# HG changeset patch
# User fangly
# Date 1375095717 14400
# Node ID 658ad8b923419de43c430394bd463c286b80036a
# Parent 7a7ecf9b9df77089d548902d60f7e408802813a4
Uploaded
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/in.biom
--- /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]
+ ]
+}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/in.qiime
--- /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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/in_db.tsv
--- /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
+
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/in_total.tsv
--- /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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/out.biom
--- /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"
+}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/out.qiime
--- /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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/out2.biom
--- /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"
+}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/out_combined.qiime
--- /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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test-data/out_total.tsv
--- /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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/in.biom
--- 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]
- ]
-}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/in.qiime
--- 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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/in_db.tsv
--- 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
-
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/in_total.tsv
--- 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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/out.biom
--- 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"
-}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/out.qiime
--- 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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/out2.biom
--- 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"
-}
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/out_combined.qiime
--- 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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 test_data/out_total.tsv
--- 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
diff -r 7a7ecf9b9df7 -r 658ad8b92341 tool-data/trait_db.loc.sample
--- /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
+
+
diff -r 7a7ecf9b9df7 -r 658ad8b92341 tool_data_table_conf.xml.sample
--- /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 @@
+
+
+
+
diff -r 7a7ecf9b9df7 -r 658ad8b92341 trait_db.loc.sample
--- 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:
-#
-#
-#
-#
-
-# 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
-
-