Mercurial > repos > fangly > copyrighter
changeset 1:658ad8b92341 draft default tip
Uploaded
| author | fangly |
|---|---|
| date | Mon, 29 Jul 2013 07:01:57 -0400 |
| parents | 7a7ecf9b9df7 |
| children | |
| files | test-data/in.biom test-data/in.qiime test-data/in_db.tsv test-data/in_total.tsv test-data/out.biom test-data/out.qiime test-data/out2.biom test-data/out_combined.qiime test-data/out_total.tsv test_data/in.biom test_data/in.qiime test_data/in_db.tsv test_data/in_total.tsv test_data/out.biom test_data/out.qiime test_data/out2.biom test_data/out_combined.qiime test_data/out_total.tsv tool-data/trait_db.loc.sample tool_data_table_conf.xml.sample trait_db.loc.sample |
| diffstat | 21 files changed, 376 insertions(+), 379 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.biom Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,46 @@ +{ + "id": "Human microbiomes", + "comment": "This is an optional comment", + "format": "Biological Observation Matrix 0.9.1-dev", + "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "type": "OTU table", + "generated_by": "QIIME revision 1.4.0-dev", + "date": "2011-12-19T19:00:00", + "rows":[ + {"id":"0", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, + {"id":"1", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, + {"id":"2", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__mazei"]}}, + {"id":"3", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__"]}}, + {"id":"4", "metadata":{"taxonomy":[]}} + ], + "columns":[ + {"id":"Sample1", "metadata":{ + "BarcodeSequence":"CGCTTATCGAGA", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample2", "metadata":{ + "BarcodeSequence":"CATACCAGTAGC", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human gut"}}, + {"id":"Sample3", "metadata":{ + "BarcodeSequence":"CTCTCTACCTGT", + "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", + "BODY_SITE":"gut", + "Description":"human skin"}} + ], + "matrix_type": "sparse", + "matrix_element_type": "int", + "shape": [5, 3], + "data":[[0,2,4], + [1,0,5], + [1,1,3], + [2,2,3], + [3,0,2], + [3,1,2], + [3,2,2], + [4,1,1], + [4,2,1] + ] +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in.qiime Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,7 @@ +# QIIME v1.3.0 OTU table +#OTU ID Sample1 Sample2 Sample3 Consensus Lineage +0 0 0 4 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ +1 5 3 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ +2 0 0 3 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei +3 2 2 2 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ +4 0 1 1 No blast hit
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_db.tsv Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,12 @@ +# ID 16S rRNA count +0 4 +1 3.31 +2 4.5 +3 4.98 + +# tax_string 16S rRNA count +k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei 3 +k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ 3.85824942205532 +k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ 4 +k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ 6.80611715914982 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/in_total.tsv Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,3 @@ +Sample1 142 +Sample2 1.31e3 +Sample3 215.3
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.biom Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,137 @@ +{ + "generated_by" : "Bio::Community version 0.1", + "matrix_type" : "sparse", + "date" : "2013-07-27T03:34:40", + "data" : [ + [ + 0, + 0, + 72.1591861673745 + ], + [ + 1, + 0, + 27.8408138326255 + ], + [ + 0, + 1, + 50.7189439619348 + ], + [ + 2, + 1, + 16.6666666666667 + ], + [ + 1, + 1, + 32.6143893713985 + ], + [ + 2, + 2, + 10 + ], + [ + 1, + 2, + 21.5547529141356 + ], + [ + 3, + 2, + 25.3357412575932 + ], + [ + 4, + 2, + 43.1095058282712 + ] + ], + "rows" : [ + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Cyanobacteria", + "c__Nostocophycideae", + "o__Nostocales", + "f__Nostocaceae", + "g__Dolichospermum", + "s__" + ] + }, + "id" : "1" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Firmicutes", + "c__Clostridia", + "o__Halanaerobiales", + "f__Halanaerobiaceae", + "g__Halanaerobium", + "s__" + ] + }, + "id" : "3" + }, + { + "metadata" : null, + "id" : "4" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Proteobacteria", + "c__Gammaproteobacteria", + "o__Enterobacteriales", + "f__Enterobacteriaceae", + "g__Escherichia", + "s__" + ] + }, + "id" : "0" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Archaea", + "p__Euryarchaeota", + "c__Methanomicrobia", + "o__Methanosarcinales", + "f__Methanosarcinaceae", + "g__Methanosarcina", + "s__mazei" + ] + }, + "id" : "2" + } + ], + "matrix_element_type" : "float", + "format_url" : "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "format" : "Biological Observation Matrix 1.0", + "columns" : [ + { + "metadata" : null, + "id" : "Sample1" + }, + { + "metadata" : null, + "id" : "Sample2" + }, + { + "metadata" : null, + "id" : "Sample3" + } + ], + "shape" : [ + 5, + 3 + ], + "id" : "", + "type" : "OTU table" +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out.qiime Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,7 @@ +# QIIME v1.3.0 OTU table +#OTU ID Sample1 Sample2 Sample3 Consensus Lineage +1 72.1591861673745 50.7189439619348 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ +3 27.8408138326255 32.6143893713985 21.5547529141356 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ +4 0 16.6666666666667 10 No blast hit +0 0 0 25.3357412575932 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ +2 0 0 43.1095058282712 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out2.biom Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,137 @@ +{ + "generated_by" : "Bio::Community version 0.1", + "matrix_type" : "sparse", + "date" : "2013-07-27T03:32:37", + "data" : [ + [ + 0, + 0, + 78.997461928934 + ], + [ + 1, + 0, + 21.002538071066 + ], + [ + 0, + 1, + 57.7458256029685 + ], + [ + 2, + 1, + 16.6666666666667 + ], + [ + 1, + 1, + 25.5875077303649 + ], + [ + 2, + 2, + 10 + ], + [ + 1, + 2, + 17.4757281553398 + ], + [ + 3, + 2, + 43.5145631067961 + ], + [ + 4, + 2, + 29.0097087378641 + ] + ], + "rows" : [ + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Cyanobacteria", + "c__Nostocophycideae", + "o__Nostocales", + "f__Nostocaceae", + "g__Dolichospermum", + "s__" + ] + }, + "id" : "1" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Firmicutes", + "c__Clostridia", + "o__Halanaerobiales", + "f__Halanaerobiaceae", + "g__Halanaerobium", + "s__" + ] + }, + "id" : "3" + }, + { + "metadata" : null, + "id" : "4" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Bacteria", + "p__Proteobacteria", + "c__Gammaproteobacteria", + "o__Enterobacteriales", + "f__Enterobacteriaceae", + "g__Escherichia", + "s__" + ] + }, + "id" : "0" + }, + { + "metadata" : { + "taxonomy" : [ + "k__Archaea", + "p__Euryarchaeota", + "c__Methanomicrobia", + "o__Methanosarcinales", + "f__Methanosarcinaceae", + "g__Methanosarcina", + "s__mazei" + ] + }, + "id" : "2" + } + ], + "matrix_element_type" : "float", + "format_url" : "http://biom-format.org/documentation/format_versions/biom-1.0.html", + "format" : "Biological Observation Matrix 1.0", + "columns" : [ + { + "metadata" : null, + "id" : "Sample1" + }, + { + "metadata" : null, + "id" : "Sample2" + }, + { + "metadata" : null, + "id" : "Sample3" + } + ], + "shape" : [ + 5, + 3 + ], + "id" : "", + "type" : "OTU table" +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_combined.qiime Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,7 @@ +# QIIME v1.3.0 OTU table +#OTU ID Sample1 Sample2 Sample3 Consensus Lineage +1 26.2887543891705 169.766111090629 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ +3 10.1428571428571 109.166666666667 10.765 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ +4 0 55.7865555514592 4.99425813085536 No blast hit +0 0 0 12.6533231776982 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ +2 0 0 21.53 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_total.tsv Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,3 @@ +Sample1 36.4316115320277 +Sample2 334.719333308755 +Sample3 49.9425813085536
--- a/test_data/in.biom Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,46 +0,0 @@ -{ - "id": "Human microbiomes", - "comment": "This is an optional comment", - "format": "Biological Observation Matrix 0.9.1-dev", - "format_url": "http://biom-format.org/documentation/format_versions/biom-1.0.html", - "type": "OTU table", - "generated_by": "QIIME revision 1.4.0-dev", - "date": "2011-12-19T19:00:00", - "rows":[ - {"id":"0", "metadata":{"taxonomy":["k__Bacteria", "p__Proteobacteria", "c__Gammaproteobacteria", "o__Enterobacteriales", "f__Enterobacteriaceae", "g__Escherichia", "s__"]}}, - {"id":"1", "metadata":{"taxonomy":["k__Bacteria", "p__Cyanobacteria", "c__Nostocophycideae", "o__Nostocales", "f__Nostocaceae", "g__Dolichospermum", "s__"]}}, - {"id":"2", "metadata":{"taxonomy":["k__Archaea", "p__Euryarchaeota", "c__Methanomicrobia", "o__Methanosarcinales", "f__Methanosarcinaceae", "g__Methanosarcina", "s__mazei"]}}, - {"id":"3", "metadata":{"taxonomy":["k__Bacteria", "p__Firmicutes", "c__Clostridia", "o__Halanaerobiales", "f__Halanaerobiaceae", "g__Halanaerobium", "s__"]}}, - {"id":"4", "metadata":{"taxonomy":[]}} - ], - "columns":[ - {"id":"Sample1", "metadata":{ - "BarcodeSequence":"CGCTTATCGAGA", - "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", - "BODY_SITE":"gut", - "Description":"human gut"}}, - {"id":"Sample2", "metadata":{ - "BarcodeSequence":"CATACCAGTAGC", - "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", - "BODY_SITE":"gut", - "Description":"human gut"}}, - {"id":"Sample3", "metadata":{ - "BarcodeSequence":"CTCTCTACCTGT", - "LinkerPrimerSequence":"CATGCTGCCTCCCGTAGGAGT", - "BODY_SITE":"gut", - "Description":"human skin"}} - ], - "matrix_type": "sparse", - "matrix_element_type": "int", - "shape": [5, 3], - "data":[[0,2,4], - [1,0,5], - [1,1,3], - [2,2,3], - [3,0,2], - [3,1,2], - [3,2,2], - [4,1,1], - [4,2,1] - ] -}
--- a/test_data/in.qiime Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# QIIME v1.3.0 OTU table -#OTU ID Sample1 Sample2 Sample3 Consensus Lineage -0 0 0 4 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ -1 5 3 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ -2 0 0 3 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei -3 2 2 2 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ -4 0 1 1 No blast hit
--- a/test_data/in_db.tsv Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -# ID 16S rRNA count -0 4 -1 3.31 -2 4.5 -3 4.98 - -# tax_string 16S rRNA count -k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei 3 -k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ 3.85824942205532 -k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ 4 -k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ 6.80611715914982 -
--- a/test_data/in_total.tsv Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample1 142 -Sample2 1.31e3 -Sample3 215.3
--- a/test_data/out.biom Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -{ - "generated_by" : "Bio::Community version 0.1", - "matrix_type" : "sparse", - "date" : "2013-07-27T03:34:40", - "data" : [ - [ - 0, - 0, - 72.1591861673745 - ], - [ - 1, - 0, - 27.8408138326255 - ], - [ - 0, - 1, - 50.7189439619348 - ], - [ - 2, - 1, - 16.6666666666667 - ], - [ - 1, - 1, - 32.6143893713985 - ], - [ - 2, - 2, - 10 - ], - [ - 1, - 2, - 21.5547529141356 - ], - [ - 3, - 2, - 25.3357412575932 - ], - [ - 4, - 2, - 43.1095058282712 - ] - ], - "rows" : [ - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Cyanobacteria", - "c__Nostocophycideae", - "o__Nostocales", - "f__Nostocaceae", - "g__Dolichospermum", - "s__" - ] - }, - "id" : "1" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Firmicutes", - "c__Clostridia", - "o__Halanaerobiales", - "f__Halanaerobiaceae", - "g__Halanaerobium", - "s__" - ] - }, - "id" : "3" - }, - { - "metadata" : null, - "id" : "4" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Proteobacteria", - "c__Gammaproteobacteria", - "o__Enterobacteriales", - "f__Enterobacteriaceae", - "g__Escherichia", - "s__" - ] - }, - "id" : "0" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Archaea", - "p__Euryarchaeota", - "c__Methanomicrobia", - "o__Methanosarcinales", - "f__Methanosarcinaceae", - "g__Methanosarcina", - "s__mazei" - ] - }, - "id" : "2" - } - ], - "matrix_element_type" : "float", - "format_url" : "http://biom-format.org/documentation/format_versions/biom-1.0.html", - "format" : "Biological Observation Matrix 1.0", - "columns" : [ - { - "metadata" : null, - "id" : "Sample1" - }, - { - "metadata" : null, - "id" : "Sample2" - }, - { - "metadata" : null, - "id" : "Sample3" - } - ], - "shape" : [ - 5, - 3 - ], - "id" : "", - "type" : "OTU table" -}
--- a/test_data/out.qiime Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# QIIME v1.3.0 OTU table -#OTU ID Sample1 Sample2 Sample3 Consensus Lineage -1 72.1591861673745 50.7189439619348 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ -3 27.8408138326255 32.6143893713985 21.5547529141356 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ -4 0 16.6666666666667 10 No blast hit -0 0 0 25.3357412575932 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ -2 0 0 43.1095058282712 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei
--- a/test_data/out2.biom Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,137 +0,0 @@ -{ - "generated_by" : "Bio::Community version 0.1", - "matrix_type" : "sparse", - "date" : "2013-07-27T03:32:37", - "data" : [ - [ - 0, - 0, - 78.997461928934 - ], - [ - 1, - 0, - 21.002538071066 - ], - [ - 0, - 1, - 57.7458256029685 - ], - [ - 2, - 1, - 16.6666666666667 - ], - [ - 1, - 1, - 25.5875077303649 - ], - [ - 2, - 2, - 10 - ], - [ - 1, - 2, - 17.4757281553398 - ], - [ - 3, - 2, - 43.5145631067961 - ], - [ - 4, - 2, - 29.0097087378641 - ] - ], - "rows" : [ - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Cyanobacteria", - "c__Nostocophycideae", - "o__Nostocales", - "f__Nostocaceae", - "g__Dolichospermum", - "s__" - ] - }, - "id" : "1" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Firmicutes", - "c__Clostridia", - "o__Halanaerobiales", - "f__Halanaerobiaceae", - "g__Halanaerobium", - "s__" - ] - }, - "id" : "3" - }, - { - "metadata" : null, - "id" : "4" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Bacteria", - "p__Proteobacteria", - "c__Gammaproteobacteria", - "o__Enterobacteriales", - "f__Enterobacteriaceae", - "g__Escherichia", - "s__" - ] - }, - "id" : "0" - }, - { - "metadata" : { - "taxonomy" : [ - "k__Archaea", - "p__Euryarchaeota", - "c__Methanomicrobia", - "o__Methanosarcinales", - "f__Methanosarcinaceae", - "g__Methanosarcina", - "s__mazei" - ] - }, - "id" : "2" - } - ], - "matrix_element_type" : "float", - "format_url" : "http://biom-format.org/documentation/format_versions/biom-1.0.html", - "format" : "Biological Observation Matrix 1.0", - "columns" : [ - { - "metadata" : null, - "id" : "Sample1" - }, - { - "metadata" : null, - "id" : "Sample2" - }, - { - "metadata" : null, - "id" : "Sample3" - } - ], - "shape" : [ - 5, - 3 - ], - "id" : "", - "type" : "OTU table" -}
--- a/test_data/out_combined.qiime Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -# QIIME v1.3.0 OTU table -#OTU ID Sample1 Sample2 Sample3 Consensus Lineage -1 26.2887543891705 169.766111090629 0 k__Bacteria; p__Cyanobacteria; c__Nostocophycideae; o__Nostocales; f__Nostocaceae; g__Dolichospermum; s__ -3 10.1428571428571 109.166666666667 10.765 k__Bacteria; p__Firmicutes; c__Clostridia; o__Halanaerobiales; f__Halanaerobiaceae; g__Halanaerobium; s__ -4 0 55.7865555514592 4.99425813085536 No blast hit -0 0 0 12.6533231776982 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Enterobacteriales; f__Enterobacteriaceae; g__Escherichia; s__ -2 0 0 21.53 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__mazei
--- a/test_data/out_total.tsv Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample1 36.4316115320277 -Sample2 334.719333308755 -Sample3 49.9425813085536
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/trait_db.loc.sample Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,10 @@ +# This file defines the locations and of available database files of microbial +# traits needed to run CopyRighter. Edit this file by adding the name and +# location of the databases you want (tab-delimited!) and move the file to the +# tool-data/ directory. + +# id name path +ssu_img40_gg201210 Short ribosomal subunit (16S) data (IMG 4.0, Greengenes 2012/10) /path/to/ssu_img40_gg201210.txt +genlength_img40_gg201210 Genome length data (IMG 4.0, Greengenes 2012/10) /path/to/genlength_img40_gg201210.txt + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jul 29 07:01:57 2013 -0400 @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of database files for CopyRighter --> + <table name="trait_db" comment_char="#"> + <columns>id, name, value</columns> + <file path="tool-data/trait_db.loc" /> + </table> +</tables>
--- a/trait_db.loc.sample Mon Jul 29 06:52:36 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -# File of pre-defined trait databases for CopyRighter -# -# This file defines the locations and of available database files of microbial -# traits needed to run CopyRighter. Edit this file by adding the name and -# location of the databases you want (tab-delimited!) and move the file to the -# tool-data/ directory. Then add this to your tool_data_table_conf.xml file: -# -# <!-- Locations of database files for CopyRighter --> -# <table name="trait_db" comment_char="#"> -# <columns>id, name, value</columns> -# <file path="tool-data/trait_db.loc" /> -# </table> -# - -# id name path -ssu_img40_gg201210 Short ribosomal subunit (16S) data (IMG 4.0, Greengenes 2012/10) /path/to/ssu_img40_gg201210.txt -genlength_img40_gg201210 Genome length data (IMG 4.0, Greengenes 2012/10) /path/to/genlength_img40_gg201210.txt -test_invalid Invalid database /path/to/db.txt - -