1\n-Contig47_chr2_25470778_25471576\t126\tG\tA\t888.0\tchr2\t25470896\tG\t12\t0\t2\t63\t14\t0\t2\t69\t14\t0\t2\t69\t10\t0\t2\t57\t18\t0\t2\t81\t13\t0\t2\t66\tN\t11\t0.289\t1\n-Contig10_chr2_40859744_40860534\t637\tG\tA\t888.0\tchr2\t40860397\tA\t3\t0\t2\t36\t3\t0\t2\t36\t2\t0\t2\t33\t7\t0\t2\t48\t6\t0\t2\t45\t8\t0\t2\t51\tY\t42\t1.435\t0\n-Contig52_chr2_41421981_41422725\t604\tC\tA\t888.0\tchr2\t41422583\tA\t17\t0\t2\t78\t18\t0\t2\t81\t14\t0\t2\t69\t17\t0\t2\t78\t12\t0\t2\t63\t14\t0\t2\t69\tY\t44\t0.882\t0\n-Contig94_chr2_43869105_43870358\t220\tG\tA\t888.0\tchr2'..b'\t0\n-Contig5_chr36_4562983_456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\t57\t13\t0\t2\t66\t6\t0\t2\t45\tY\t59\t1.686\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/add_fst_column/add_fst_column.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_out/add_fst_column/add_fst_column.snp Wed Apr 18 11:12:21 2012 -0400 |
| b |
| @@ -0,0 +1,21 @@ +Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0 0.1636 +Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0 0.3846 +Contig132_chr7_20426224_20428145 1815 A G 28.3 chr7 20428041 A 11 1 2 43 12 0 2 63 19 0 2 84 23 0 2 96 14 0 2 69 10 0 2 57 N 11 0.264 0 0.0213 +Contig30_chr8_17147743_17147923 13 G A 105.0 chr8 17147756 A 1 3 1 19 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 3 0 2 36 N 6 +99. 0 0.4286 +Contig44_chr8_71186368_71188207 1455 G T 147.0 chr8 71187818 G 4 10 1 74 3 0 2 36 20 0 2 87 12 0 2 63 8 0 2 51 10 0 2 57 Y 88 0.036 0 0.4167 +Contig103_chr11_8844784_8845095 214 T G 135.0 chr11 8844993 T 1 1 2 12 10 0 2 57 5 4 1 26 2 3 1 13 2 7 1 34 1 1 2 13 Y 75 0.731 0 0.2101 +Contig37_chr13_15910164_15910426 245 G A 32.9 chr13 -1 N 3 4 1 41 4 0 2 39 3 0 2 36 4 0 2 39 3 0 2 36 10 0 2 57 N -1 2.159 1 0.2222 +Contig50_chr17_12247973_12249183 889 G T 47.6 chr17 12248878 G 0 1 2 9 8 0 2 51 9 2 2 21 7 2 2 21 15 0 2 72 0 3 0 9 Y 1 1.181 0 0.0150 +Contig159_chr22_7896450_7896974 109 G C 151.0 chr22 7896570 G 16 0 2 75 5 7 1 62 14 0 2 69 16 0 2 75 13 0 2 66 13 0 2 66 Y 16 0.465 0 0.1429 +Contig77_chr22_49764414_49764875 353 C A 148.0 chr22 49764777 C 7 4 1 65 18 0 2 81 16 0 2 75 20 0 2 87 4 3 1 52 9 4 1 67 Y 12 0.941 0 0.0741 +Contig61_chr24_30465488_30465834 149 G T 68.2 chr24 30465637 G 13 0 2 66 4 2 2 11 18 0 2 81 11 0 2 60 11 0 2 60 9 0 2 54 N 99 0.105 2 0.0556 +Contig59_chr25_18196776_18197707 785 G A 112.0 chr25 18197551 G 8 10 1 42 27 0 2 108 21 0 2 90 18 0 2 81 10 0 2 57 14 0 2 69 N 36 3.625 0 0.1250 +Contig85_chr27_45471750_45472022 211 G A 53.1 chr27 45471964 G 18 0 2 81 10 0 2 57 15 0 2 72 0 13 0 36 16 0 2 75 14 0 2 69 N 75 2.502 1 0.3023 +Contig175_chr28_36441165_36441915 68 T C 3.83 chr28 36441234 T 4 4 1 15 6 0 2 45 12 0 2 63 15 0 2 72 6 0 2 45 9 0 2 54 N 4 1.610 2 0.1667 +Contig114_chr30_33636712_33637208 34 C T 142.0 chr30 33636744 C 7 0 2 48 4 1 2 20 6 0 2 45 6 0 2 45 3 4 1 29 5 0 2 42 Y 14 8.028 0 0.0435 +Contig42_chr32_38900713_38901320 320 A G 134.0 chr32 38901021 T 12 0 2 63 10 0 2 57 9 11 1 104 5 0 2 42 19 0 2 84 7 6 1 56 Y 71 0.165 0 0.2821 +Contig41_chr34_16544482_16545449 46 T C 102.0 chr34 16544523 T 5 0 2 42 11 0 2 60 6 0 2 45 0 2 0 3 7 0 2 48 8 0 2 51 Y 215 1.156 0 0.1429 +Contig19_chr35_23887144_23888282 90 C A 10.1 chr35 23887242 - 3 3 1 12 4 4 1 19 8 6 1 37 4 3 1 11 8 3 2 7 9 3 2 11 Y 105 0.199 0 0.0051 +Contig74_chr35_25394343_25394813 303 A T 221.0 chr35 25394646 G 23 0 2 96 15 0 2 72 25 0 2 105 7 7 1 49 18 0 2 81 16 0 2 75 Y 58 4.298 0 0.0986 +Contig18_chr37_17147806_17149851 291 T G 112.0 chr37 17148084 T 4 6 1 45 16 0 2 75 17 0 2 78 14 0 2 69 22 0 2 93 13 0 2 66 Y 41 4.442 0 0.1304 +Contig12_chrX_23243561_23244412 479 C G 67.7 chrX 23244037 C 2 0 2 33 4 2 2 8 2 6 1 43 7 0 2 48 6 0 2 45 4 0 2 39 Y 208 1.620 0 0.0256 |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/add_fst_column/add_fst_column.wsf --- a/test-data/test_out/add_fst_column/add_fst_column.wsf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,21 +0,0 @@ -Contig113_chr5_11052263_11052603 28 C T 38.2 chr5 11052280 C 1 2 1 12 3 2 1 10 5 0 2 42 2 1 2 13 3 0 2 36 8 0 2 51 Y 161 +99. 0 0.1636 -Contig215_chr5_70946445_70947428 363 T G 28.2 chr5 70946809 C 4 0 2 39 0 5 0 12 9 0 2 54 6 0 2 45 3 3 2 1 9 0 2 54 N 43 0.153 0 0.3846 -Contig132_chr7_20426224_20428145 1815 A G 28.3 chr7 20428041 A 11 1 2 43 12 0 2 63 19 0 2 84 23 0 2 96 14 0 2 69 10 0 2 57 N 11 0.264 0 0.0213 -Contig30_chr8_17147743_17147923 13 G A 105.0 chr8 17147756 A 1 3 1 19 1 0 2 30 3 0 2 36 1 0 2 30 1 0 2 30 3 0 2 36 N 6 +99. 0 0.4286 -Contig44_chr8_71186368_71188207 1455 G T 147.0 chr8 71187818 G 4 10 1 74 3 0 2 36 20 0 2 87 12 0 2 63 8 0 2 51 10 0 2 57 Y 88 0.036 0 0.4167 -Contig103_chr11_8844784_8845095 214 T G 135.0 chr11 8844993 T 1 1 2 12 10 0 2 57 5 4 1 26 2 3 1 13 2 7 1 34 1 1 2 13 Y 75 0.731 0 0.2101 -Contig37_chr13_15910164_15910426 245 G A 32.9 chr13 -1 N 3 4 1 41 4 0 2 39 3 0 2 36 4 0 2 39 3 0 2 36 10 0 2 57 N -1 2.159 1 0.2222 -Contig50_chr17_12247973_12249183 889 G T 47.6 chr17 12248878 G 0 1 2 9 8 0 2 51 9 2 2 21 7 2 2 21 15 0 2 72 0 3 0 9 Y 1 1.181 0 0.0150 -Contig159_chr22_7896450_7896974 109 G C 151.0 chr22 7896570 G 16 0 2 75 5 7 1 62 14 0 2 69 16 0 2 75 13 0 2 66 13 0 2 66 Y 16 0.465 0 0.1429 -Contig77_chr22_49764414_49764875 353 C A 148.0 chr22 49764777 C 7 4 1 65 18 0 2 81 16 0 2 75 20 0 2 87 4 3 1 52 9 4 1 67 Y 12 0.941 0 0.0741 -Contig61_chr24_30465488_30465834 149 G T 68.2 chr24 30465637 G 13 0 2 66 4 2 2 11 18 0 2 81 11 0 2 60 11 0 2 60 9 0 2 54 N 99 0.105 2 0.0556 -Contig59_chr25_18196776_18197707 785 G A 112.0 chr25 18197551 G 8 10 1 42 27 0 2 108 21 0 2 90 18 0 2 81 10 0 2 57 14 0 2 69 N 36 3.625 0 0.1250 -Contig85_chr27_45471750_45472022 211 G A 53.1 chr27 45471964 G 18 0 2 81 10 0 2 57 15 0 2 72 0 13 0 36 16 0 2 75 14 0 2 69 N 75 2.502 1 0.3023 -Contig175_chr28_36441165_36441915 68 T C 3.83 chr28 36441234 T 4 4 1 15 6 0 2 45 12 0 2 63 15 0 2 72 6 0 2 45 9 0 2 54 N 4 1.610 2 0.1667 -Contig114_chr30_33636712_33637208 34 C T 142.0 chr30 33636744 C 7 0 2 48 4 1 2 20 6 0 2 45 6 0 2 45 3 4 1 29 5 0 2 42 Y 14 8.028 0 0.0435 -Contig42_chr32_38900713_38901320 320 A G 134.0 chr32 38901021 T 12 0 2 63 10 0 2 57 9 11 1 104 5 0 2 42 19 0 2 84 7 6 1 56 Y 71 0.165 0 0.2821 -Contig41_chr34_16544482_16545449 46 T C 102.0 chr34 16544523 T 5 0 2 42 11 0 2 60 6 0 2 45 0 2 0 3 7 0 2 48 8 0 2 51 Y 215 1.156 0 0.1429 -Contig19_chr35_23887144_23888282 90 C A 10.1 chr35 23887242 - 3 3 1 12 4 4 1 19 8 6 1 37 4 3 1 11 8 3 2 7 9 3 2 11 Y 105 0.199 0 0.0051 -Contig74_chr35_25394343_25394813 303 A T 221.0 chr35 25394646 G 23 0 2 96 15 0 2 72 25 0 2 105 7 7 1 49 18 0 2 81 16 0 2 75 Y 58 4.298 0 0.0986 -Contig18_chr37_17147806_17149851 291 T G 112.0 chr37 17148084 T 4 6 1 45 16 0 2 75 17 0 2 78 14 0 2 69 22 0 2 93 13 0 2 66 Y 41 4.442 0 0.1304 -Contig12_chrX_23243561_23244412 479 C G 67.7 chrX 23244037 C 2 0 2 33 4 2 2 8 2 6 1 43 7 0 2 48 6 0 2 45 4 0 2 39 Y 208 1.620 0 0.0256 |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/modify_snp_table/modify.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_out/modify_snp_table/modify.snp Wed Apr 18 11:12:21 2012 -0400 |
| b |
| b'@@ -0,0 +1,338 @@\n+Contig161_chr1_4641264_4641879\t115\tC\tT\t73.5\tchr1\t4641382\tC\t6\t0\t2\t45\t8\t0\t2\t51\t15\t0\t2\t72\t5\t0\t2\t42\t6\t0\t2\t45\t10\t0\t2\t57\tY\t54\t0.323\t0\n+Contig20_chr1_21313469_21313570\t66\tC\tT\t54.0\tchr1\t21313534\tC\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\t4\t0\t2\t39\t4\t0\t2\t39\t5\t0\t2\t42\tN\t1\t+99.\t0\n+Contig86_chr1_30984450_30985684\t670\tC\tT\t365.0\tchr1\t30985133\tC\t9\t0\t2\t54\t10\t0\t2\t57\t13\t0\t2\t66\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\tY\t145\t0.031\t0\n+Contig5_chr1_32562160_32563940\t1215\tG\tT\t163.0\tchr1\t32563356\tG\t17\t0\t2\t78\t19\t0\t2\t84\t20\t0\t2\t87\t14\t0\t2\t69\t12\t0\t2\t63\t10\t0\t2\t57\tY\t17\t0.251\t0\n+Contig110_chr1_33385093_33386888\t510\tC\tT\t270.0\tchr1\t33385587\tA\t14\t0\t2\t69\t11\t0\t2\t60\t19\t0\t2\t84\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\tY\t13\t0.126\t0\n+Contig100_chr1_33562920_33564288\t743\tC\tT\t178.0\tchr1\t33563655\tC\t6\t0\t2\t45\t10\t0\t2\t57\t8\t0\t2\t51\t5\t0\t2\t42\t13\t0\t2\t66\t7\t0\t2\t48\tY\t13\t0.090\t3\n+Contig7_chr1_37302355_37302489\t97\tA\tG\t59.2\tchr1\t37302452\tG\t3\t0\t2\t36\t8\t0\t2\t51\t5\t0\t2\t42\t8\t0\t2\t51\t7\t0\t2\t48\t6\t0\t2\t45\tN\t56\t2.812\t0\n+Contig62_chr1_41880715_41882180\t1078\tT\tG\t57.6\tchr1\t41881785\tT\t14\t0\t2\t69\t15\t0\t2\t72\t16\t0\t2\t75\t13\t0\t2\t66\t8\t0\t2\t51\t10\t0\t2\t57\tY\t21\t0.477\t0\n+Contig47_chr1_48409178_48409384\t37\tC\tT\t134.0\tchr1\t48409215\tT\t5\t0\t2\t42\t6\t0\t2\t45\t8\t0\t2\t51\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\tN\t66\t+99.\t0\n+Contig119_chr1_49647683_49650077\t1618\tC\tA\t99.7\tchr1\t49649276\tA\t8\t0\t2\t51\t11\t0\t2\t60\t10\t0\t2\t57\t9\t0\t2\t54\t10\t0\t2\t57\t14\t0\t2\t69\tY\t16\t0.166\t0\n+Contig21_chr1_60697952_60699446\t307\tG\tA\t51.9\tchr1\t60698265\tG\t12\t0\t2\t63\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\t9\t0\t2\t54\t4\t0\t2\t39\tY\t98\t0.507\t0\n+Contig131_chr1_62319542_62320564\t169\tC\tG\t103.0\tchr1\t62319709\tC\t12\t0\t2\t63\t12\t0\t2\t66\t14\t0\t2\t69\t12\t0\t2\t63\t9\t0\t2\t54\t9\t0\t2\t54\tY\t73\t0.307\t1\n+Contig14_chr1_63450425_63450680\t101\tT\tA\t102.0\tchr1\t63450530\tT\t8\t0\t2\t51\t10\t0\t2\t57\t18\t0\t2\t81\t8\t0\t2\t51\t8\t0\t2\t34\t8\t0\t2\t51\tN\t99\t1.085\t0\n+Contig83_chr1_63869778_63869942\t40\tT\tC\t23.7\tchr1\t63869819\tC\t5\t0\t2\t42\t7\t0\t2\t48\t2\t0\t2\t33\t4\t0\t2\t39\t6\t0\t2\t48\t4\t0\t2\t39\tN\t654\t1.364\t0\n+Contig30_chr1_64702572_64703138\t178\tA\tT\t117.0\tchr1\t64702750\tT\t10\t0\t2\t57\t10\t0\t2\t57\t20\t0\t2\t87\t21\t0\t2\t90\t6\t0\t2\t45\t12\t0\t2\t63\tY\t50\t3.872\t0\n+Contig101_chr1_69868406_69868872\t287\tG\tA\t14.6\tchr1\t69868689\tG\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t8\t0\t2\t51\t7\t0\t2\t48\t8\t0\t2\t51\tN\t137\t0.305\t0\n+Contig35_chr1_74482577_74482791\t170\tG\tA\t45.4\tchr1\t74482751\tA\t3\t0\t2\t36\t4\t0\t2\t39\t13\t0\t2\t66\t2\t0\t2\t33\t5\t0\t2\t42\t2\t0\t2\t33\tN\t20\t+99.\t3\n+Contig49_chr1_83865731_83865944\t85\tG\tA\t34.1\tchr1\t-1\tN\t4\t0\t2\t39\t4\t0\t2\t39\t8\t0\t2\t51\t2\t0\t2\t33\t5\t0\t2\t42\t4\t0\t2\t39\tN\t-1\t1.485\t0\n+Contig129_chr1_117547123_117548666\t926\tG\tA\t126.0\tchr1\t117548059\tG\t19\t0\t2\t84\t9\t0\t2\t54\t11\t0\t2\t60\t10\t0\t2\t57\t12\t0\t2\t63\t11\t0\t2\t60\tY\t64\t0.049\t0\n+Contig7_chr1_125154638_125154844\t190\tG\tT\t130.0\tchr1\t125154818\tA\t5\t0\t2\t42\t4\t0\t2\t39\t7\t0\t2\t48\t2\t0\t2\t33\t7\t0\t2\t48\t4\t0\t2\t39\tN\t33\t+99.\t0\n+Contig222_chr2_9817738_9818143\t220\tC\tT\t888.0\tchr2\t9817960\tC\t17\t0\t2\t78\t12\t0\t2\t63\t20\t0\t2\t87\t8\t0\t2\t51\t11\t0\t2\t60\t12\t0\t2\t63\tY\t76\t0.093\t1\n+Contig47_chr2_25470778_25471576\t126\tG\tA\t888.0\tchr2\t25470896\tG\t12\t0\t2\t63\t14\t0\t2\t69\t14\t0\t2\t69\t10\t0\t2\t57\t18\t0\t2\t81\t13\t0\t2\t66\tN\t11\t0.289\t1\n+Contig10_chr2_40859744_40860534\t637\tG\tA\t888.0\tchr2\t40860397\tA\t3\t0\t2\t36\t3\t0\t2\t36\t2\t0\t2\t33\t7\t0\t2\t48\t6\t0\t2\t45\t8\t0\t2\t51\tY\t42\t1.435\t0\n+Contig52_chr2_41421981_41422725\t604\tC\tA\t888.0\tchr2\t41422583\tA\t17\t0\t2\t78\t18\t0\t2\t81\t14\t0\t2\t69\t17\t0\t2\t78\t12\t0\t2\t63\t14\t0\t2\t69\tY\t44\t0.882\t0\n+Contig94_chr2_43869105_43870358\t220\tG\tA\t888.0\tchr2\t43869333\tG\t12\t0\t2\t63\t18\t0\t2\t81\t11\t0\t2\t60\t15\t0\t2\t72\t12\t0\t2\t63\t13\t0\t2\t66\tY\t1\t0.156\t0\n+Contig34_chr2_48444129_48444939\t695\tC\tT\t134.0\tchr2\t48444828\tC\t14\t0\t2\t69\t8\t0\t2\t51\t16\t0\t2\t75\t17\t0\t2\t78\t9\t0\t2\t54\t15\t0\t2\t72\tY\t161\t0.375\t0\n+Contig6_chr2_56859179_56859956\t671\tT\tC\t999.9\tchr2\t56859851\tT\t15\t0\t2\t72\t18\t0\t2\t81\t20\t0\t2\t90\t19\t0\t2\t84\t19\t0\t2\t84\t24\t0\t2\t99\tN\t28\t5.308\t1\n+Contig115_chr2_61631913_61632510\t310\tG\tT\t999.3\tchr2\t61632216\tG\t7\t0\t2\t48\t9\t0\t2\t54\t7\t0\t2\t48\t11\t0\t2\t60\t10\t0\t2\t57\t10\t0\t2\t57\tN\t13\t0.184\t0\n+Contig31_chr2_67331584_67331785\t39\tC\tT\t999.0\tchr2\t67331623\tC\t11\t0\t2\t60\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t2\t0\t2\t33\t4\t0\t2\t39\tN\t110\t0.647\t1\n+Contig92_chr2_75906683_75907774\t773\tT\tC\t85.4\tchr2\t75907438\tC\t12\t0\t2\t63\t12\t0\t2\t63\t17\t0\t2\t78\t8\t0\t2\t51\t8\t0\t2\t51\t13\t0\t2\t66\tY\t93\t0.166\t0\n+Contig'..b'73_3667898\t348\tG\tT\t124.0\tchr35\t3667121\tG\t9\t0\t2\t54\t20\t0\t2\t87\t18\t0\t2\t81\t15\t0\t2\t72\t12\t0\t2\t63\t14\t0\t2\t69\tY\t285\t0.235\t0\n+Contig195_chr35_15722500_15722741\t205\tG\tA\t4.08\tchr35\t15722718\tG\t3\t0\t2\t36\t5\t0\t2\t42\t1\t0\t2\t30\t6\t0\t2\t45\t1\t0\t2\t30\t1\t0\t2\t30\tN\t43\t+99.\t0\n+Contig101_chr35_19513178_19513697\t62\tC\tT\t112.0\tchr35\t19513238\tC\t12\t0\t2\t63\t7\t0\t2\t48\t13\t0\t2\t66\t7\t0\t2\t48\t5\t0\t2\t42\t8\t0\t2\t51\tN\t115\t3.135\t0\n+Contig47_chr35_24382042_24382526\t33\tG\tA\t87.0\tchr35\t24382076\tG\t5\t0\t2\t42\t4\t0\t2\t39\t6\t0\t2\t45\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\tY\t71\t+99.\t0\n+Contig77_chr35_24796947_24797172\t65\tA\tG\t52.1\tchr35\t24797009\tA\t7\t0\t2\t48\t5\t0\t2\t42\t8\t0\t2\t51\t6\t0\t2\t45\t12\t0\t2\t63\t10\t0\t2\t57\tN\t11\t1.401\t3\n+Contig74_chr35_25394343_25394813\t303\tA\tT\t221.0\tchr35\t25394646\tG\t23\t0\t2\t96\t15\t0\t2\t72\t25\t0\t2\t105\t7\t7\t1\t49\t18\t0\t2\t81\t16\t0\t2\t75\tY\t58\t4.298\t0\n+Contig5_chr36_4562983_4563634\t343\tC\tT\t151.0\tchr36\t4563324\tT\t20\t0\t2\t87\t20\t0\t2\t87\t23\t0\t2\t96\t24\t0\t2\t99\t9\t0\t2\t54\t8\t0\t2\t51\tY\t40\t1.169\t0\n+Contig75_chr36_7885319_7885588\t53\tG\tA\t25.7\tchr36\t7885372\tG\t10\t0\t2\t57\t8\t0\t2\t51\t13\t0\t2\t66\t7\t0\t2\t48\t4\t0\t2\t39\t7\t0\t2\t48\tN\t7\t2.653\t0\n+Contig184_chr36_18956191_18958552\t187\tA\tG\t11.5\tchr36\t18956371\tG\t10\t0\t2\t57\t11\t0\t2\t60\t21\t0\t2\t90\t14\t0\t2\t69\t7\t0\t2\t48\t4\t0\t2\t39\tN\t278\t1.434\t2\n+Contig12_chr36_21557176_21557828\t513\tT\tA\t159.0\tchr36\t21557695\tA\t11\t0\t2\t60\t14\t0\t2\t69\t21\t0\t2\t90\t12\t0\t2\t63\t15\t0\t2\t72\t11\t0\t2\t60\tY\t55\t0.222\t0\n+Contig2_chr36_22436067_22436794\t653\tC\tT\t73.0\tchr36\t22436730\tC\t11\t0\t2\t60\t16\t0\t2\t75\t13\t0\t2\t66\t11\t0\t2\t60\t21\t0\t2\t90\t21\t0\t2\t90\tY\t9\t0.534\t0\n+Contig133_chr36_32954045_32955409\t136\tA\tG\t116.0\tchr36\t32954182\tA\t16\t0\t2\t75\t15\t0\t2\t72\t20\t0\t2\t87\t11\t0\t2\t60\t18\t0\t2\t81\t13\t0\t2\t66\tY\t74\t3.772\t1\n+Contig53_chr37_6665763_6665919\t116\tC\tT\t111.0\tchr37\t6665875\tC\t9\t0\t2\t54\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t8\t0\t2\t51\t10\t0\t2\t57\tN\t15\t10.875\t1\n+Contig42_chr37_9589176_9591269\t252\tG\tA\t25.1\tchr37\t9589430\tG\t10\t0\t2\t40\t13\t0\t2\t66\t18\t0\t2\t81\t21\t0\t2\t90\t9\t0\t2\t54\t17\t0\t2\t78\tN\t67\t1.170\t2\n+Contig2_chr37_17134963_17136513\t1140\tA\tC\t158.0\tchr37\t17136092\tA\t14\t0\t2\t69\t24\t0\t2\t99\t17\t0\t2\t78\t16\t0\t2\t75\t15\t0\t2\t75\t13\t0\t2\t66\tY\t12\t0.053\t1\n+Contig18_chr37_17147806_17149851\t291\tT\tG\t112.0\tchr37\t17148084\tT\t4\t6\t1\t45\t16\t0\t2\t75\t17\t0\t2\t78\t14\t0\t2\t69\t22\t0\t2\t93\t13\t0\t2\t66\tY\t41\t4.442\t0\n+Contig64_chr37_17606895_17607534\t565\tC\tT\t30.2\tchr37\t17607439\tA\t9\t0\t2\t54\t16\t0\t2\t75\t20\t0\t2\t87\t14\t0\t2\t69\t16\t0\t2\t75\t10\t0\t2\t57\tN\t20\t1.622\t0\n+Contig126_chr37_21587881_21590621\t373\tG\tT\t132.0\tchr37\t21588256\tG\t11\t0\t2\t60\t11\t0\t2\t60\t23\t0\t2\t96\t12\t0\t2\t63\t8\t0\t2\t51\t18\t0\t2\t81\tY\t12\t0.549\t0\n+Contig2_chr37_31197993_31198256\t182\tC\tT\t39.6\tchr37\t31198171\tT\t6\t0\t2\t45\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t12\t0\t2\t63\tN\t2\t0.595\t0\n+Contig46_chr37_31852376_31853555\t825\tA\tG\t111.0\tchr37\t31853191\tG\t19\t0\t2\t84\t14\t0\t2\t69\t15\t0\t2\t72\t7\t0\t2\t48\t8\t0\t2\t51\t16\t0\t2\t75\tY\t17\t0.128\t1\n+Contig7_chr38_12217200_12218387\t1163\tA\tT\t44.4\tchr38\t12218353\tA\t11\t0\t2\t60\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t11\t0\t2\t60\t11\t0\t2\t60\tY\t67\t+99.\t0\n+Contig15_chr38_12282020_12282253\t150\tC\tT\t156.0\tchr38\t12282164\tA\t17\t0\t2\t78\t11\t0\t2\t60\t19\t0\t2\t84\t14\t0\t2\t69\t5\t0\t2\t42\t14\t0\t2\t69\tY\t26\t2.952\t1\n+Contig6_chr38_16185744_16186110\t325\tA\tG\t74.9\tchr38\t16186061\tA\t5\t0\t2\t42\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\t1\t0\t2\t30\t12\t0\t2\t63\tY\t40\t+99.\t0\n+Contig265_chrX_2689247_2689484\t114\tC\tG\t103.0\tchrX\t2689356\tC\t11\t0\t2\t60\t9\t0\t2\t54\t13\t0\t2\t66\t16\t0\t2\t75\t14\t0\t2\t69\t10\t0\t2\t57\tN\t2\t9.232\t1\n+Contig122_chrX_6026976_6027327\t330\tC\tT\t79.4\tchrX\t6027303\tC\t3\t0\t2\t36\t3\t0\t2\t36\t3\t0\t2\t36\t4\t0\t2\t39\t3\t0\t2\t36\t6\t0\t2\t45\tY\t30\t+99.\t0\n+Contig113_chrX_26287829_26288398\t385\tC\tT\t59.6\tchrX\t26288213\tC\t9\t0\t2\t54\t9\t0\t2\t54\t17\t0\t2\t78\t11\t0\t2\t60\t3\t8\t1\t44\t4\t0\t2\t39\tN\t13\t0.077\t0\n+Contig237_chrX_31256648_31257654\t165\tT\tA\t246.0\tchrX\t31256814\tT\t7\t0\t2\t48\t23\t0\t2\t96\t19\t0\t2\t84\t17\t0\t2\t78\t14\t0\t2\t69\t8\t0\t2\t51\tY\t37\t1.481\t0\n+Contig90_chrX_57430715_57431566\t548\tC\tT\t116.0\tchrX\t57431266\tT\t9\t0\t2\t54\t18\t0\t2\t81\t13\t0\t2\t66\t14\t0\t2\t69\t8\t0\t2\t54\t7\t0\t2\t48\tY\t261\t0.154\t1\n+Contig133_chrX_84833782_84834125\t182\tG\tA\t69.7\tchrX\t84833962\tG\t5\t0\t2\t42\t18\t0\t2\t81\t12\t0\t2\t63\t19\t0\t2\t84\t6\t3\t1\t27\t7\t0\t2\t48\tN\t619\t0.278\t0\n+Contig125_chrX_93319363_93320877\t349\tA\tC\t145.0\tchrX\t93319721\tA\t4\t0\t2\t39\t6\t0\t2\t45\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\t6\t0\t2\t45\tY\t59\t1.686\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/modify_snp_table/modify.wsf --- a/test-data/test_out/modify_snp_table/modify.wsf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,338 +0,0 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t8\t0\t2\t51\t8\t0\t2\t51\t13\t0\t2\t66\tY\t93\t0.166\t0\n-Contig'..b'73_3667898\t348\tG\tT\t124.0\tchr35\t3667121\tG\t9\t0\t2\t54\t20\t0\t2\t87\t18\t0\t2\t81\t15\t0\t2\t72\t12\t0\t2\t63\t14\t0\t2\t69\tY\t285\t0.235\t0\n-Contig195_chr35_15722500_15722741\t205\tG\tA\t4.08\tchr35\t15722718\tG\t3\t0\t2\t36\t5\t0\t2\t42\t1\t0\t2\t30\t6\t0\t2\t45\t1\t0\t2\t30\t1\t0\t2\t30\tN\t43\t+99.\t0\n-Contig101_chr35_19513178_19513697\t62\tC\tT\t112.0\tchr35\t19513238\tC\t12\t0\t2\t63\t7\t0\t2\t48\t13\t0\t2\t66\t7\t0\t2\t48\t5\t0\t2\t42\t8\t0\t2\t51\tN\t115\t3.135\t0\n-Contig47_chr35_24382042_24382526\t33\tG\tA\t87.0\tchr35\t24382076\tG\t5\t0\t2\t42\t4\t0\t2\t39\t6\t0\t2\t45\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\tY\t71\t+99.\t0\n-Contig77_chr35_24796947_24797172\t65\tA\tG\t52.1\tchr35\t24797009\tA\t7\t0\t2\t48\t5\t0\t2\t42\t8\t0\t2\t51\t6\t0\t2\t45\t12\t0\t2\t63\t10\t0\t2\t57\tN\t11\t1.401\t3\n-Contig74_chr35_25394343_25394813\t303\tA\tT\t221.0\tchr35\t25394646\tG\t23\t0\t2\t96\t15\t0\t2\t72\t25\t0\t2\t105\t7\t7\t1\t49\t18\t0\t2\t81\t16\t0\t2\t75\tY\t58\t4.298\t0\n-Contig5_chr36_4562983_4563634\t343\tC\tT\t151.0\tchr36\t4563324\tT\t20\t0\t2\t87\t20\t0\t2\t87\t23\t0\t2\t96\t24\t0\t2\t99\t9\t0\t2\t54\t8\t0\t2\t51\tY\t40\t1.169\t0\n-Contig75_chr36_7885319_7885588\t53\tG\tA\t25.7\tchr36\t7885372\tG\t10\t0\t2\t57\t8\t0\t2\t51\t13\t0\t2\t66\t7\t0\t2\t48\t4\t0\t2\t39\t7\t0\t2\t48\tN\t7\t2.653\t0\n-Contig184_chr36_18956191_18958552\t187\tA\tG\t11.5\tchr36\t18956371\tG\t10\t0\t2\t57\t11\t0\t2\t60\t21\t0\t2\t90\t14\t0\t2\t69\t7\t0\t2\t48\t4\t0\t2\t39\tN\t278\t1.434\t2\n-Contig12_chr36_21557176_21557828\t513\tT\tA\t159.0\tchr36\t21557695\tA\t11\t0\t2\t60\t14\t0\t2\t69\t21\t0\t2\t90\t12\t0\t2\t63\t15\t0\t2\t72\t11\t0\t2\t60\tY\t55\t0.222\t0\n-Contig2_chr36_22436067_22436794\t653\tC\tT\t73.0\tchr36\t22436730\tC\t11\t0\t2\t60\t16\t0\t2\t75\t13\t0\t2\t66\t11\t0\t2\t60\t21\t0\t2\t90\t21\t0\t2\t90\tY\t9\t0.534\t0\n-Contig133_chr36_32954045_32955409\t136\tA\tG\t116.0\tchr36\t32954182\tA\t16\t0\t2\t75\t15\t0\t2\t72\t20\t0\t2\t87\t11\t0\t2\t60\t18\t0\t2\t81\t13\t0\t2\t66\tY\t74\t3.772\t1\n-Contig53_chr37_6665763_6665919\t116\tC\tT\t111.0\tchr37\t6665875\tC\t9\t0\t2\t54\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t8\t0\t2\t51\t10\t0\t2\t57\tN\t15\t10.875\t1\n-Contig42_chr37_9589176_9591269\t252\tG\tA\t25.1\tchr37\t9589430\tG\t10\t0\t2\t40\t13\t0\t2\t66\t18\t0\t2\t81\t21\t0\t2\t90\t9\t0\t2\t54\t17\t0\t2\t78\tN\t67\t1.170\t2\n-Contig2_chr37_17134963_17136513\t1140\tA\tC\t158.0\tchr37\t17136092\tA\t14\t0\t2\t69\t24\t0\t2\t99\t17\t0\t2\t78\t16\t0\t2\t75\t15\t0\t2\t75\t13\t0\t2\t66\tY\t12\t0.053\t1\n-Contig18_chr37_17147806_17149851\t291\tT\tG\t112.0\tchr37\t17148084\tT\t4\t6\t1\t45\t16\t0\t2\t75\t17\t0\t2\t78\t14\t0\t2\t69\t22\t0\t2\t93\t13\t0\t2\t66\tY\t41\t4.442\t0\n-Contig64_chr37_17606895_17607534\t565\tC\tT\t30.2\tchr37\t17607439\tA\t9\t0\t2\t54\t16\t0\t2\t75\t20\t0\t2\t87\t14\t0\t2\t69\t16\t0\t2\t75\t10\t0\t2\t57\tN\t20\t1.622\t0\n-Contig126_chr37_21587881_21590621\t373\tG\tT\t132.0\tchr37\t21588256\tG\t11\t0\t2\t60\t11\t0\t2\t60\t23\t0\t2\t96\t12\t0\t2\t63\t8\t0\t2\t51\t18\t0\t2\t81\tY\t12\t0.549\t0\n-Contig2_chr37_31197993_31198256\t182\tC\tT\t39.6\tchr37\t31198171\tT\t6\t0\t2\t45\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t12\t0\t2\t63\tN\t2\t0.595\t0\n-Contig46_chr37_31852376_31853555\t825\tA\tG\t111.0\tchr37\t31853191\tG\t19\t0\t2\t84\t14\t0\t2\t69\t15\t0\t2\t72\t7\t0\t2\t48\t8\t0\t2\t51\t16\t0\t2\t75\tY\t17\t0.128\t1\n-Contig7_chr38_12217200_12218387\t1163\tA\tT\t44.4\tchr38\t12218353\tA\t11\t0\t2\t60\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t11\t0\t2\t60\t11\t0\t2\t60\tY\t67\t+99.\t0\n-Contig15_chr38_12282020_12282253\t150\tC\tT\t156.0\tchr38\t12282164\tA\t17\t0\t2\t78\t11\t0\t2\t60\t19\t0\t2\t84\t14\t0\t2\t69\t5\t0\t2\t42\t14\t0\t2\t69\tY\t26\t2.952\t1\n-Contig6_chr38_16185744_16186110\t325\tA\tG\t74.9\tchr38\t16186061\tA\t5\t0\t2\t42\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\t1\t0\t2\t30\t12\t0\t2\t63\tY\t40\t+99.\t0\n-Contig265_chrX_2689247_2689484\t114\tC\tG\t103.0\tchrX\t2689356\tC\t11\t0\t2\t60\t9\t0\t2\t54\t13\t0\t2\t66\t16\t0\t2\t75\t14\t0\t2\t69\t10\t0\t2\t57\tN\t2\t9.232\t1\n-Contig122_chrX_6026976_6027327\t330\tC\tT\t79.4\tchrX\t6027303\tC\t3\t0\t2\t36\t3\t0\t2\t36\t3\t0\t2\t36\t4\t0\t2\t39\t3\t0\t2\t36\t6\t0\t2\t45\tY\t30\t+99.\t0\n-Contig113_chrX_26287829_26288398\t385\tC\tT\t59.6\tchrX\t26288213\tC\t9\t0\t2\t54\t9\t0\t2\t54\t17\t0\t2\t78\t11\t0\t2\t60\t3\t8\t1\t44\t4\t0\t2\t39\tN\t13\t0.077\t0\n-Contig237_chrX_31256648_31257654\t165\tT\tA\t246.0\tchrX\t31256814\tT\t7\t0\t2\t48\t23\t0\t2\t96\t19\t0\t2\t84\t17\t0\t2\t78\t14\t0\t2\t69\t8\t0\t2\t51\tY\t37\t1.481\t0\n-Contig90_chrX_57430715_57431566\t548\tC\tT\t116.0\tchrX\t57431266\tT\t9\t0\t2\t54\t18\t0\t2\t81\t13\t0\t2\t66\t14\t0\t2\t69\t8\t0\t2\t54\t7\t0\t2\t48\tY\t261\t0.154\t1\n-Contig133_chrX_84833782_84834125\t182\tG\tA\t69.7\tchrX\t84833962\tG\t5\t0\t2\t42\t18\t0\t2\t81\t12\t0\t2\t63\t19\t0\t2\t84\t6\t3\t1\t27\t7\t0\t2\t48\tN\t619\t0.278\t0\n-Contig125_chrX_93319363_93320877\t349\tA\tC\t145.0\tchrX\t93319721\tA\t4\t0\t2\t39\t6\t0\t2\t45\t11\t0\t2\t60\t10\t0\t2\t57\t13\t0\t2\t66\t6\t0\t2\t45\tY\t59\t1.686\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/select_snps/select_snps.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_out/select_snps/select_snps.snp Wed Apr 18 11:12:21 2012 -0400 |
| [ |
| b'@@ -0,0 +1,102 @@\n+#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",\n+#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}\n+Contig161_chr1_4641264_4641879\t115\tC\tT\t73.5\tchr1\t4641382\tC\t6\t0\t2\t45\t8\t0\t2\t51\t15\t0\t2\t72\t5\t0\t2\t42\t6\t0\t2\t45\t10\t0\t2\t57\tY\t54\t0.323\t0\n+Contig86_chr1_30984450_30985684\t670\tC\tT\t365.0\tchr1\t30985133\tC\t9\t0\t2\t54\t10\t0\t2\t57\t13\t0\t2\t66\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\tY\t145\t0.031\t0\n+Contig21_chr1_60697952_60699446\t307\tG\tA\t51.9\tchr1\t60698265\tG\t12\t0\t2\t63\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\t9\t0\t2\t54\t4\t0\t2\t39\tY\t98\t0.507\t0\n+Contig64_chr1_87343284_87345672\t163\tT\tA\t3.76\tchr1\t87343443\tC\t0\t2\t2\t1\t0\t0\t-1\t0\t5\t0\t2\t42\t2\t0\t2\t33\t0\t1\t2\t14\t0\t0\t-1\t0\tN\t3\t0.039\t2\n+Contig20_chr1_110679280_110679687\t181\tC\tT\t87.4\tchr1\t110679454\t-\t1\t0\t2\t30\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\t2\t0\t2\t33\t0\t0\t-1\t0\tN\t31\t0.660\t2\n+Contig222_chr2_9817738_9818143\t220\tC\tT\t888.0\tchr2\t9817960\tC\t17\t0\t2\t78\t12\t0\t2\t63\t20\t0\t2\t87\t8\t0\t2\t51\t11\t0\t2\t60\t12\t0\t2\t63\tY\t76\t0.093\t1\n+Contig47_chr2_25470778_25471576\t126\tG\tA\t888.0\tchr2\t25470896\tG\t12\t0\t2\t63\t14\t0\t2\t69\t14\t0\t2\t69\t10\t0\t2\t57\t18\t0\t2\t81\t13\t0\t2\t66\tN\t11\t0.289\t1\n+Contig6_chr2_56859179_56859956\t671\tT\tC\t999.9\tchr2\t56859851\tT\t15\t0\t2\t72\t18\t0\t2\t81\t20\t0\t2\t90\t19\t0\t2\t84\t19\t0\t2\t84\t24\t0\t2\t99\tN\t28\t5.308\t1\n+Contig163_chr2_76402959_76404830\t221\tC\tT\t127.0\tchr2\t76403181\tC\t4\t0\t2\t42\t10\t0\t2\t57\t9\t0\t2\t54\t11\t0\t2\t60\t7\t0\t2\t48\t9\t0\t2\t54\tY\t54\t0.178\t1\n+Contig56_chr3_17326225_17327548\t387\tG\tC\t91.2\tchr3\t17326591\tG\t14\t0\t2\t69\t13\t0\t2\t66\t15\t0\t2\t72\t15\t0\t2\t72\t13\t0\t2\t66\t12\t0\t2\t63\tY\t20\t0.225\t3\n+Contig108_chr3_46210055_46210874\t367\tA\tG\t21.0\tchr3\t46210423\tA\t19\t0\t2\t84\t10\t0\t2\t57\t16\t0\t2\t75\t14\t0\t2\t69\t20\t0\t2\t87\t11\t0\t2\t60\tN\t236\t0.028\t1\n+Contig1_chr3_51588422_51589409\t926\tA\tG\t51.0\tchr3\t51589353\tG\t2\t0\t2\t33\t2\t0\t2\t33\t6\t0\t2\t45\t4\t0\t2\t39\t9\t0\t2\t54\t11\t0\t2\t60\tN\t21\t1.147\t0\n+Contig65_chr3_80727952_80728283\t39\tT\tC\t71.2\tchr3\t80727990\tT\t7\t0\t2\t48\t3\t0\t2\t36\t8\t0\t2\t51\t6\t0\t2\t45\t8\t0\t2\t51\t11\t0\t2\t60\tN\t22\t7.078\t0\n+Contig134_chr4_12145648_12148225\t1326\tC\tT\t164.0\tchr4\t12146961\tC\t9\t0\t2\t54\t8\t0\t2\t51\t7\t0\t2\t48\t3\t0\t2\t36\t5\t0\t2\t42\t5\t0\t2\t42\tY\t4\t0.080\t1\n+Contig19_chr4_26233601_26233991\t146\tG\tC\t51.6\tchr4\t26233744\tG\t10\t0\t2\t57\t8\t0\t2\t51\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t4\t0\t2\t39\tN\t41\t0.163\t3\n+Contig17_chr4_61310346_61311158\t267\tC\tT\t49.9\tchr4\t61310604\tT\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t14\t0\t2\t69\t7\t0\t2\t48\tY\t219\t0.098\t0\n+Contig31_chr5_4734956_4736547\t1166\tC\tT\t133.0\tchr5\t4736132\tC\t14\t0\t2\t69\t8\t0\t2\t51\t17\t0\t2\t78\t4\t0\t2\t39\t9\t0\t2\t54\t12\t0\t2\t63\tY\t1\t0.021\t0\n+Contig6_chr5_26899813_26900498\t97\tA\tC\t88.6\tchr5\t26899910\tA\t15\t0\t2\t72\t14\t0\t2\t69\t27\t0\t2\t108\t15\t0\t2\t72\t13\t0\t2\t69\t12\t0\t2\t63\tY\t92\t7.370\t3\n+Contig45_chr5_50892738_50892968\t169\tC\tA\t25.8\tchr5\t50892911\tC\t10\t0\t2\t57\t7\t0\t2\t48\t10\t0\t2\t60\t6\t0\t2\t45\t6\t0\t2\t45\t13\t0\t2\t66\tN\t244\t0.497\t1\n+Contig45_chr5_76133561_76134403\t388\tA\tG\t103.0\tchr5\t76133941\tG\t3\t0\t2\t36\t8\t0\t2\t51\t8\t0\t2\t51\t5\t0\t2\t42\t6\t0\t2\t45\t7\t0\t2\t48\tY\t57\t0.038\t0\n+Contig111_chr6_5821219_5822519\t1060\tA\tG\t68.1\tchr6\t5822321\tT\t7\t0\t2\t48\t6\t0\t2\t45\t11\t0\t2\t60\t9\t0\t2\t54\t3\t0\t2\t36\t12\t0\t2\t63\tY\t7\t0.231\t1\n+Contig102_chr6_30271329_30271577\t39\tT\tG\t139.0\tchr6\t30271371\tG\t3\t0\t2\t36\t4\t0\t2\t39\t6\t0\t2\t45\t1\t0\t2\t30\t4\t0\t2\t39\t4\t0\t2\t39\tN\t15\t1.159\t0\n+Contig112_chr6_51024554_51024851\t100\tA\tG\t121.0\tchr6\t51024654\tA\t10\t0\t2\t57\t12\t0\t2\t63\t9\t0\t2\t54\t13\t0\t2\t66\t14\t0\t2\t69\t17\t0\t2\t78\tN\t75\t4.287\t0\n+Contig84_chr7_6648683_6650255\t1297\tG\tA\t110.0\tchr7\t6649988\tG\t18\t0\t2\t81\t9\t0\t2\t54\t22\t0\t2\t77\t16\t0\t2\t75\t20\t0\t2\t87\t6\t0\t2\t45\tY\t83\t0.166\t0\n+Contig206_chr7_26281823_26282074\t103\tC\tA\t101.0\tchr7\t26281925\tT\t11\t0\t2\t60\t16\t0\t2\t61\t19\t0\t2\t84\t6\t0\t2\t45\t19\t0\t2\t84\t16\t0\t2\t75\tN\t-1\t0.947\t1\n+Contig38_chr7_50681997_50682600\t42\tT\tC\t92.4\tchr7\t50682037\tG\t6\t0\t2\t45\t2\t0\t2\t33\t10\t0\t2\t57\t12\t0\t2\t63\t5\t0\t2\t42\t6\t0\t2\t45\tY\t94\t0.146\t0\n+Contig91_chr8_12804505_12805470\t409\tC\tA\t111.0\tchr8\t12804906\tC\t8\t0\t2\t51\t10\t0\t2\t57\t15\t0\t2\t72\t12\t0\t2\t63\t14\t0\t2\t69\t15\t0\t2\t72\tN\t145\t0.175\t0\n+Contig8_chr8_27811135_27812620\t333\tC\tT'..b'0\tchr25\t4011690\tA\t12\t0\t2\t63\t17\t0\t2\t78\t13\t0\t2\t66\t13\t0\t2\t66\t13\t0\t2\t66\t13\t0\t2\t66\tY\t5\t0.087\t0\n+Contig103_chr25_38891221_38892140\t407\tG\tA\t131.0\tchr25\t38891644\tG\t8\t0\t2\t51\t14\t0\t2\t69\t18\t0\t2\t81\t8\t0\t2\t51\t8\t0\t2\t51\t11\t0\t2\t60\tY\t149\t0.167\t4\n+Contig204_chr26_4311195_4311778\t170\tC\tT\t16.9\tchr26\t4311363\tT\t20\t0\t2\t87\t8\t0\t2\t51\t13\t0\t2\t66\t18\t0\t2\t81\t11\t0\t2\t60\t14\t0\t2\t69\tN\t35\t0.085\t0\n+Contig146_chr26_26622638_26623906\t574\tG\tA\t186.0\tchr26\t26623219\tA\t11\t0\t2\t60\t12\t0\t2\t63\t9\t0\t2\t54\t11\t0\t2\t60\t9\t0\t2\t54\t12\t0\t2\t63\tY\t1\t0.318\t0\n+Contig135_chr27_6853874_6854079\t158\tC\tT\t116.0\tchr27\t6854032\tT\t18\t0\t2\t81\t19\t0\t2\t84\t13\t0\t2\t66\t7\t0\t2\t48\t8\t0\t2\t51\t11\t0\t2\t60\tN\t4\t0.060\t1\n+Contig64_chr27_34654435_34654621\t132\tC\tA\t115.0\tchr27\t34654567\tT\t2\t0\t2\t33\t2\t0\t2\t33\t5\t0\t2\t42\t3\t0\t2\t36\t3\t0\t2\t36\t8\t0\t2\t51\tN\t12\t0.297\t1\n+Contig131_chr28_6481806_6483783\t138\tC\tT\t36.2\tchr28\t6481953\tC\t12\t0\t2\t63\t12\t0\t2\t63\t20\t0\t2\t87\t11\t0\t2\t60\t10\t0\t2\t57\t12\t0\t2\t63\tY\t10\t0.387\t0\n+Contig60_chr28_30197166_30197364\t92\tT\tC\t164.0\tchr28\t30197258\tT\t10\t0\t2\t57\t13\t0\t2\t66\t15\t0\t2\t72\t16\t0\t2\t75\t12\t0\t2\t63\t11\t0\t2\t60\tN\t369\t1.139\t0\n+Contig29_chr29_4726399_4727143\t559\tA\tT\t163.0\tchr29\t4726955\tA\t15\t0\t2\t72\t18\t0\t2\t81\t18\t0\t2\t81\t16\t0\t2\t75\t11\t0\t2\t60\t14\t0\t2\t72\tY\t161\t3.114\t0\n+Contig1_chr30_5992217_5993068\t106\tC\tT\t129.0\tchr30\t5992319\tC\t10\t0\t2\t57\t11\t0\t2\t60\t7\t0\t2\t48\t11\t0\t2\t60\t10\t0\t2\t57\t12\t0\t2\t63\tY\t76\t1.079\t0\n+Contig165_chr30_25804389_25804926\t190\tT\tC\t126.0\tchr30\t25804592\tC\t3\t0\t2\t36\t8\t0\t2\t51\t7\t0\t2\t48\t10\t0\t2\t57\t7\t0\t2\t48\t4\t0\t2\t39\tY\t113\t0.329\t0\n+Contig38_chr31_5164423_5166573\t2074\tC\tT\t134.0\tchr31\t5166501\tT\t13\t0\t2\t66\t10\t0\t2\t57\t17\t0\t2\t78\t11\t0\t2\t60\t17\t0\t2\t78\t10\t0\t2\t57\tY\t58\t+99.\t0\n+Contig17_chr31_26433828_26434459\t498\tT\tC\t9.79\tchr31\t26434322\tT\t18\t0\t2\t81\t10\t0\t2\t57\t15\t0\t2\t72\t13\t0\t2\t66\t16\t0\t2\t75\t15\t0\t2\t72\tY\t137\t4.814\t0\n+Contig9_chr32_19479532_19479735\t12\tA\tG\t20.7\tchr32\t19479544\tA\t1\t0\t2\t30\t2\t0\t2\t33\t1\t0\t2\t30\t5\t0\t2\t42\t3\t0\t2\t36\t3\t0\t2\t36\tN\t17\t+99.\t0\n+Contig30_chr32_25902721_25905783\t208\tC\tG\t162.0\tchr32\t25902927\tG\t11\t0\t2\t60\t13\t0\t2\t66\t11\t0\t2\t60\t12\t0\t2\t63\t7\t0\t2\t48\t11\t0\t2\t60\tY\t145\t0.322\t2\n+Contig18_chr33_22207246_22209159\t1363\tG\tT\t51.5\tchr33\t22208619\t-\t16\t0\t2\t75\t8\t0\t2\t51\t11\t0\t2\t60\t10\t0\t2\t57\t15\t0\t2\t72\t12\t0\t2\t63\tY\t59\t2.560\t0\n+Contig170_chr33_26189421_26189940\t292\tT\tC\t98.4\tchr33\t26189703\tT\t21\t0\t2\t90\t13\t0\t2\t66\t15\t0\t2\t72\t13\t0\t2\t66\t19\t0\t2\t84\t13\t0\t2\t66\tY\t23\t0.307\t0\n+Contig113_chr34_13341080_13341643\t236\tC\tT\t90.7\tchr34\t13341316\tC\t4\t0\t2\t39\t2\t0\t2\t33\t8\t0\t2\t51\t4\t0\t2\t39\t8\t0\t2\t51\t3\t0\t2\t36\tY\t47\t0.412\t3\n+Contig152_chr34_31794848_31795540\t242\tG\tA\t93.2\tchr34\t31795093\tG\t11\t0\t2\t60\t24\t0\t2\t99\t17\t0\t2\t78\t15\t0\t2\t72\t18\t0\t2\t81\t17\t0\t2\t78\tY\t123\t2.780\t0\n+Contig47_chr35_3666773_3667898\t348\tG\tT\t124.0\tchr35\t3667121\tG\t9\t0\t2\t54\t20\t0\t2\t87\t18\t0\t2\t81\t15\t0\t2\t72\t12\t0\t2\t63\t14\t0\t2\t69\tY\t285\t0.235\t0\n+Contig74_chr35_25394343_25394813\t303\tA\tT\t221.0\tchr35\t25394646\tG\t23\t0\t2\t96\t15\t0\t2\t72\t25\t0\t2\t105\t7\t7\t1\t49\t18\t0\t2\t81\t16\t0\t2\t75\tY\t58\t4.298\t0\n+Contig5_chr36_4562983_4563634\t343\tC\tT\t151.0\tchr36\t4563324\tT\t20\t0\t2\t87\t20\t0\t2\t87\t23\t0\t2\t96\t24\t0\t2\t99\t9\t0\t2\t54\t8\t0\t2\t51\tY\t40\t1.169\t0\n+Contig133_chr36_32954045_32955409\t136\tA\tG\t116.0\tchr36\t32954182\tA\t16\t0\t2\t75\t15\t0\t2\t72\t20\t0\t2\t87\t11\t0\t2\t60\t18\t0\t2\t81\t13\t0\t2\t66\tY\t74\t3.772\t1\n+Contig53_chr37_6665763_6665919\t116\tC\tT\t111.0\tchr37\t6665875\tC\t9\t0\t2\t54\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t8\t0\t2\t51\t10\t0\t2\t57\tN\t15\t10.875\t1\n+Contig2_chr37_31197993_31198256\t182\tC\tT\t39.6\tchr37\t31198171\tT\t6\t0\t2\t45\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t12\t0\t2\t63\tN\t2\t0.595\t0\n+Contig7_chr38_12217200_12218387\t1163\tA\tT\t44.4\tchr38\t12218353\tA\t11\t0\t2\t60\t13\t0\t2\t66\t17\t0\t2\t78\t10\t0\t2\t57\t11\t0\t2\t60\t11\t0\t2\t60\tY\t67\t+99.\t0\n+Contig265_chrX_2689247_2689484\t114\tC\tG\t103.0\tchrX\t2689356\tC\t11\t0\t2\t60\t9\t0\t2\t54\t13\t0\t2\t66\t16\t0\t2\t75\t14\t0\t2\t69\t10\t0\t2\t57\tN\t2\t9.232\t1\n+Contig113_chrX_26287829_26288398\t385\tC\tT\t59.6\tchrX\t26288213\tC\t9\t0\t2\t54\t9\t0\t2\t54\t17\t0\t2\t78\t11\t0\t2\t60\t3\t8\t1\t44\t4\t0\t2\t39\tN\t13\t0.077\t0\n+Contig90_chrX_57430715_57431566\t548\tC\tT\t116.0\tchrX\t57431266\tT\t9\t0\t2\t54\t18\t0\t2\t81\t13\t0\t2\t66\t14\t0\t2\t69\t8\t0\t2\t54\t7\t0\t2\t48\tY\t261\t0.154\t1\n+Contig133_chrX_84833782_84834125\t182\tG\tA\t69.7\tchrX\t84833962\tG\t5\t0\t2\t42\t18\t0\t2\t81\t12\t0\t2\t63\t19\t0\t2\t84\t6\t3\t1\t27\t7\t0\t2\t48\tN\t619\t0.278\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/select_snps/select_snps.wsf --- a/test-data/test_out/select_snps/select_snps.wsf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,102 +0,0 @@\n-#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist",\n-#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"}\n-Contig161_chr1_4641264_4641879\t115\tC\tT\t73.5\tchr1\t4641382\tC\t6\t0\t2\t45\t8\t0\t2\t51\t15\t0\t2\t72\t5\t0\t2\t42\t6\t0\t2\t45\t10\t0\t2\t57\tY\t54\t0.323\t0\n-Contig86_chr1_30984450_30985684\t670\tC\tT\t365.0\tchr1\t30985133\tC\t9\t0\t2\t54\t10\t0\t2\t57\t13\t0\t2\t66\t3\t0\t2\t36\t9\t0\t2\t54\t7\t0\t2\t48\tY\t145\t0.031\t0\n-Contig21_chr1_60697952_60699446\t307\tG\tA\t51.9\tchr1\t60698265\tG\t12\t0\t2\t63\t9\t0\t2\t54\t4\t0\t2\t39\t6\t0\t2\t45\t9\t0\t2\t54\t4\t0\t2\t39\tY\t98\t0.507\t0\n-Contig64_chr1_87343284_87345672\t163\tT\tA\t3.76\tchr1\t87343443\tC\t0\t2\t2\t1\t0\t0\t-1\t0\t5\t0\t2\t42\t2\t0\t2\t33\t0\t1\t2\t14\t0\t0\t-1\t0\tN\t3\t0.039\t2\n-Contig20_chr1_110679280_110679687\t181\tC\tT\t87.4\tchr1\t110679454\t-\t1\t0\t2\t30\t7\t0\t2\t48\t4\t0\t2\t39\t2\t0\t2\t33\t2\t0\t2\t33\t0\t0\t-1\t0\tN\t31\t0.660\t2\n-Contig222_chr2_9817738_9818143\t220\tC\tT\t888.0\tchr2\t9817960\tC\t17\t0\t2\t78\t12\t0\t2\t63\t20\t0\t2\t87\t8\t0\t2\t51\t11\t0\t2\t60\t12\t0\t2\t63\tY\t76\t0.093\t1\n-Contig47_chr2_25470778_25471576\t126\tG\tA\t888.0\tchr2\t25470896\tG\t12\t0\t2\t63\t14\t0\t2\t69\t14\t0\t2\t69\t10\t0\t2\t57\t18\t0\t2\t81\t13\t0\t2\t66\tN\t11\t0.289\t1\n-Contig6_chr2_56859179_56859956\t671\tT\tC\t999.9\tchr2\t56859851\tT\t15\t0\t2\t72\t18\t0\t2\t81\t20\t0\t2\t90\t19\t0\t2\t84\t19\t0\t2\t84\t24\t0\t2\t99\tN\t28\t5.308\t1\n-Contig163_chr2_76402959_76404830\t221\tC\tT\t127.0\tchr2\t76403181\tC\t4\t0\t2\t42\t10\t0\t2\t57\t9\t0\t2\t54\t11\t0\t2\t60\t7\t0\t2\t48\t9\t0\t2\t54\tY\t54\t0.178\t1\n-Contig56_chr3_17326225_17327548\t387\tG\tC\t91.2\tchr3\t17326591\tG\t14\t0\t2\t69\t13\t0\t2\t66\t15\t0\t2\t72\t15\t0\t2\t72\t13\t0\t2\t66\t12\t0\t2\t63\tY\t20\t0.225\t3\n-Contig108_chr3_46210055_46210874\t367\tA\tG\t21.0\tchr3\t46210423\tA\t19\t0\t2\t84\t10\t0\t2\t57\t16\t0\t2\t75\t14\t0\t2\t69\t20\t0\t2\t87\t11\t0\t2\t60\tN\t236\t0.028\t1\n-Contig1_chr3_51588422_51589409\t926\tA\tG\t51.0\tchr3\t51589353\tG\t2\t0\t2\t33\t2\t0\t2\t33\t6\t0\t2\t45\t4\t0\t2\t39\t9\t0\t2\t54\t11\t0\t2\t60\tN\t21\t1.147\t0\n-Contig65_chr3_80727952_80728283\t39\tT\tC\t71.2\tchr3\t80727990\tT\t7\t0\t2\t48\t3\t0\t2\t36\t8\t0\t2\t51\t6\t0\t2\t45\t8\t0\t2\t51\t11\t0\t2\t60\tN\t22\t7.078\t0\n-Contig134_chr4_12145648_12148225\t1326\tC\tT\t164.0\tchr4\t12146961\tC\t9\t0\t2\t54\t8\t0\t2\t51\t7\t0\t2\t48\t3\t0\t2\t36\t5\t0\t2\t42\t5\t0\t2\t42\tY\t4\t0.080\t1\n-Contig19_chr4_26233601_26233991\t146\tG\tC\t51.6\tchr4\t26233744\tG\t10\t0\t2\t57\t8\t0\t2\t51\t9\t0\t2\t54\t5\t0\t2\t42\t9\t0\t2\t54\t4\t0\t2\t39\tN\t41\t0.163\t3\n-Contig17_chr4_61310346_61311158\t267\tC\tT\t49.9\tchr4\t61310604\tT\t10\t0\t2\t57\t7\t0\t2\t48\t9\t0\t2\t54\t10\t0\t2\t57\t14\t0\t2\t69\t7\t0\t2\t48\tY\t219\t0.098\t0\n-Contig31_chr5_4734956_4736547\t1166\tC\tT\t133.0\tchr5\t4736132\tC\t14\t0\t2\t69\t8\t0\t2\t51\t17\t0\t2\t78\t4\t0\t2\t39\t9\t0\t2\t54\t12\t0\t2\t63\tY\t1\t0.021\t0\n-Contig6_chr5_26899813_26900498\t97\tA\tC\t88.6\tchr5\t26899910\tA\t15\t0\t2\t72\t14\t0\t2\t69\t27\t0\t2\t108\t15\t0\t2\t72\t13\t0\t2\t69\t12\t0\t2\t63\tY\t92\t7.370\t3\n-Contig45_chr5_50892738_50892968\t169\tC\tA\t25.8\tchr5\t50892911\tC\t10\t0\t2\t57\t7\t0\t2\t48\t10\t0\t2\t60\t6\t0\t2\t45\t6\t0\t2\t45\t13\t0\t2\t66\tN\t244\t0.497\t1\n-Contig45_chr5_76133561_76134403\t388\tA\tG\t103.0\tchr5\t76133941\tG\t3\t0\t2\t36\t8\t0\t2\t51\t8\t0\t2\t51\t5\t0\t2\t42\t6\t0\t2\t45\t7\t0\t2\t48\tY\t57\t0.038\t0\n-Contig111_chr6_5821219_5822519\t1060\tA\tG\t68.1\tchr6\t5822321\tT\t7\t0\t2\t48\t6\t0\t2\t45\t11\t0\t2\t60\t9\t0\t2\t54\t3\t0\t2\t36\t12\t0\t2\t63\tY\t7\t0.231\t1\n-Contig102_chr6_30271329_30271577\t39\tT\tG\t139.0\tchr6\t30271371\tG\t3\t0\t2\t36\t4\t0\t2\t39\t6\t0\t2\t45\t1\t0\t2\t30\t4\t0\t2\t39\t4\t0\t2\t39\tN\t15\t1.159\t0\n-Contig112_chr6_51024554_51024851\t100\tA\tG\t121.0\tchr6\t51024654\tA\t10\t0\t2\t57\t12\t0\t2\t63\t9\t0\t2\t54\t13\t0\t2\t66\t14\t0\t2\t69\t17\t0\t2\t78\tN\t75\t4.287\t0\n-Contig84_chr7_6648683_6650255\t1297\tG\tA\t110.0\tchr7\t6649988\tG\t18\t0\t2\t81\t9\t0\t2\t54\t22\t0\t2\t77\t16\t0\t2\t75\t20\t0\t2\t87\t6\t0\t2\t45\tY\t83\t0.166\t0\n-Contig206_chr7_26281823_26282074\t103\tC\tA\t101.0\tchr7\t26281925\tT\t11\t0\t2\t60\t16\t0\t2\t61\t19\t0\t2\t84\t6\t0\t2\t45\t19\t0\t2\t84\t16\t0\t2\t75\tN\t-1\t0.947\t1\n-Contig38_chr7_50681997_50682600\t42\tT\tC\t92.4\tchr7\t50682037\tG\t6\t0\t2\t45\t2\t0\t2\t33\t10\t0\t2\t57\t12\t0\t2\t63\t5\t0\t2\t42\t6\t0\t2\t45\tY\t94\t0.146\t0\n-Contig91_chr8_12804505_12805470\t409\tC\tA\t111.0\tchr8\t12804906\tC\t8\t0\t2\t51\t10\t0\t2\t57\t15\t0\t2\t72\t12\t0\t2\t63\t14\t0\t2\t69\t15\t0\t2\t72\tN\t145\t0.175\t0\n-Contig8_chr8_27811135_27812620\t333\tC\tT'..b'0\tchr25\t4011690\tA\t12\t0\t2\t6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t3\t1\t27\t7\t0\t2\t48\tN\t619\t0.278\t0\n' |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.snp Wed Apr 18 11:12:21 2012 -0400 |
| [ |
| @@ -0,0 +1,10 @@ +#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist", +#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"} +Contig47_chr2_25470778_25471576 126 G A 888.0 chr2 25470896 G 12 0 2 63 14 0 2 69 14 0 2 69 10 0 2 57 18 0 2 81 13 0 2 66 N 11 0.289 1 +Contig73_chr9_29451535_29452248 616 A G 24.7 chr9 29452127 G 4 0 2 39 7 0 2 48 1 0 2 30 4 0 2 39 7 0 2 48 6 0 2 45 N 49 0.448 4 +Contig69_chr10_40547265_40548153 371 G A 58.1 chr10 40547649 A 9 0 2 54 8 0 2 51 8 0 2 51 9 0 2 54 4 0 2 39 5 0 2 42 Y 20 0.138 4 +Contig99_chr17_26021506_26022200 505 C T 88.8 chr17 26022017 T 15 0 2 72 13 0 2 66 19 0 2 84 9 0 2 54 10 0 2 57 11 0 2 60 Y 1 0.172 1 +Contig27_chr17_61713766_61716585 1056 G C 40.0 chr17 61714821 G 4 0 2 39 8 0 2 51 10 0 2 57 6 0 2 45 6 0 2 45 3 0 2 36 N 6 2.200 4 +Contig26_chr22_57817664_57819633 1453 A G 150.0 chr22 57819121 G 9 0 2 54 9 0 2 54 13 0 2 66 15 0 2 72 11 0 2 60 14 0 2 69 N 15 0.471 1 +Contig103_chr25_38891221_38892140 407 G A 131.0 chr25 38891644 G 8 0 2 51 14 0 2 69 18 0 2 81 8 0 2 51 8 0 2 51 11 0 2 60 Y 149 0.167 4 +Contig64_chr27_34654435_34654621 132 C A 115.0 chr27 34654567 T 2 0 2 33 2 0 2 33 5 0 2 42 3 0 2 36 3 0 2 36 8 0 2 51 N 12 0.297 1 |
| b |
| diff -r 626b714f72bb -r e29f4d801bb0 test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.wsf --- a/test-data/test_out/specify_restriction_enzymes/specify_restriction_enzymes.wsf Tue Apr 10 13:51:19 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,10 +0,0 @@ -#{"column_names":["scaf","pos","A","B","qual","ref","rpos","rnuc","1A","1B","1G","1Q","2A","2B","2G","2Q","3A","3B","3G","3Q","4A","4B","4G","4Q","5A","5B","5G","5Q","6A","6B","6G","6Q","pair","dist", -#"prim","rflp"],"dbkey":"canFam2","individuals":[["PB1",9],["PB2",13],["PB3",17],["PB4",21],["PB6",25],["PB8",29]],"pos":2,"rPos":7,"ref":6,"scaffold":1,"species":"bear"} -Contig47_chr2_25470778_25471576 126 G A 888.0 chr2 25470896 G 12 0 2 63 14 0 2 69 14 0 2 69 10 0 2 57 18 0 2 81 13 0 2 66 N 11 0.289 1 -Contig73_chr9_29451535_29452248 616 A G 24.7 chr9 29452127 G 4 0 2 39 7 0 2 48 1 0 2 30 4 0 2 39 7 0 2 48 6 0 2 45 N 49 0.448 4 -Contig69_chr10_40547265_40548153 371 G A 58.1 chr10 40547649 A 9 0 2 54 8 0 2 51 8 0 2 51 9 0 2 54 4 0 2 39 5 0 2 42 Y 20 0.138 4 -Contig99_chr17_26021506_26022200 505 C T 88.8 chr17 26022017 T 15 0 2 72 13 0 2 66 19 0 2 84 9 0 2 54 10 0 2 57 11 0 2 60 Y 1 0.172 1 -Contig27_chr17_61713766_61716585 1056 G C 40.0 chr17 61714821 G 4 0 2 39 8 0 2 51 10 0 2 57 6 0 2 45 6 0 2 45 3 0 2 36 N 6 2.200 4 -Contig26_chr22_57817664_57819633 1453 A G 150.0 chr22 57819121 G 9 0 2 54 9 0 2 54 13 0 2 66 15 0 2 72 11 0 2 60 14 0 2 69 N 15 0.471 1 -Contig103_chr25_38891221_38892140 407 G A 131.0 chr25 38891644 G 8 0 2 51 14 0 2 69 18 0 2 81 8 0 2 51 8 0 2 51 11 0 2 60 Y 149 0.167 4 -Contig64_chr27_34654435_34654621 132 C A 115.0 chr27 34654567 T 2 0 2 33 2 0 2 33 5 0 2 42 3 0 2 36 3 0 2 36 8 0 2 51 N 12 0.297 1 |