| Previous changeset 7:243be7a79d9c (2018-05-31) Next changeset 9:a6cd59f35832 (2018-06-26) |
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Commit message:
planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit d6aa0144475c93626400a46e933acbbd77fefb01-dirty |
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modified:
data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml tools/mentalist_call/mentalist_call.xml tools/mentalist_distance/mentalist_distance.xml |
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added:
test-data/mentalist_distance/large_input_00.tsv test-data/mentalist_distance/large_output_00.tsv test-data/mentalist_distance/med_input_00.tsv test-data/mentalist_distance/med_output_00.tsv test-data/mentalist_distance/small_input_00.tsv test-data/mentalist_distance/small_output_00.tsv test-data/mentalist_tree/med_input_00.tsv test-data/mentalist_tree/med_output_00.nwk test-data/mentalist_tree/small_input_00.tsv test-data/mentalist_tree/small_output_00.nwk tools/mentalist_tree/mentalist_tree tools/mentalist_tree/mentalist_tree.xml |
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removed:
test-data/large_input_00.tsv test-data/large_output_00.tsv test-data/med_input_00.tsv test-data/med_output_00.tsv test-data/small_input_00.tsv test-data/small_output_00.tsv |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 data_managers/data_manager_conf.xml --- a/data_managers/data_manager_conf.xml Thu May 31 14:29:28 2018 -0400 +++ b/data_managers/data_manager_conf.xml Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <data_managers> - <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.8"> + <data_manager tool_file="data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml" id="mentalist_build_db" version="0.1.9"> <data_table name="mentalist_databases"> <output> <column name="value" /> @@ -15,7 +15,7 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.8"> + <data_manager tool_file="data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml" id="mentalist_download_cgmlst" version="0.1.9"> <data_table name="mentalist_databases"> <output> <column name="value" /> @@ -30,7 +30,7 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.8"> + <data_manager tool_file="data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml" id="mentalist_download_pubmlst" version="0.1.9"> <data_table name="mentalist_databases"> <output> <column name="value" /> @@ -45,7 +45,7 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.8"> + <data_manager tool_file="data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml" id="mentalist_download_enterobase" version="0.1.9"> <data_table name="mentalist_databases"> <output> <column name="value" /> |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml --- a/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Thu May 31 14:29:28 2018 -0400 +++ b/data_managers/data_manager_mentalist_build_db/data_manager/mentalist_build_db.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.8"> +<tool id="mentalist_build_db" name="MentaLiST Build DB" tool_type="manage_data" version="0.1.9"> <requirements> - <requirement type="package" version="0.1.8">mentalist</requirement> + <requirement type="package" version="0.1.9">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml --- a/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Thu May 31 14:29:28 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_cgmlst/data_manager/mentalist_download_cgmlst.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.8"> +<tool id="mentalist_download_cgmlst" name="MentaLiST Download from cgMLST" tool_type="manage_data" version="0.1.9"> <requirements> - <requirement type="package" version="0.1.8">mentalist</requirement> + <requirement type="package" version="0.1.9">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml --- a/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml Thu May 31 14:29:28 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_enterobase/data_manager/mentalist_download_enterobase.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.8"> +<tool id="mentalist_download_enterobase" name="MentaLiST Download from Enterobase" tool_type="manage_data" version="0.1.9"> <requirements> - <requirement type="package" version="0.1.8">mentalist</requirement> + <requirement type="package" version="0.1.9">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml --- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Thu May 31 14:29:28 2018 -0400 +++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,7 +1,7 @@ <?xml version="1.0"?> -<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.8"> +<tool id="mentalist_download_pubmlst" name="MentaLiST Download from pubMLST" tool_type="manage_data" version="0.1.9"> <requirements> - <requirement type="package" version="0.1.8">mentalist</requirement> + <requirement type="package" version="0.1.9">mentalist</requirement> </requirements> <command detect_errors="exit_code"> <![CDATA[ |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/large_input_00.tsv --- a/test-data/large_input_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1001 +0,0 @@\n-Sample\tlocus-0\tlocus-1\tlocus-2\tlocus-3\tlocus-4\tlocus-5\tlocus-6\tlocus-7\tlocus-8\tlocus-9\tlocus-10\tlocus-11\tlocus-12\tlocus-13\tlocus-14\tlocus-15\tlocus-16\tlocus-17\tlocus-18\tlocus-19\tlocus-20\tlocus-21\tlocus-22\tlocus-23\tlocus-24\tlocus-25\tlocus-26\tlocus-27\tlocus-28\tlocus-29\tlocus-30\tlocus-31\tlocus-32\tlocus-33\tlocus-34\tlocus-35\tlocus-36\tlocus-37\tlocus-38\tlocus-39\tlocus-40\tlocus-41\tlocus-42\tlocus-43\tlocus-44\tlocus-45\tlocus-46\tlocus-47\tlocus-48\tlocus-49\tlocus-50\tlocus-51\tlocus-52\tlocus-53\tlocus-54\tlocus-55\tlocus-56\tlocus-57\tlocus-58\tlocus-59\tlocus-60\tlocus-61\tlocus-62\tlocus-63\tlocus-64\tlocus-65\tlocus-66\tlocus-67\tlocus-68\tlocus-69\tlocus-70\tlocus-71\tlocus-72\tlocus-73\tlocus-74\tlocus-75\tlocus-76\tlocus-77\tlocus-78\tlocus-79\tlocus-80\tlocus-81\tlocus-82\tlocus-83\tlocus-84\tlocus-85\tlocus-86\tlocus-87\tlocus-88\tlocus-89\tlocus-90\tlocus-91\tlocus-92\tlocus-93\tlocus-94\tlocus-95\tlocus-96\tlocus-97\tlocus-98\tlocus-99\n-sample-0\t9\t9\t0\t0\t2\t2\t2\t0\t1\t7\t7\t1\t6\t7\t0\t7\t4\t1\t6\t0\t8\t5\t7\t5\t1\t3\t0\t1\t8\t6\t2\t2\t4\t3\t6\t5\t1\t2\t2\t5\t3\t3\t5\t6\t4\t8\t5\t9\t1\t3\t3\t9\t7\t6\t1\t8\t5\t3\t9\t3\t4\t6\t0\t1\t5\t7\t1\t2\t6\t5\t1\t8\t7\t1\t5\t2\t1\t9\t5\t0\t0\t2\t1\t1\t8\t3\t3\t4\t0\t2\t5\t3\t6\t1\t7\t0\t6\t6\t1\t0\n-sample-1\t6\t5\t0\t1\t9\t8\t5\t8\t1\t8\t2\t1\t1\t0\t6\t2\t4\t4\t2\t3\t5\t9\t6\t8\t0\t5\t6\t1\t7\t8\t9\t7\t9\t9\t4\t1\t0\t4\t3\t4\t4\t3\t1\t8\t8\t3\t5\t7\t9\t9\t2\t1\t1\t3\t1\t1\t4\t4\t9\t6\t8\t2\t3\t6\t5\t6\t1\t5\t4\t7\t1\t7\t8\t8\t1\t7\t2\t7\t5\t0\t1\t2\t8\t5\t6\t6\t5\t4\t4\t4\t5\t4\t2\t8\t6\t5\t7\t2\t1\t9\n-sample-2\t1\t2\t7\t3\t4\t9\t1\t0\t7\t5\t7\t0\t6\t1\t8\t8\t8\t5\t9\t0\t6\t5\t7\t0\t9\t2\t9\t7\t9\t2\t9\t1\t9\t7\t5\t7\t7\t3\t6\t9\t5\t4\t2\t8\t2\t4\t4\t9\t3\t9\t2\t0\t3\t9\t0\t1\t3\t1\t1\t7\t6\t8\t6\t1\t1\t0\t5\t7\t6\t8\t7\t6\t2\t8\t8\t4\t2\t4\t0\t7\t7\t8\t3\t0\t6\t2\t3\t2\t1\t8\t6\t3\t4\t4\t1\t2\t7\t6\t3\t9\n-sample-3\t1\t0\t1\t9\t6\t8\t1\t1\t3\t2\t9\t5\t2\t9\t7\t8\t5\t3\t7\t2\t2\t8\t7\t0\t8\t3\t5\t9\t8\t0\t5\t0\t5\t9\t2\t2\t2\t0\t8\t5\t6\t4\t0\t3\t4\t7\t3\t3\t2\t6\t9\t2\t8\t9\t8\t5\t9\t5\t3\t3\t5\t5\t1\t3\t7\t3\t9\t5\t6\t9\t4\t6\t1\t8\t0\t6\t7\t5\t0\t5\t4\t6\t3\t3\t3\t0\t8\t4\t0\t5\t3\t8\t7\t9\t4\t4\t6\t8\t9\t6\n-sample-4\t9\t5\t8\t1\t6\t8\t4\t6\t9\t9\t3\t0\t7\t8\t4\t2\t9\t0\t6\t7\t2\t3\t0\t0\t3\t0\t9\t9\t8\t9\t0\t3\t5\t3\t1\t4\t8\t0\t3\t9\t6\t6\t8\t8\t6\t8\t2\t5\t9\t9\t2\t8\t3\t9\t8\t4\t6\t7\t7\t5\t9\t1\t0\t6\t3\t6\t3\t4\t6\t1\t7\t7\t6\t2\t1\t9\t2\t5\t2\t9\t8\t5\t2\t9\t8\t0\t9\t2\t5\t3\t3\t5\t0\t5\t1\t2\t2\t5\t4\t9\n-sample-5\t9\t5\t8\t0\t1\t9\t4\t0\t8\t6\t3\t6\t3\t3\t0\t3\t5\t9\t4\t2\t6\t1\t5\t4\t1\t5\t0\t9\t1\t8\t4\t5\t3\t3\t2\t2\t3\t9\t6\t5\t0\t8\t4\t9\t9\t8\t0\t4\t4\t5\t2\t3\t9\t9\t9\t3\t2\t0\t9\t7\t2\t5\t5\t1\t1\t8\t7\t0\t6\t4\t3\t9\t7\t4\t2\t7\t7\t6\t4\t5\t5\t7\t6\t4\t1\t2\t7\t3\t4\t5\t0\t8\t5\t7\t8\t7\t9\t4\t1\t0\n-sample-6\t4\t7\t1\t4\t8\t3\t0\t0\t5\t7\t7\t0\t7\t1\t8\t2\t4\t6\t9\t7\t2\t2\t4\t6\t8\t4\t9\t3\t2\t5\t3\t5\t3\t9\t1\t1\t4\t6\t6\t8\t5\t8\t5\t4\t9\t2\t6\t3\t6\t9\t7\t0\t9\t5\t7\t4\t4\t8\t6\t1\t2\t3\t2\t9\t8\t4\t4\t4\t0\t2\t2\t1\t3\t8\t9\t4\t6\t8\t2\t4\t1\t3\t5\t6\t7\t8\t0\t1\t3\t7\t1\t3\t7\t9\t5\t5\t3\t4\t8\t2\n-sample-7\t0\t5\t9\t3\t8\t5\t1\t3\t0\t4\t9\t1\t8\t6\t9\t2\t3\t8\t5\t0\t4\t6\t6\t3\t2\t0\t7\t7\t1\t9\t9\t4\t6\t5\t4\t9\t0\t8\t5\t7\t9\t5\t6\t0\t6\t4\t5\t4\t6\t3\t0\t2\t2\t1\t5\t2\t3\t5\t1\t5\t3\t1\t9\t9\t7\t4\t0\t1\t4\t1\t0\t8\t6\t8\t7\t0\t1\t9\t6\t0\t2\t7\t4\t5\t8\t2\t9\t1\t5\t5\t2\t2\t5\t9\t5\t2\t6\t9\t7\t0\n-sample-8\t5\t7\t3\t5\t1\t1\t4\t4\t6\t2\t1\t4\t4\t8\t1\t7\t6\t8\t9\t8\t7\t3\t6\t3\t2\t9\t2\t8\t9\t8\t6\t2\t9\t4\t0\t8\t0\t1\t1\t9\t3\t3\t7\t2\t5\t0\t8\t7\t9\t1\t9\t5\t8\t2\t9\t6\t3\t4\t5\t8\t9\t3\t5\t0\t5\t6\t5\t2\t1\t1\t5\t1\t7\t9\t1\t3\t2\t4\t4\t4\t2\t4\t3\t9\t9\t4\t6\t5\t8\t8\t8\t9\t4\t7\t3\t8\t2\t9\t3\t1\n-sample-9\t1\t4\t0\t0\t7\t1\t8\t0\t6\t2\t2\t7\t2\t2\t3\t7\t0\t5\t8\t6\t1\t7\t8\t4\t7\t6\t9\t1\t6\t5\t0\t3\t5\t9\t1\t5\t1\t0\t7\t3\t3\t9\t6\t7\t9\t9\t0\t5\t7\t9\t5\t6\t3\t5\t1\t4\t6\t9\t0\t0\t0\t8\t1\t2\t4\t4\t8\t0\t9\t4\t3\t3\t3\t1\t9\t2\t0\t8\t9\t4\t4\t6\t7\t3\t3\t2\t9\t0\t1\t6\t3\t9\t8\t4\t4\t3\t9\t5\t3\t3\n-sample-10\t7\t2\t7\t0\t1\t8\t2\t4\t3\t9\t6\t8\t7\t8\t7\t1\t2\t8\t4\t3\t4\t7\t7\t8\t9\t3\t3\t1\t0\t7\t6\t3\t9\t1\t1\t6\t0\t9\t2\t9\t8\t9\t7\t6\t1\t6\t7\t0\t3\t3\t7\t7\t9\t2\t1\t9\t2\t5\t8\t0\t1\t2\t8\t4\t6\t3\t2\t8\t8\t4\t0\t5\t5\t2\t9\t8\t6\t2\t2\t4\t3\t9\t2\t9\t7\t8\t1\t9\t5\t2\t6\t8\t6\t9\t8\t4\t7\t8\t9\t2\n-sample-11\t7\t1\t0\t8\t1\t4\t7\t2\t3\t9\t4\t6\t3\t5\t6\t7\t1\t1\t2\t5\t2\t7\t2\t6\t0\t4\t3\t7\t0\t7\t6\t7\t6\t7\t4\t9\t3\t8\t0\t4\t7\t0\t1\t7\t7\t9\t3\t1\t9\t0\t2\t7\t6\t2\t6\t3\t8\t0\t1\t2\t1\t3\t7\t5\t0\t8\t0\t2\t7\t6\t6\t1\t1\t0\t5\t1\t7\t5\t2\t3\t7\t1\t4\t3\t7\t5\t1\t8\t5\t5\t9\t3\t4\t8\t6\t5\t0\t8\t8\t0\n-sample-12\t2\t1\t0\t0\t2\t8\t4\t3\t2\t2\t3\t4\t7\t7\t6\t8\t8\t5\t7\t8\t2\t7\t1\t5\t7\t0\t9\t9\t1\t4\t0\t1\t9\t0\t5\t4\t0\t8\t8\t0\t4\t7\t2\t5\t0\t3\t0\t2\t4\t0\t9\t8\t7\t8\t1\t6\t3\t6\t0\t3\t9\t3\t0\t8\t3\t3\t6\t6\t8\t5\t9\t0\t6\t3\t4\t7\t7\t1\t9\t1\t6\t0\t7\t8\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|
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/large_output_00.tsv --- a/test-data/large_output_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1001 +0,0 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|
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/med_input_00.tsv --- a/test-data/med_input_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,101 +0,0 @@\n-Sample\tlocus-0\tlocus-1\tlocus-2\tlocus-3\tlocus-4\tlocus-5\tlocus-6\tlocus-7\tlocus-8\tlocus-9\tlocus-10\tlocus-11\tlocus-12\tlocus-13\tlocus-14\tlocus-15\tlocus-16\tlocus-17\tlocus-18\tlocus-19\tlocus-20\tlocus-21\tlocus-22\tlocus-23\tlocus-24\tlocus-25\tlocus-26\tlocus-27\tlocus-28\tlocus-29\tlocus-30\tlocus-31\tlocus-32\tlocus-33\tlocus-34\tlocus-35\tlocus-36\tlocus-37\tlocus-38\tlocus-39\tlocus-40\tlocus-41\tlocus-42\tlocus-43\tlocus-44\tlocus-45\tlocus-46\tlocus-47\tlocus-48\tlocus-49\tlocus-50\tlocus-51\tlocus-52\tlocus-53\tlocus-54\tlocus-55\tlocus-56\tlocus-57\tlocus-58\tlocus-59\tlocus-60\tlocus-61\tlocus-62\tlocus-63\tlocus-64\tlocus-65\tlocus-66\tlocus-67\tlocus-68\tlocus-69\tlocus-70\tlocus-71\tlocus-72\tlocus-73\tlocus-74\tlocus-75\tlocus-76\tlocus-77\tlocus-78\tlocus-79\tlocus-80\tlocus-81\tlocus-82\tlocus-83\tlocus-84\tlocus-85\tlocus-86\tlocus-87\tlocus-88\tlocus-89\tlocus-90\tlocus-91\tlocus-92\tlocus-93\tlocus-94\tlocus-95\tlocus-96\tlocus-97\tlocus-98\tlocus-99\n-sample-0\t9\t8\t5\t2\t6\t6\t2\t3\t3\t9\t6\t8\t2\t8\t0\t6\t8\t5\t1\t5\t9\t1\t9\t0\t1\t5\t6\t7\t1\t6\t2\t8\t1\t8\t3\t2\t5\t4\t7\t2\t8\t6\t2\t1\t6\t2\t5\t8\t7\t5\t0\t7\t9\t3\t0\t6\t7\t2\t1\t9\t6\t0\t4\t5\t3\t4\t0\t5\t1\t6\t6\t7\t0\t3\t9\t9\t5\t7\t2\t3\t9\t9\t5\t6\t6\t8\t7\t1\t6\t7\t4\t5\t6\t0\t9\t0\t0\t0\t5\t4\n-sample-1\t4\t2\t8\t2\t3\t9\t0\t6\t0\t9\t0\t1\t4\t1\t5\t0\t9\t6\t1\t4\t5\t3\t1\t7\t6\t1\t5\t8\t3\t3\t4\t9\t9\t6\t9\t7\t9\t1\t6\t4\t7\t3\t8\t6\t0\t6\t7\t8\t8\t8\t4\t1\t5\t4\t8\t7\t4\t0\t7\t8\t2\t2\t5\t7\t9\t8\t8\t7\t3\t2\t7\t0\t9\t1\t4\t7\t6\t5\t2\t5\t2\t8\t6\t5\t5\t4\t5\t2\t2\t8\t6\t7\t8\t6\t1\t3\t6\t9\t8\t7\n-sample-2\t9\t6\t5\t2\t3\t1\t1\t8\t6\t2\t0\t8\t0\t9\t7\t4\t7\t2\t1\t6\t1\t4\t4\t1\t6\t9\t2\t7\t1\t9\t4\t5\t4\t5\t5\t7\t3\t0\t4\t1\t0\t0\t4\t6\t9\t6\t9\t8\t0\t4\t2\t6\t6\t9\t3\t4\t6\t6\t6\t8\t4\t9\t2\t2\t8\t0\t8\t9\t7\t1\t9\t9\t4\t5\t6\t2\t4\t7\t4\t0\t7\t4\t8\t3\t8\t6\t2\t9\t9\t5\t8\t5\t8\t6\t8\t5\t0\t7\t6\t4\n-sample-3\t2\t9\t9\t7\t9\t4\t2\t5\t1\t0\t1\t4\t2\t8\t5\t6\t4\t9\t3\t8\t0\t5\t8\t4\t8\t4\t0\t2\t1\t6\t1\t5\t4\t2\t5\t8\t2\t6\t5\t6\t3\t9\t7\t9\t3\t2\t8\t0\t2\t1\t1\t9\t1\t0\t7\t2\t0\t2\t4\t4\t5\t4\t6\t0\t3\t5\t7\t7\t8\t6\t9\t5\t1\t0\t7\t1\t9\t2\t9\t7\t7\t4\t4\t6\t4\t3\t4\t1\t4\t3\t6\t9\t7\t5\t2\t4\t7\t6\t6\t4\n-sample-4\t3\t6\t8\t5\t1\t9\t7\t7\t0\t6\t4\t7\t2\t9\t9\t6\t8\t8\t0\t0\t3\t9\t7\t1\t6\t6\t0\t1\t3\t9\t1\t5\t3\t6\t9\t8\t9\t6\t3\t3\t2\t3\t6\t2\t3\t2\t2\t3\t9\t2\t0\t9\t1\t2\t3\t6\t1\t0\t4\t0\t0\t7\t0\t9\t9\t3\t3\t4\t5\t8\t8\t1\t7\t5\t3\t3\t1\t9\t9\t5\t8\t2\t5\t6\t4\t3\t6\t0\t8\t7\t0\t7\t3\t8\t4\t1\t8\t4\t0\t2\n-sample-5\t8\t7\t6\t7\t0\t5\t1\t0\t5\t7\t1\t4\t5\t0\t1\t8\t0\t2\t1\t4\t6\t1\t6\t3\t7\t1\t0\t0\t8\t2\t8\t4\t5\t3\t0\t1\t7\t1\t6\t8\t9\t7\t2\t3\t9\t3\t9\t2\t8\t0\t9\t8\t1\t5\t9\t9\t7\t2\t0\t4\t5\t1\t1\t5\t5\t8\t1\t9\t2\t9\t8\t6\t1\t5\t2\t7\t6\t4\t5\t3\t0\t3\t5\t3\t0\t1\t4\t8\t7\t7\t1\t8\t1\t7\t9\t2\t0\t3\t3\t1\n-sample-6\t6\t5\t3\t2\t6\t5\t6\t8\t9\t7\t6\t1\t0\t2\t8\t2\t3\t7\t8\t2\t1\t8\t6\t7\t6\t2\t4\t9\t8\t7\t6\t0\t5\t4\t8\t0\t4\t5\t1\t7\t4\t3\t2\t7\t9\t9\t4\t9\t0\t7\t9\t9\t4\t3\t8\t7\t8\t1\t6\t6\t5\t4\t6\t5\t3\t3\t9\t3\t6\t1\t5\t7\t2\t7\t8\t5\t3\t9\t6\t4\t4\t1\t9\t1\t0\t5\t7\t5\t7\t4\t5\t4\t5\t7\t3\t2\t6\t0\t5\t1\n-sample-7\t7\t5\t3\t1\t3\t9\t3\t6\t5\t9\t6\t2\t2\t3\t9\t9\t5\t1\t3\t1\t3\t1\t3\t8\t9\t4\t4\t0\t7\t5\t2\t7\t7\t8\t6\t9\t9\t1\t2\t3\t1\t4\t3\t8\t5\t4\t2\t5\t0\t6\t5\t8\t9\t9\t5\t5\t2\t5\t5\t1\t8\t3\t9\t4\t7\t4\t2\t1\t7\t7\t5\t0\t2\t3\t2\t1\t9\t4\t3\t1\t7\t5\t8\t3\t9\t3\t4\t1\t2\t3\t8\t1\t1\t2\t2\t3\t2\t5\t5\t2\n-sample-8\t6\t8\t0\t7\t5\t0\t8\t5\t0\t5\t1\t7\t7\t5\t2\t1\t3\t6\t0\t7\t4\t0\t3\t6\t5\t7\t2\t8\t5\t1\t3\t9\t3\t7\t6\t3\t8\t2\t8\t2\t5\t4\t7\t1\t6\t3\t4\t3\t1\t1\t4\t9\t0\t3\t5\t3\t3\t6\t2\t6\t7\t9\t4\t3\t4\t2\t6\t6\t0\t6\t8\t2\t4\t5\t9\t7\t2\t2\t5\t5\t2\t3\t2\t8\t8\t0\t5\t5\t7\t9\t4\t5\t5\t7\t6\t5\t4\t9\t7\t9\n-sample-9\t5\t2\t3\t8\t1\t1\t9\t3\t0\t5\t1\t3\t2\t5\t6\t4\t9\t5\t0\t9\t9\t2\t4\t9\t8\t7\t0\t7\t5\t8\t9\t5\t6\t6\t7\t7\t8\t2\t6\t3\t5\t9\t6\t2\t7\t2\t5\t6\t7\t1\t9\t9\t9\t1\t9\t2\t5\t5\t7\t7\t5\t5\t3\t0\t4\t1\t4\t1\t5\t0\t9\t9\t1\t1\t9\t0\t8\t3\t0\t2\t9\t9\t7\t9\t2\t3\t1\t3\t7\t2\t0\t4\t1\t8\t1\t7\t8\t9\t5\t2\n-sample-10\t8\t1\t3\t3\t2\t2\t7\t9\t0\t6\t5\t7\t6\t3\t5\t7\t5\t2\t3\t7\t1\t3\t3\t2\t9\t9\t4\t1\t7\t2\t7\t1\t5\t7\t4\t0\t0\t5\t4\t6\t9\t0\t8\t9\t2\t6\t2\t5\t2\t8\t5\t8\t0\t0\t9\t0\t4\t0\t6\t2\t3\t5\t6\t7\t4\t4\t3\t1\t7\t8\t1\t7\t6\t7\t6\t1\t2\t6\t1\t8\t4\t2\t8\t5\t7\t3\t0\t0\t8\t0\t9\t5\t0\t0\t4\t2\t1\t0\t2\t6\n-sample-11\t7\t4\t0\t1\t3\t3\t7\t8\t8\t9\t9\t1\t6\t1\t6\t0\t4\t3\t8\t7\t3\t7\t2\t7\t2\t0\t6\t4\t5\t3\t8\t0\t8\t0\t4\t4\t4\t2\t6\t1\t9\t5\t6\t3\t0\t8\t5\t3\t7\t8\t9\t9\t2\t1\t1\t3\t4\t1\t0\t8\t2\t7\t0\t8\t8\t9\t3\t2\t0\t7\t9\t2\t5\t8\t2\t4\t5\t7\t7\t1\t0\t4\t9\t1\t2\t6\t4\t0\t2\t7\t7\t1\t3\t2\t3\t0\t8\t4\t5\t7\n-sample-12\t3\t6\t6\t4\t8\t5\t1\t0\t8\t7\t8\t2\t9\t7\t1\t3\t8\t7\t3\t0\t7\t9\t2\t6\t5\t2\t3\t8\t1\t1\t1\t9\t9\t0\t0\t8\t5\t8\t1\t7\t7\t3\t8\t2\t3\t0\t6\t2\t9\t7\t6\t3\t7\t8\t6\t2\t2\t6\t0\t0\t8\t8\t7\t6\t0\t7\t2\t7\t6\t9\t0\t4\t0\t6\t4\t8\t1\t9\t0\t0\t9\t3\t9\t6\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|
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/med_output_00.tsv --- a/test-data/med_output_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,101 +0,0 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t90\t93\t88\t91\t89\t93\t90\t92\t93\t91\t94\t89\t93\t90\t91\t84\t89\t88\t87\t88\t90\t91\t90\t94\t91\t90\t89\t90\t91\t88\t97\t93\t89\t83\t94\t91\t90\t89\t92\t86\t88\t95\t95\t91\t85\t88\t91\t90\t91\t93\t94\t94\t86\t93\t93\t90\t87\t89\t90\t93\t90\t94\t83\t92\t94\t91\t93\t85\t88\t92\t88\t91\t91\t93\t93\t91\t87\t90\t89\t94\t93\t88\t89\t89\t94\t92\t88\t90\t92\t94\t93\t91\t0\n' 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| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/large_input_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/large_input_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,1001 @@\n+Sample\tlocus-0\tlocus-1\tlocus-2\tlocus-3\tlocus-4\tlocus-5\tlocus-6\tlocus-7\tlocus-8\tlocus-9\tlocus-10\tlocus-11\tlocus-12\tlocus-13\tlocus-14\tlocus-15\tlocus-16\tlocus-17\tlocus-18\tlocus-19\tlocus-20\tlocus-21\tlocus-22\tlocus-23\tlocus-24\tlocus-25\tlocus-26\tlocus-27\tlocus-28\tlocus-29\tlocus-30\tlocus-31\tlocus-32\tlocus-33\tlocus-34\tlocus-35\tlocus-36\tlocus-37\tlocus-38\tlocus-39\tlocus-40\tlocus-41\tlocus-42\tlocus-43\tlocus-44\tlocus-45\tlocus-46\tlocus-47\tlocus-48\tlocus-49\tlocus-50\tlocus-51\tlocus-52\tlocus-53\tlocus-54\tlocus-55\tlocus-56\tlocus-57\tlocus-58\tlocus-59\tlocus-60\tlocus-61\tlocus-62\tlocus-63\tlocus-64\tlocus-65\tlocus-66\tlocus-67\tlocus-68\tlocus-69\tlocus-70\tlocus-71\tlocus-72\tlocus-73\tlocus-74\tlocus-75\tlocus-76\tlocus-77\tlocus-78\tlocus-79\tlocus-80\tlocus-81\tlocus-82\tlocus-83\tlocus-84\tlocus-85\tlocus-86\tlocus-87\tlocus-88\tlocus-89\tlocus-90\tlocus-91\tlocus-92\tlocus-93\tlocus-94\tlocus-95\tlocus-96\tlocus-97\tlocus-98\tlocus-99\n+sample-0\t9\t9\t0\t0\t2\t2\t2\t0\t1\t7\t7\t1\t6\t7\t0\t7\t4\t1\t6\t0\t8\t5\t7\t5\t1\t3\t0\t1\t8\t6\t2\t2\t4\t3\t6\t5\t1\t2\t2\t5\t3\t3\t5\t6\t4\t8\t5\t9\t1\t3\t3\t9\t7\t6\t1\t8\t5\t3\t9\t3\t4\t6\t0\t1\t5\t7\t1\t2\t6\t5\t1\t8\t7\t1\t5\t2\t1\t9\t5\t0\t0\t2\t1\t1\t8\t3\t3\t4\t0\t2\t5\t3\t6\t1\t7\t0\t6\t6\t1\t0\n+sample-1\t6\t5\t0\t1\t9\t8\t5\t8\t1\t8\t2\t1\t1\t0\t6\t2\t4\t4\t2\t3\t5\t9\t6\t8\t0\t5\t6\t1\t7\t8\t9\t7\t9\t9\t4\t1\t0\t4\t3\t4\t4\t3\t1\t8\t8\t3\t5\t7\t9\t9\t2\t1\t1\t3\t1\t1\t4\t4\t9\t6\t8\t2\t3\t6\t5\t6\t1\t5\t4\t7\t1\t7\t8\t8\t1\t7\t2\t7\t5\t0\t1\t2\t8\t5\t6\t6\t5\t4\t4\t4\t5\t4\t2\t8\t6\t5\t7\t2\t1\t9\n+sample-2\t1\t2\t7\t3\t4\t9\t1\t0\t7\t5\t7\t0\t6\t1\t8\t8\t8\t5\t9\t0\t6\t5\t7\t0\t9\t2\t9\t7\t9\t2\t9\t1\t9\t7\t5\t7\t7\t3\t6\t9\t5\t4\t2\t8\t2\t4\t4\t9\t3\t9\t2\t0\t3\t9\t0\t1\t3\t1\t1\t7\t6\t8\t6\t1\t1\t0\t5\t7\t6\t8\t7\t6\t2\t8\t8\t4\t2\t4\t0\t7\t7\t8\t3\t0\t6\t2\t3\t2\t1\t8\t6\t3\t4\t4\t1\t2\t7\t6\t3\t9\n+sample-3\t1\t0\t1\t9\t6\t8\t1\t1\t3\t2\t9\t5\t2\t9\t7\t8\t5\t3\t7\t2\t2\t8\t7\t0\t8\t3\t5\t9\t8\t0\t5\t0\t5\t9\t2\t2\t2\t0\t8\t5\t6\t4\t0\t3\t4\t7\t3\t3\t2\t6\t9\t2\t8\t9\t8\t5\t9\t5\t3\t3\t5\t5\t1\t3\t7\t3\t9\t5\t6\t9\t4\t6\t1\t8\t0\t6\t7\t5\t0\t5\t4\t6\t3\t3\t3\t0\t8\t4\t0\t5\t3\t8\t7\t9\t4\t4\t6\t8\t9\t6\n+sample-4\t9\t5\t8\t1\t6\t8\t4\t6\t9\t9\t3\t0\t7\t8\t4\t2\t9\t0\t6\t7\t2\t3\t0\t0\t3\t0\t9\t9\t8\t9\t0\t3\t5\t3\t1\t4\t8\t0\t3\t9\t6\t6\t8\t8\t6\t8\t2\t5\t9\t9\t2\t8\t3\t9\t8\t4\t6\t7\t7\t5\t9\t1\t0\t6\t3\t6\t3\t4\t6\t1\t7\t7\t6\t2\t1\t9\t2\t5\t2\t9\t8\t5\t2\t9\t8\t0\t9\t2\t5\t3\t3\t5\t0\t5\t1\t2\t2\t5\t4\t9\n+sample-5\t9\t5\t8\t0\t1\t9\t4\t0\t8\t6\t3\t6\t3\t3\t0\t3\t5\t9\t4\t2\t6\t1\t5\t4\t1\t5\t0\t9\t1\t8\t4\t5\t3\t3\t2\t2\t3\t9\t6\t5\t0\t8\t4\t9\t9\t8\t0\t4\t4\t5\t2\t3\t9\t9\t9\t3\t2\t0\t9\t7\t2\t5\t5\t1\t1\t8\t7\t0\t6\t4\t3\t9\t7\t4\t2\t7\t7\t6\t4\t5\t5\t7\t6\t4\t1\t2\t7\t3\t4\t5\t0\t8\t5\t7\t8\t7\t9\t4\t1\t0\n+sample-6\t4\t7\t1\t4\t8\t3\t0\t0\t5\t7\t7\t0\t7\t1\t8\t2\t4\t6\t9\t7\t2\t2\t4\t6\t8\t4\t9\t3\t2\t5\t3\t5\t3\t9\t1\t1\t4\t6\t6\t8\t5\t8\t5\t4\t9\t2\t6\t3\t6\t9\t7\t0\t9\t5\t7\t4\t4\t8\t6\t1\t2\t3\t2\t9\t8\t4\t4\t4\t0\t2\t2\t1\t3\t8\t9\t4\t6\t8\t2\t4\t1\t3\t5\t6\t7\t8\t0\t1\t3\t7\t1\t3\t7\t9\t5\t5\t3\t4\t8\t2\n+sample-7\t0\t5\t9\t3\t8\t5\t1\t3\t0\t4\t9\t1\t8\t6\t9\t2\t3\t8\t5\t0\t4\t6\t6\t3\t2\t0\t7\t7\t1\t9\t9\t4\t6\t5\t4\t9\t0\t8\t5\t7\t9\t5\t6\t0\t6\t4\t5\t4\t6\t3\t0\t2\t2\t1\t5\t2\t3\t5\t1\t5\t3\t1\t9\t9\t7\t4\t0\t1\t4\t1\t0\t8\t6\t8\t7\t0\t1\t9\t6\t0\t2\t7\t4\t5\t8\t2\t9\t1\t5\t5\t2\t2\t5\t9\t5\t2\t6\t9\t7\t0\n+sample-8\t5\t7\t3\t5\t1\t1\t4\t4\t6\t2\t1\t4\t4\t8\t1\t7\t6\t8\t9\t8\t7\t3\t6\t3\t2\t9\t2\t8\t9\t8\t6\t2\t9\t4\t0\t8\t0\t1\t1\t9\t3\t3\t7\t2\t5\t0\t8\t7\t9\t1\t9\t5\t8\t2\t9\t6\t3\t4\t5\t8\t9\t3\t5\t0\t5\t6\t5\t2\t1\t1\t5\t1\t7\t9\t1\t3\t2\t4\t4\t4\t2\t4\t3\t9\t9\t4\t6\t5\t8\t8\t8\t9\t4\t7\t3\t8\t2\t9\t3\t1\n+sample-9\t1\t4\t0\t0\t7\t1\t8\t0\t6\t2\t2\t7\t2\t2\t3\t7\t0\t5\t8\t6\t1\t7\t8\t4\t7\t6\t9\t1\t6\t5\t0\t3\t5\t9\t1\t5\t1\t0\t7\t3\t3\t9\t6\t7\t9\t9\t0\t5\t7\t9\t5\t6\t3\t5\t1\t4\t6\t9\t0\t0\t0\t8\t1\t2\t4\t4\t8\t0\t9\t4\t3\t3\t3\t1\t9\t2\t0\t8\t9\t4\t4\t6\t7\t3\t3\t2\t9\t0\t1\t6\t3\t9\t8\t4\t4\t3\t9\t5\t3\t3\n+sample-10\t7\t2\t7\t0\t1\t8\t2\t4\t3\t9\t6\t8\t7\t8\t7\t1\t2\t8\t4\t3\t4\t7\t7\t8\t9\t3\t3\t1\t0\t7\t6\t3\t9\t1\t1\t6\t0\t9\t2\t9\t8\t9\t7\t6\t1\t6\t7\t0\t3\t3\t7\t7\t9\t2\t1\t9\t2\t5\t8\t0\t1\t2\t8\t4\t6\t3\t2\t8\t8\t4\t0\t5\t5\t2\t9\t8\t6\t2\t2\t4\t3\t9\t2\t9\t7\t8\t1\t9\t5\t2\t6\t8\t6\t9\t8\t4\t7\t8\t9\t2\n+sample-11\t7\t1\t0\t8\t1\t4\t7\t2\t3\t9\t4\t6\t3\t5\t6\t7\t1\t1\t2\t5\t2\t7\t2\t6\t0\t4\t3\t7\t0\t7\t6\t7\t6\t7\t4\t9\t3\t8\t0\t4\t7\t0\t1\t7\t7\t9\t3\t1\t9\t0\t2\t7\t6\t2\t6\t3\t8\t0\t1\t2\t1\t3\t7\t5\t0\t8\t0\t2\t7\t6\t6\t1\t1\t0\t5\t1\t7\t5\t2\t3\t7\t1\t4\t3\t7\t5\t1\t8\t5\t5\t9\t3\t4\t8\t6\t5\t0\t8\t8\t0\n+sample-12\t2\t1\t0\t0\t2\t8\t4\t3\t2\t2\t3\t4\t7\t7\t6\t8\t8\t5\t7\t8\t2\t7\t1\t5\t7\t0\t9\t9\t1\t4\t0\t1\t9\t0\t5\t4\t0\t8\t8\t0\t4\t7\t2\t5\t0\t3\t0\t2\t4\t0\t9\t8\t7\t8\t1\t6\t3\t6\t0\t3\t9\t3\t0\t8\t3\t3\t6\t6\t8\t5\t9\t0\t6\t3\t4\t7\t7\t1\t9\t1\t6\t0\t7\t8\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3\t3\t4\t8\t0\t2\t2\t3\t2\t2\t4\t5\t1\t8\t0\t8\t1\t9\t6\t1\t7\t2\t6\t7\t3\t4\t1\t9\t4\t6\t2\t0\t9\t5\t8\t4\t4\t8\t3\t2\t4\t2\t3\t5\t0\t9\t5\t6\t9\t1\t7\t2\t7\t4\t0\t8\t2\t5\t1\t2\t7\t0\t4\t3\t4\t3\t8\t3\t2\t7\t3\t4\t0\t5\t0\n+sample-996\t4\t3\t8\t7\t0\t0\t4\t1\t4\t3\t2\t7\t9\t0\t7\t3\t0\t8\t4\t7\t3\t6\t8\t5\t4\t9\t7\t9\t1\t8\t2\t0\t0\t1\t6\t8\t2\t1\t6\t6\t6\t3\t6\t6\t3\t2\t6\t8\t8\t6\t2\t1\t0\t7\t2\t4\t0\t7\t7\t9\t2\t8\t6\t9\t0\t3\t0\t5\t6\t9\t2\t6\t8\t0\t4\t9\t0\t6\t6\t1\t7\t3\t8\t4\t7\t4\t1\t3\t9\t3\t0\t1\t5\t5\t2\t8\t7\t7\t9\t7\n+sample-997\t5\t7\t9\t3\t1\t3\t9\t2\t7\t9\t9\t0\t9\t4\t9\t2\t8\t6\t1\t3\t5\t2\t0\t5\t4\t3\t4\t3\t4\t6\t9\t8\t9\t1\t9\t2\t3\t1\t9\t1\t0\t1\t0\t4\t7\t6\t6\t7\t1\t7\t6\t9\t4\t3\t5\t3\t7\t0\t9\t5\t0\t7\t2\t9\t9\t1\t2\t7\t7\t6\t8\t6\t2\t8\t6\t9\t4\t5\t4\t2\t3\t0\t1\t3\t7\t5\t1\t7\t2\t6\t1\t9\t8\t3\t8\t5\t1\t6\t3\t8\n+sample-998\t4\t9\t6\t4\t1\t6\t2\t2\t0\t2\t5\t7\t3\t6\t2\t7\t0\t8\t9\t4\t7\t5\t4\t3\t2\t4\t5\t2\t7\t2\t9\t1\t2\t7\t4\t4\t4\t9\t2\t6\t2\t0\t1\t9\t6\t9\t4\t7\t5\t7\t1\t8\t9\t2\t1\t9\t6\t3\t0\t6\t2\t0\t8\t5\t5\t3\t7\t1\t6\t3\t9\t3\t5\t1\t8\t1\t7\t3\t9\t4\t9\t8\t6\t6\t8\t0\t9\t7\t5\t2\t0\t0\t1\t6\t1\t2\t8\t4\t5\t4\n+sample-999\t5\t7\t3\t6\t8\t8\t1\t9\t9\t5\t8\t2\t4\t0\t4\t9\t8\t0\t2\t0\t9\t0\t3\t3\t3\t2\t7\t1\t0\t8\t1\t4\t5\t0\t2\t4\t8\t9\t2\t4\t7\t1\t8\t6\t6\t3\t4\t4\t2\t5\t0\t3\t8\t5\t2\t8\t5\t0\t1\t1\t2\t2\t8\t2\t4\t4\t5\t8\t4\t7\t0\t0\t1\t0\t6\t9\t2\t1\t4\t7\t9\t1\t2\t1\t1\t5\t1\t0\t8\t4\t9\t4\t5\t0\t8\t9\t3\t3\t8\t8\n' |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/large_output_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/large_output_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,1001 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| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/med_input_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/med_input_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,101 @@\n+Sample\tlocus-0\tlocus-1\tlocus-2\tlocus-3\tlocus-4\tlocus-5\tlocus-6\tlocus-7\tlocus-8\tlocus-9\tlocus-10\tlocus-11\tlocus-12\tlocus-13\tlocus-14\tlocus-15\tlocus-16\tlocus-17\tlocus-18\tlocus-19\tlocus-20\tlocus-21\tlocus-22\tlocus-23\tlocus-24\tlocus-25\tlocus-26\tlocus-27\tlocus-28\tlocus-29\tlocus-30\tlocus-31\tlocus-32\tlocus-33\tlocus-34\tlocus-35\tlocus-36\tlocus-37\tlocus-38\tlocus-39\tlocus-40\tlocus-41\tlocus-42\tlocus-43\tlocus-44\tlocus-45\tlocus-46\tlocus-47\tlocus-48\tlocus-49\tlocus-50\tlocus-51\tlocus-52\tlocus-53\tlocus-54\tlocus-55\tlocus-56\tlocus-57\tlocus-58\tlocus-59\tlocus-60\tlocus-61\tlocus-62\tlocus-63\tlocus-64\tlocus-65\tlocus-66\tlocus-67\tlocus-68\tlocus-69\tlocus-70\tlocus-71\tlocus-72\tlocus-73\tlocus-74\tlocus-75\tlocus-76\tlocus-77\tlocus-78\tlocus-79\tlocus-80\tlocus-81\tlocus-82\tlocus-83\tlocus-84\tlocus-85\tlocus-86\tlocus-87\tlocus-88\tlocus-89\tlocus-90\tlocus-91\tlocus-92\tlocus-93\tlocus-94\tlocus-95\tlocus-96\tlocus-97\tlocus-98\tlocus-99\n+sample-0\t9\t8\t5\t2\t6\t6\t2\t3\t3\t9\t6\t8\t2\t8\t0\t6\t8\t5\t1\t5\t9\t1\t9\t0\t1\t5\t6\t7\t1\t6\t2\t8\t1\t8\t3\t2\t5\t4\t7\t2\t8\t6\t2\t1\t6\t2\t5\t8\t7\t5\t0\t7\t9\t3\t0\t6\t7\t2\t1\t9\t6\t0\t4\t5\t3\t4\t0\t5\t1\t6\t6\t7\t0\t3\t9\t9\t5\t7\t2\t3\t9\t9\t5\t6\t6\t8\t7\t1\t6\t7\t4\t5\t6\t0\t9\t0\t0\t0\t5\t4\n+sample-1\t4\t2\t8\t2\t3\t9\t0\t6\t0\t9\t0\t1\t4\t1\t5\t0\t9\t6\t1\t4\t5\t3\t1\t7\t6\t1\t5\t8\t3\t3\t4\t9\t9\t6\t9\t7\t9\t1\t6\t4\t7\t3\t8\t6\t0\t6\t7\t8\t8\t8\t4\t1\t5\t4\t8\t7\t4\t0\t7\t8\t2\t2\t5\t7\t9\t8\t8\t7\t3\t2\t7\t0\t9\t1\t4\t7\t6\t5\t2\t5\t2\t8\t6\t5\t5\t4\t5\t2\t2\t8\t6\t7\t8\t6\t1\t3\t6\t9\t8\t7\n+sample-2\t9\t6\t5\t2\t3\t1\t1\t8\t6\t2\t0\t8\t0\t9\t7\t4\t7\t2\t1\t6\t1\t4\t4\t1\t6\t9\t2\t7\t1\t9\t4\t5\t4\t5\t5\t7\t3\t0\t4\t1\t0\t0\t4\t6\t9\t6\t9\t8\t0\t4\t2\t6\t6\t9\t3\t4\t6\t6\t6\t8\t4\t9\t2\t2\t8\t0\t8\t9\t7\t1\t9\t9\t4\t5\t6\t2\t4\t7\t4\t0\t7\t4\t8\t3\t8\t6\t2\t9\t9\t5\t8\t5\t8\t6\t8\t5\t0\t7\t6\t4\n+sample-3\t2\t9\t9\t7\t9\t4\t2\t5\t1\t0\t1\t4\t2\t8\t5\t6\t4\t9\t3\t8\t0\t5\t8\t4\t8\t4\t0\t2\t1\t6\t1\t5\t4\t2\t5\t8\t2\t6\t5\t6\t3\t9\t7\t9\t3\t2\t8\t0\t2\t1\t1\t9\t1\t0\t7\t2\t0\t2\t4\t4\t5\t4\t6\t0\t3\t5\t7\t7\t8\t6\t9\t5\t1\t0\t7\t1\t9\t2\t9\t7\t7\t4\t4\t6\t4\t3\t4\t1\t4\t3\t6\t9\t7\t5\t2\t4\t7\t6\t6\t4\n+sample-4\t3\t6\t8\t5\t1\t9\t7\t7\t0\t6\t4\t7\t2\t9\t9\t6\t8\t8\t0\t0\t3\t9\t7\t1\t6\t6\t0\t1\t3\t9\t1\t5\t3\t6\t9\t8\t9\t6\t3\t3\t2\t3\t6\t2\t3\t2\t2\t3\t9\t2\t0\t9\t1\t2\t3\t6\t1\t0\t4\t0\t0\t7\t0\t9\t9\t3\t3\t4\t5\t8\t8\t1\t7\t5\t3\t3\t1\t9\t9\t5\t8\t2\t5\t6\t4\t3\t6\t0\t8\t7\t0\t7\t3\t8\t4\t1\t8\t4\t0\t2\n+sample-5\t8\t7\t6\t7\t0\t5\t1\t0\t5\t7\t1\t4\t5\t0\t1\t8\t0\t2\t1\t4\t6\t1\t6\t3\t7\t1\t0\t0\t8\t2\t8\t4\t5\t3\t0\t1\t7\t1\t6\t8\t9\t7\t2\t3\t9\t3\t9\t2\t8\t0\t9\t8\t1\t5\t9\t9\t7\t2\t0\t4\t5\t1\t1\t5\t5\t8\t1\t9\t2\t9\t8\t6\t1\t5\t2\t7\t6\t4\t5\t3\t0\t3\t5\t3\t0\t1\t4\t8\t7\t7\t1\t8\t1\t7\t9\t2\t0\t3\t3\t1\n+sample-6\t6\t5\t3\t2\t6\t5\t6\t8\t9\t7\t6\t1\t0\t2\t8\t2\t3\t7\t8\t2\t1\t8\t6\t7\t6\t2\t4\t9\t8\t7\t6\t0\t5\t4\t8\t0\t4\t5\t1\t7\t4\t3\t2\t7\t9\t9\t4\t9\t0\t7\t9\t9\t4\t3\t8\t7\t8\t1\t6\t6\t5\t4\t6\t5\t3\t3\t9\t3\t6\t1\t5\t7\t2\t7\t8\t5\t3\t9\t6\t4\t4\t1\t9\t1\t0\t5\t7\t5\t7\t4\t5\t4\t5\t7\t3\t2\t6\t0\t5\t1\n+sample-7\t7\t5\t3\t1\t3\t9\t3\t6\t5\t9\t6\t2\t2\t3\t9\t9\t5\t1\t3\t1\t3\t1\t3\t8\t9\t4\t4\t0\t7\t5\t2\t7\t7\t8\t6\t9\t9\t1\t2\t3\t1\t4\t3\t8\t5\t4\t2\t5\t0\t6\t5\t8\t9\t9\t5\t5\t2\t5\t5\t1\t8\t3\t9\t4\t7\t4\t2\t1\t7\t7\t5\t0\t2\t3\t2\t1\t9\t4\t3\t1\t7\t5\t8\t3\t9\t3\t4\t1\t2\t3\t8\t1\t1\t2\t2\t3\t2\t5\t5\t2\n+sample-8\t6\t8\t0\t7\t5\t0\t8\t5\t0\t5\t1\t7\t7\t5\t2\t1\t3\t6\t0\t7\t4\t0\t3\t6\t5\t7\t2\t8\t5\t1\t3\t9\t3\t7\t6\t3\t8\t2\t8\t2\t5\t4\t7\t1\t6\t3\t4\t3\t1\t1\t4\t9\t0\t3\t5\t3\t3\t6\t2\t6\t7\t9\t4\t3\t4\t2\t6\t6\t0\t6\t8\t2\t4\t5\t9\t7\t2\t2\t5\t5\t2\t3\t2\t8\t8\t0\t5\t5\t7\t9\t4\t5\t5\t7\t6\t5\t4\t9\t7\t9\n+sample-9\t5\t2\t3\t8\t1\t1\t9\t3\t0\t5\t1\t3\t2\t5\t6\t4\t9\t5\t0\t9\t9\t2\t4\t9\t8\t7\t0\t7\t5\t8\t9\t5\t6\t6\t7\t7\t8\t2\t6\t3\t5\t9\t6\t2\t7\t2\t5\t6\t7\t1\t9\t9\t9\t1\t9\t2\t5\t5\t7\t7\t5\t5\t3\t0\t4\t1\t4\t1\t5\t0\t9\t9\t1\t1\t9\t0\t8\t3\t0\t2\t9\t9\t7\t9\t2\t3\t1\t3\t7\t2\t0\t4\t1\t8\t1\t7\t8\t9\t5\t2\n+sample-10\t8\t1\t3\t3\t2\t2\t7\t9\t0\t6\t5\t7\t6\t3\t5\t7\t5\t2\t3\t7\t1\t3\t3\t2\t9\t9\t4\t1\t7\t2\t7\t1\t5\t7\t4\t0\t0\t5\t4\t6\t9\t0\t8\t9\t2\t6\t2\t5\t2\t8\t5\t8\t0\t0\t9\t0\t4\t0\t6\t2\t3\t5\t6\t7\t4\t4\t3\t1\t7\t8\t1\t7\t6\t7\t6\t1\t2\t6\t1\t8\t4\t2\t8\t5\t7\t3\t0\t0\t8\t0\t9\t5\t0\t0\t4\t2\t1\t0\t2\t6\n+sample-11\t7\t4\t0\t1\t3\t3\t7\t8\t8\t9\t9\t1\t6\t1\t6\t0\t4\t3\t8\t7\t3\t7\t2\t7\t2\t0\t6\t4\t5\t3\t8\t0\t8\t0\t4\t4\t4\t2\t6\t1\t9\t5\t6\t3\t0\t8\t5\t3\t7\t8\t9\t9\t2\t1\t1\t3\t4\t1\t0\t8\t2\t7\t0\t8\t8\t9\t3\t2\t0\t7\t9\t2\t5\t8\t2\t4\t5\t7\t7\t1\t0\t4\t9\t1\t2\t6\t4\t0\t2\t7\t7\t1\t3\t2\t3\t0\t8\t4\t5\t7\n+sample-12\t3\t6\t6\t4\t8\t5\t1\t0\t8\t7\t8\t2\t9\t7\t1\t3\t8\t7\t3\t0\t7\t9\t2\t6\t5\t2\t3\t8\t1\t1\t1\t9\t9\t0\t0\t8\t5\t8\t1\t7\t7\t3\t8\t2\t3\t0\t6\t2\t9\t7\t6\t3\t7\t8\t6\t2\t2\t6\t0\t0\t8\t8\t7\t6\t0\t7\t2\t7\t6\t9\t0\t4\t0\t6\t4\t8\t1\t9\t0\t0\t9\t3\t9\t6\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|
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/med_output_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/med_output_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,101 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t87\t88\t79\t91\t92\t89\t92\t87\t91\t91\t90\t92\t89\t96\t88\t8'..b'\t93\t84\t89\t92\t93\t87\t89\t89\t92\t88\t94\t91\t83\t88\t91\t90\t87\t93\t86\t89\t92\t89\t89\t89\t90\t88\t87\t89\t85\t94\t92\t94\t87\t88\t88\t91\t92\t93\t90\t92\t88\t84\t93\t88\t92\t90\t93\t96\t92\t89\t84\t92\t89\t92\t90\t94\t90\t92\t89\t87\t89\t87\t93\t87\t94\t92\t88\t96\t91\t91\t84\t92\t88\t93\t87\t95\t86\t83\t91\t95\t0\t93\t87\t90\t86\t88\t86\t90\t87\t87\t84\t89\t93\n+sample-88\t88\t94\t90\t86\t93\t92\t85\t87\t89\t87\t90\t89\t95\t86\t91\t85\t91\t92\t86\t88\t88\t90\t91\t91\t90\t90\t92\t90\t89\t92\t93\t88\t91\t89\t98\t85\t92\t90\t92\t91\t93\t97\t90\t92\t94\t93\t92\t86\t91\t92\t93\t88\t86\t92\t85\t92\t89\t93\t93\t95\t92\t85\t92\t90\t95\t93\t95\t88\t86\t93\t88\t88\t93\t93\t94\t90\t93\t89\t89\t92\t89\t89\t94\t92\t90\t93\t88\t93\t0\t96\t97\t87\t93\t83\t85\t91\t89\t95\t90\t88\n+sample-89\t90\t93\t87\t88\t88\t87\t91\t83\t90\t88\t80\t87\t95\t87\t88\t94\t91\t93\t92\t89\t87\t89\t90\t82\t82\t95\t90\t89\t90\t88\t93\t88\t91\t88\t81\t86\t95\t90\t90\t95\t88\t87\t94\t89\t85\t83\t89\t90\t95\t95\t91\t87\t93\t82\t91\t89\t87\t94\t87\t90\t88\t88\t87\t92\t88\t92\t88\t93\t95\t88\t93\t95\t80\t91\t92\t92\t83\t88\t90\t88\t85\t91\t91\t84\t88\t86\t87\t87\t96\t0\t93\t92\t89\t90\t86\t89\t95\t91\t88\t89\n+sample-90\t89\t88\t90\t93\t95\t92\t88\t95\t81\t91\t88\t93\t91\t86\t93\t90\t92\t85\t90\t89\t89\t97\t91\t94\t88\t89\t93\t91\t90\t88\t85\t94\t89\t90\t94\t90\t93\t93\t90\t86\t84\t89\t95\t91\t91\t90\t84\t91\t88\t85\t86\t90\t92\t89\t90\t89\t85\t86\t94\t88\t92\t93\t86\t95\t89\t87\t83\t93\t94\t90\t92\t90\t92\t91\t84\t91\t89\t84\t85\t88\t85\t88\t89\t88\t86\t93\t91\t90\t97\t93\t0\t88\t87\t93\t93\t85\t95\t92\t90\t89\n+sample-91\t96\t92\t94\t93\t91\t88\t89\t93\t90\t92\t94\t94\t87\t94\t89\t90\t93\t93\t88\t88\t83\t90\t96\t84\t91\t89\t96\t88\t96\t89\t87\t88\t90\t86\t97\t91\t85\t90\t95\t91\t87\t87\t92\t93\t88\t95\t88\t93\t88\t87\t89\t86\t88\t91\t92\t91\t91\t96\t90\t86\t90\t89\t88\t95\t92\t90\t91\t89\t94\t91\t89\t90\t89\t89\t90\t88\t89\t93\t88\t86\t92\t86\t87\t88\t89\t91\t88\t86\t87\t92\t88\t0\t88\t93\t96\t92\t91\t88\t94\t94\n+sample-92\t87\t93\t89\t95\t87\t91\t89\t88\t86\t91\t88\t87\t85\t87\t91\t86\t95\t95\t90\t89\t90\t88\t85\t93\t85\t91\t87\t87\t90\t85\t91\t90\t87\t91\t90\t89\t84\t91\t89\t94\t80\t88\t87\t91\t92\t87\t95\t87\t87\t92\t88\t85\t93\t89\t92\t87\t92\t89\t89\t83\t91\t89\t87\t87\t89\t90\t91\t90\t86\t95\t87\t92\t88\t91\t93\t86\t88\t93\t90\t87\t89\t89\t89\t86\t96\t88\t87\t88\t93\t89\t87\t88\t0\t87\t92\t84\t89\t83\t89\t92\n+sample-93\t94\t85\t95\t89\t95\t92\t85\t89\t89\t91\t86\t94\t94\t78\t87\t93\t90\t90\t91\t89\t88\t84\t91\t93\t86\t94\t91\t90\t87\t93\t91\t92\t91\t85\t88\t93\t93\t93\t95\t88\t90\t91\t87\t87\t91\t93\t93\t91\t88\t87\t87\t90\t87\t93\t92\t95\t94\t93\t87\t89\t88\t91\t93\t91\t90\t96\t90\t94\t90\t94\t88\t91\t85\t88\t94\t95\t95\t91\t97\t90\t90\t88\t95\t86\t86\t93\t91\t86\t83\t90\t93\t93\t87\t0\t84\t90\t91\t95\t85\t88\n+sample-94\t95\t93\t85\t89\t84\t92\t89\t88\t93\t91\t88\t85\t91\t96\t90\t91\t89\t89\t85\t95\t95\t93\t87\t84\t90\t87\t90\t87\t90\t92\t91\t86\t87\t89\t92\t90\t91\t86\t93\t92\t92\t94\t93\t92\t90\t89\t92\t91\t91\t91\t93\t84\t89\t90\t90\t89\t89\t89\t88\t86\t87\t95\t91\t93\t88\t82\t86\t92\t92\t88\t96\t91\t92\t85\t88\t88\t92\t85\t86\t87\t86\t94\t92\t91\t90\t93\t87\t90\t85\t86\t93\t96\t92\t84\t0\t96\t91\t90\t88\t90\n+sample-95\t86\t89\t84\t91\t92\t87\t91\t92\t92\t93\t93\t88\t90\t91\t92\t92\t90\t87\t90\t91\t92\t85\t84\t93\t88\t86\t96\t93\t91\t86\t92\t93\t90\t88\t84\t90\t92\t92\t93\t86\t96\t86\t88\t83\t89\t91\t94\t87\t90\t86\t88\t95\t95\t92\t82\t91\t97\t89\t94\t89\t88\t83\t89\t91\t92\t91\t90\t88\t94\t87\t93\t87\t91\t88\t89\t84\t94\t91\t91\t94\t90\t94\t89\t88\t93\t91\t87\t87\t91\t89\t85\t92\t84\t90\t96\t0\t90\t95\t87\t92\n+sample-96\t90\t91\t92\t94\t89\t93\t87\t93\t85\t88\t95\t89\t95\t91\t90\t89\t91\t93\t94\t93\t91\t95\t90\t84\t91\t91\t90\t93\t89\t86\t93\t86\t88\t91\t90\t87\t92\t91\t93\t90\t96\t92\t86\t83\t87\t93\t92\t90\t90\t91\t89\t89\t90\t91\t89\t92\t89\t91\t88\t90\t94\t92\t85\t88\t93\t91\t80\t90\t96\t91\t87\t87\t95\t91\t94\t83\t93\t86\t92\t91\t89\t88\t89\t86\t92\t93\t86\t87\t89\t95\t95\t91\t89\t91\t91\t90\t0\t89\t89\t94\n+sample-97\t93\t86\t84\t90\t86\t96\t89\t82\t87\t90\t89\t92\t90\t88\t93\t93\t92\t92\t87\t86\t91\t88\t91\t91\t94\t93\t90\t92\t94\t92\t82\t90\t92\t95\t85\t88\t86\t91\t95\t92\t86\t92\t90\t97\t92\t91\t94\t88\t84\t89\t89\t84\t90\t87\t93\t90\t88\t88\t87\t88\t85\t90\t91\t85\t93\t81\t90\t87\t91\t90\t90\t93\t88\t91\t91\t91\t79\t94\t95\t86\t89\t83\t92\t94\t87\t88\t87\t84\t95\t91\t92\t88\t83\t95\t90\t95\t89\t0\t92\t93\n+sample-98\t94\t89\t88\t88\t93\t92\t90\t87\t87\t90\t82\t93\t89\t88\t91\t89\t93\t90\t90\t89\t88\t88\t94\t91\t91\t93\t93\t84\t89\t91\t91\t88\t89\t88\t93\t90\t94\t88\t85\t87\t95\t92\t92\t89\t88\t90\t88\t88\t93\t88\t89\t92\t91\t91\t94\t92\t92\t89\t89\t91\t90\t93\t93\t93\t93\t93\t91\t94\t96\t89\t91\t88\t91\t87\t90\t88\t91\t94\t93\t94\t86\t90\t90\t90\t92\t96\t83\t89\t90\t88\t90\t94\t89\t85\t88\t87\t89\t92\t0\t91\n+sample-99\t85\t93\t94\t88\t89\t90\t86\t90\t93\t88\t91\t89\t93\t90\t92\t93\t91\t94\t89\t93\t90\t91\t84\t89\t88\t87\t88\t90\t91\t90\t94\t91\t90\t89\t90\t91\t88\t97\t93\t89\t83\t94\t91\t90\t89\t92\t86\t88\t95\t95\t91\t85\t88\t91\t90\t91\t93\t94\t94\t86\t93\t93\t90\t87\t89\t90\t93\t90\t94\t83\t92\t94\t91\t93\t85\t88\t92\t88\t91\t91\t93\t93\t91\t87\t90\t89\t94\t93\t88\t89\t89\t94\t92\t88\t90\t92\t94\t93\t91\t0\n' |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/small_input_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/small_input_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ +Sample locus-0 locus-1 locus-2 locus-3 locus-4 locus-5 locus-6 locus-7 locus-8 locus-9 +sample-0 2 0 5 2 4 4 2 5 2 8 +sample-1 5 3 2 7 6 8 1 7 0 4 +sample-2 6 4 7 8 5 8 6 1 9 5 +sample-3 7 9 2 1 1 9 3 4 2 3 +sample-4 5 2 9 7 2 3 5 9 8 5 +sample-5 0 3 8 7 2 5 1 9 4 1 +sample-6 8 1 0 1 3 8 5 2 2 8 +sample-7 0 0 6 0 6 5 9 7 3 4 +sample-8 8 7 0 9 9 0 8 7 4 3 +sample-9 5 7 9 1 3 3 5 8 3 3 |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_distance/small_output_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_distance/small_output_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + sample-0 sample-1 sample-2 sample-3 sample-4 sample-5 sample-6 sample-7 sample-8 sample-9 +sample-0 0 10 10 9 10 10 8 9 10 10 +sample-1 10 0 9 9 8 7 9 7 9 9 +sample-2 10 9 0 10 9 10 9 10 10 10 +sample-3 9 9 10 0 10 10 8 10 9 8 +sample-4 10 8 9 10 0 7 9 10 10 6 +sample-5 10 7 10 10 7 0 10 8 9 10 +sample-6 8 9 9 8 9 10 0 10 8 7 +sample-7 9 7 10 10 10 8 10 0 9 9 +sample-8 10 9 10 9 10 9 8 9 0 8 +sample-9 10 9 10 8 6 10 7 9 8 0 |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_tree/med_input_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_tree/med_input_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| b'@@ -0,0 +1,101 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|
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_tree/med_output_00.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_tree/med_output_00.nwk Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +(((((sample-55:41.71429,sample-46:41.28571)Inner36:2.08594,(sample-12:42.79847,sample-6:42.20153)Inner50:1.41406)Inner73:1.17639,(((((sample-89:39.37228,sample-72:40.62772)Inner7:2.88906,(sample-45:40.87658,sample-41:41.12342)Inner20:2.11094)Inner59:0.95241,(sample-27:41.71186,sample-24:41.28814)Inner40:2.29759)Inner77:0.51510,(sample-80:41.63672,(sample-82:40.88750,sample-21:41.11250)Inner19:0.86328)Inner35:2.70365)Inner84:0.48215,(((sample-53:39.58763,sample-9:39.41237)Inner2:3.35795,(sample-4:41.68852,sample-3:42.31148)Inner38:1.14205)Inner55:1.86063,(((sample-99:43.18750,(sample-69:40.72472,sample-11:40.27528)Inner10:2.31250)Inner57:0.78292,(sample-59:40.65000,sample-5:40.35000)Inner9:3.21708)Inner71:0.49007,((sample-64:42.29009,sample-51:41.70991)Inner46:1.50781,((sample-92:39.63235,sample-40:40.36765)Inner14:2.19477,(sample-36:41.94129,sample-0:42.05871)Inner33:1.30523)Inner56:0.99219)Inner72:0.29118)Inner75:0.68624)Inner85:0.26394)Inner90:0.19666)Inner95:0.08868,(((sample-98:41.20513,sample-10:40.79487)Inner21:2.48769,((sample-97:39.56720,sample-76:39.43280)Inner6:1.17105,sample-7:41.32895)Inner23:2.51231)Inner66:1.14558,((sample-74:41.75746,sample-60:41.24254)Inner32:2.66667,(sample-57:40.47159,sample-1:40.52841)Inner11:3.58333)Inner81:0.38567)Inner86:0.41473)Inner97:0.06049,((((((sample-85:40.63889,sample-79:40.36111)Inner18:2.67318,(sample-34:41.67500,(sample-61:41.34740,sample-29:40.65260)Inner22:0.82500)Inner39:1.57682)Inner63:0.86737,(sample-28:42.59722,sample-26:42.40278)Inner45:1.94513)Inner78:0.65710,((sample-68:41.90893,sample-25:41.09107)Inner29:2.04375,(sample-50:42.40701,(sample-38:39.78646,sample-20:39.21354)Inner3:3.09299)Inner58:0.45625)Inner64:1.28040)Inner91:0.18081,(((sample-75:43.23395,(sample-63:42.24892,(sample-49:40.47632,sample-47:39.52368)Inner4:2.25108)Inner41:1.01605)Inner62:0.40142,(sample-67:40.70640,sample-22:41.29360)Inner13:2.78608)Inner65:1.37617,(((sample-73:40.43750,sample-42:40.56250)Inner15:2.78987,(sample-54:40.93373,sample-33:41.06627)Inner16:2.71013)Inner70:0.76270,((sample-95:41.60769,sample-43:41.39231)Inner34:1.04255,(sample-39:39.71809,sample-17:40.28191)Inner5:2.70745)Inner52:1.79980)Inner83:0.34258)Inner89:0.30845)Inner94:0.14628,(((sample-87:41.83004,(sample-48:41.19366,sample-19:40.80634)Inner28:0.66996)Inner42:2.31867,((sample-91:43.22596,(sample-81:42.31971,sample-30:42.68029)Inner47:0.77404)Inner60:0.92154,(sample-90:40.65854,sample-8:40.34146)Inner17:2.82846)Inner76:0.33758)Inner80:0.63334,(((sample-52:42.86528,(sample-71:41.14062,sample-16:41.85938)Inner27:1.63472)Inner54:1.13031,(sample-88:42.35491,(sample-93:39.14796,sample-13:38.85204)Inner1:3.14509)Inner43:1.93219)Inner74:0.91706,(((sample-83:40.94000,sample-70:41.06000)Inner24:2.54713,(sample-58:42.45098,(sample-32:40.81926,sample-15:41.18074)Inner25:1.04902)Inner48:1.32787)Inner68:0.77832,((sample-84:40.79281,sample-56:41.20719)Inner26:1.93092,(sample-18:42.71250,sample-2:42.28750)Inner49:0.81908)Inner61:1.22168)Inner79:0.55950)Inner92:0.07174)Inner93:0.17696)Inner96:0.08099,(((sample-96:40.31319,sample-66:39.68681)Inner8:3.27246,(sample-62:42.03226,sample-35:40.96774)Inner37:1.72754)Inner67:1.19815,((sample-31:42.10677,(sample-44:40.49425,sample-23:40.50575)Inner12:1.89323)Inner51:1.99544,(((sample-78:42.29891,sample-77:42.70109)Inner53:0.82760,(sample-94:40.98713,sample-65:41.01287)Inner31:2.17240)Inner69:0.84881,(sample-86:41.76705,(sample-37:41.45833,sample-14:41.54167)Inner30:0.73295)Inner44:2.08869)Inner82:0.34831)Inner87:0.14560)Inner88:0.30133)Inner98:0.00000; |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_tree/small_input_00.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_tree/small_input_00.tsv Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -0,0 +1,11 @@ + sample-0 sample-1 sample-2 sample-3 sample-4 sample-5 sample-6 sample-7 sample-8 sample-9 +sample-0 0 10 10 9 10 10 8 9 10 10 +sample-1 10 0 9 9 8 7 9 7 9 9 +sample-2 10 9 0 10 9 10 9 10 10 10 +sample-3 9 9 10 0 10 10 8 10 9 8 +sample-4 10 8 9 10 0 7 9 10 10 6 +sample-5 10 7 10 10 7 0 10 8 9 10 +sample-6 8 9 9 8 9 10 0 10 8 7 +sample-7 9 7 10 10 10 8 10 0 9 9 +sample-8 10 9 10 9 10 9 8 9 0 8 +sample-9 10 9 10 8 6 10 7 9 8 0 |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/mentalist_tree/small_output_00.nwk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mentalist_tree/small_output_00.nwk Mon Jun 18 15:52:32 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +((sample-8:4.42708,(sample-3:4.32812,(sample-6:3.42500,sample-0:4.57500)Inner4:0.17188)Inner5:0.32292)Inner6:0.17969,(sample-2:5.13281,(sample-7:3.87500,(sample-5:3.78571,sample-1:3.21429)Inner2:0.12500)Inner3:0.86719)Inner7:0.05469,(sample-9:2.87500,sample-4:3.12500)Inner1:1.32031)Inner8:0.00000; |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/small_input_00.tsv --- a/test-data/small_input_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ -Sample locus-0 locus-1 locus-2 locus-3 locus-4 locus-5 locus-6 locus-7 locus-8 locus-9 -sample-0 2 0 5 2 4 4 2 5 2 8 -sample-1 5 3 2 7 6 8 1 7 0 4 -sample-2 6 4 7 8 5 8 6 1 9 5 -sample-3 7 9 2 1 1 9 3 4 2 3 -sample-4 5 2 9 7 2 3 5 9 8 5 -sample-5 0 3 8 7 2 5 1 9 4 1 -sample-6 8 1 0 1 3 8 5 2 2 8 -sample-7 0 0 6 0 6 5 9 7 3 4 -sample-8 8 7 0 9 9 0 8 7 4 3 -sample-9 5 7 9 1 3 3 5 8 3 3 |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 test-data/small_output_00.tsv --- a/test-data/small_output_00.tsv Thu May 31 14:29:28 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,11 +0,0 @@ - sample-0 sample-1 sample-2 sample-3 sample-4 sample-5 sample-6 sample-7 sample-8 sample-9 -sample-0 0 10 10 9 10 10 8 9 10 10 -sample-1 10 0 9 9 8 7 9 7 9 9 -sample-2 10 9 0 10 9 10 9 10 10 10 -sample-3 9 9 10 0 10 10 8 10 9 8 -sample-4 10 8 9 10 0 7 9 10 10 6 -sample-5 10 7 10 10 7 0 10 8 9 10 -sample-6 8 9 9 8 9 10 0 10 8 7 -sample-7 9 7 10 10 10 8 10 0 9 9 -sample-8 10 9 10 9 10 9 8 9 0 8 -sample-9 10 9 10 8 6 10 7 9 8 0 |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 tools/mentalist_call/mentalist_call.xml --- a/tools/mentalist_call/mentalist_call.xml Thu May 31 14:29:28 2018 -0400 +++ b/tools/mentalist_call/mentalist_call.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,6 +1,6 @@ -<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.8"> +<tool id="mentalist_call" name="MentaLiST MLST Analysis" version="0.1.9"> <requirements> - <requirement type="package" version="0.1.8">mentalist</requirement> + <requirement type="package" version="0.1.9">mentalist</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ mentalist |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 tools/mentalist_distance/mentalist_distance.xml --- a/tools/mentalist_distance/mentalist_distance.xml Thu May 31 14:29:28 2018 -0400 +++ b/tools/mentalist_distance/mentalist_distance.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id="mentalist_distance" name="MentaLiST Distance Matrix" version="0.1.8"> +<tool id="mentalist_distance" name="MentaLiST Distance Matrix" version="0.1.9"> <requirements> <requirement type="package" version="3.4.1">r-base</requirement> </requirements> @@ -15,16 +15,16 @@ </outputs> <tests> <test> - <param name="input" value="small_input_00.tsv" /> - <output name="output" file="small_output_00.tsv" /> + <param name="input" value="mentalist_distance/small_input_00.tsv" /> + <output name="output" file="mentalist_distance/small_output_00.tsv" /> </test> <test> - <param name="input" value="med_input_00.tsv" /> - <output name="output" file="med_output_00.tsv" /> + <param name="input" value="mentalist_distance/med_input_00.tsv" /> + <output name="output" file="mentalist_distance/med_output_00.tsv" /> </test> <test> - <param name="input" value="large_input_00.tsv" /> - <output name="output" file="large_output_00.tsv" /> + <param name="input" value="mentalist_distance/large_input_00.tsv" /> + <output name="output" file="mentalist_distance/large_output_00.tsv" /> </test> </tests> <help><![CDATA[ |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 tools/mentalist_tree/mentalist_tree --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mentalist_tree/mentalist_tree Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -0,0 +1,66 @@ +#!/usr/bin/env python + +import sys +import csv +import numpy as np + +import Bio.Phylo +from Bio.Phylo.TreeConstruction import DistanceMatrix, DistanceTreeConstructor + +def usage(): + print("usage: mentalist_tree <input.tsv>\n") + +def process_input_matrix(input_matrix): + """ Converts an array-of-arrays containting sample IDs and distances + into a BioPython DistanceMatrix object + """ + input_matrix.pop(0) + sample_names = [row[0] for row in input_matrix] + for row in input_matrix: + row.pop(0) + distance_matrix = [] + for input_matrix_row in input_matrix: + distance_matrix.append([int(i) for i in input_matrix_row]) + """ np.tril() converts a matrix like this: [[0 1 2] + [1 0 1] + [2 1 0]] + ...into this: [[0 0 0] + [1 0 0] + [2 1 0]] + ...but what we need to pass to DistanceMatrix() is this: [[0] + [1 0] + [2 1 0]] + ...so that's what the (somewhat cryptic) code below does. + """ + distance_matrix = np.tril(np.array(distance_matrix)) + num_rows = distance_matrix.shape[0] + """ masking the distance matrix with tril_indices gives a linearized + distance matrix [0 1 0 2 1 0] that we need to re-construct into [[0], [1, 0], [2, 1, 0]] + """ + lower_triangular_idx_mask = np.tril_indices(num_rows) + linear_distance_matrix = distance_matrix[lower_triangular_idx_mask] + distance_matrix = [] + min = 0 + max = 1 + for i in range(num_rows): + distance_matrix.append(linear_distance_matrix[min:max].tolist()) + min = max + max = max + (i + 2) + distance_matrix = DistanceMatrix(names=sample_names, matrix=distance_matrix) + return distance_matrix + +def main(): + if len(sys.argv) < 2: + usage() + sys.exit(1) + + input_file = sys.argv[1] + reader = csv.reader(open(input_file, "r"), delimiter="\t") + input_matrix = list(reader) + distance_matrix = process_input_matrix(input_matrix) + constructor = DistanceTreeConstructor() + tree = constructor.nj(distance_matrix) + Bio.Phylo.write(tree, sys.stdout, 'newick') + +if __name__ == '__main__': + main() |
| b |
| diff -r 243be7a79d9c -r f29e7738bb64 tools/mentalist_tree/mentalist_tree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mentalist_tree/mentalist_tree.xml Mon Jun 18 15:52:32 2018 -0400 |
| [ |
| @@ -0,0 +1,32 @@ +<tool id="mentalist_tree" name="MentaLiST Tree" version="0.1.9"> + <requirements> + <requirement type="package" version="1.71">biopython</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + $__tool_directory__/mentalist_tree + '${input}' + > '${output}' + ]]></command> + <inputs> + <param name="input" type="data" format="tabular" label="MentaLiST Distance Matrix" help=""/> + </inputs> + <outputs> + <data name="output" format="txt"/> + </outputs> + <tests> + <test> + <param name="input" value="mentalist_tree/small_input_00.tsv" /> + <output name="output" file="mentalist_tree/small_output_00.nwk" /> + </test> + <test> + <param name="input" value="mentalist_tree/med_input_00.tsv" /> + <output name="output" file="mentalitst_tree/med_output_00.nwk" /> + </test> + </tests> + <help><![CDATA[ + mentalist_distance <input.tsv> + ]]></help> + <citations> + <citation type="doi">10.1101/172858</citation> + </citations> +</tool> |