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Added test data director for make_prefs_file.py

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1 parent ed2fa80 commit 01f8309105126a7181388aef886198ad8c024f43 Luke Ursell committed Oct 16, 2012
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11 make_prefs_file/mapping.txt
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+#SampleID BarcodeSequence LinkerPrimerSequence Treatment DOB Description
+#Example mapping file for the QIIME analysis package. These 9 samples are from a study of the effects of exercise and diet on mouse cardiac physiology (Crawford, et al, PNAS, 2009).
+PC.354 AGCACGAGCCTA YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._354
+PC.355 AACTCGTCGATG YATGCTGCCTCCCGTAGGAGT Control 20061218 Control_mouse_I.D._355
+PC.356 ACAGACCACTCA YATGCTGCCTCCCGTAGGAGT Control 20061126 Control_mouse_I.D._356
+PC.481 ACCAGCGACTAG YATGCTGCCTCCCGTAGGAGT Control 20070314 Control_mouse_I.D._481
+PC.593 AGCAGCACTTGT YATGCTGCCTCCCGTAGGAGT Control 20071210 Control_mouse_I.D._593
+PC.607 AACTGTGCGTAC YATGCTGCCTCCCGTAGGAGT Fast 20071112 Fasting_mouse_I.D._607
+PC.634 ACAGAGTCGGCT YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._634
+PC.635 ACCGCAGAGTCA YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._635
+PC.636 ACGGTGAGTGTC YATGCTGCCTCCCGTAGGAGT Fast 20080116 Fasting_mouse_I.D._636
View
69 make_prefs_file/prefs_out.txt
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+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'BarcodeSequence': 10,
+ 'LinkerPrimerSequence': 10,
+ 'Treatment': 10,
+ 'DOB': 10,
+ 'Description': 10
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
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47 make_prefs_file/prefs_out_1.txt
@@ -0,0 +1,47 @@
+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'SampleID&&Treatment':
+ {
+ 'column':'SampleID&&Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'Treatment': 10,
+ 'SampleID&&Treatment': 10
+ },
+'FIELDS':
+ [
+ 'SampleID',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
View
69 make_prefs_file/prefs_out_d15.txt
@@ -0,0 +1,69 @@
+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 15,
+ 'BarcodeSequence': 15,
+ 'LinkerPrimerSequence': 15,
+ 'Treatment': 15,
+ 'DOB': 15,
+ 'Description': 15
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
View
69 make_prefs_file/prefs_out_procrustes.txt
@@ -0,0 +1,69 @@
+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'BarcodeSequence': 10,
+ 'LinkerPrimerSequence': 10,
+ 'Treatment': 10,
+ 'DOB': 10,
+ 'Description': 10
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'blue',
+'arrow_head_color':'black'
+}
View
69 make_prefs_file/prefs_out_s3.txt
@@ -0,0 +1,69 @@
+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'BarcodeSequence': 10,
+ 'LinkerPrimerSequence': 10,
+ 'Treatment': 10,
+ 'DOB': 10,
+ 'Description': 10
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'3.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
View
76 make_prefs_file/prefs_out_taxa_l3.txt
@@ -0,0 +1,76 @@
+{
+'background_color':'black',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'BarcodeSequence': 10,
+ 'LinkerPrimerSequence': 10,
+ 'Treatment': 10,
+ 'DOB': 10,
+ 'Description': 10
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_2':
+ {
+ 'column':'2',
+ 'colors':
+ {
+ 'Root;k__Bacteria;Other':('red0',(0,100,100)),
+ 'Root;k__Bacteria;p__Actinobacteria':('red26.6666666667',(26,100,100)),
+ 'Root;k__Bacteria;p__Bacteroidetes':('red53.3333333333',(53,100,100)),
+ 'Root;k__Bacteria;p__Deferribacteres':('red80.0',(80,100,100)),
+ 'Root;k__Bacteria;p__Firmicutes':('red106.666666667',(106,100,100)),
+ 'Root;k__Bacteria;p__Proteobacteria':('red133.333333333',(133,100,100)),
+ 'Root;k__Bacteria;p__TM7':('red160.0',(160,100,100)),
+ 'Root;k__Bacteria;p__Tenericutes':('red186.666666667',(186,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
View
69 make_prefs_file/prefs_out_white.txt
@@ -0,0 +1,69 @@
+{
+'background_color':'white',
+
+'sample_coloring':
+ {
+ 'SampleID':
+ {
+ 'column':'SampleID',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'BarcodeSequence':
+ {
+ 'column':'BarcodeSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'LinkerPrimerSequence':
+ {
+ 'column':'LinkerPrimerSequence',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Treatment':
+ {
+ 'column':'Treatment',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'DOB':
+ {
+ 'column':'DOB',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ },
+ 'Description':
+ {
+ 'column':'Description',
+ 'colors':(('red',(0,100,100)),('blue',(240,100,100)))
+ }
+ },
+'MONTE_CARLO_GROUP_DISTANCES':
+ {
+ 'SampleID': 10,
+ 'BarcodeSequence': 10,
+ 'LinkerPrimerSequence': 10,
+ 'Treatment': 10,
+ 'DOB': 10,
+ 'Description': 10
+ },
+'FIELDS':
+ [
+ 'Description',
+ 'DOB',
+ 'BarcodeSequence',
+ 'SampleID',
+ 'LinkerPrimerSequence',
+ 'Treatment'
+ ],
+'taxonomy_coloring':
+ {
+ 'Level_1':
+ {
+ 'column':'1',
+ 'colors':
+ {
+ 'Root;Bacteria':('red0',(0,100,100))
+ }
+ }
+ },
+'ball_scale':'1.000000',
+'arrow_line_color':'white',
+'arrow_head_color':'red'
+}
View
9 make_prefs_file/taxa_level_3.txt
@@ -0,0 +1,9 @@
+Taxon PC.636 PC.635 PC.356 PC.481 PC.354 PC.593 PC.355 PC.607 PC.634
+Root;k__Bacteria;Other 0.0202702702703 0.0469798657718 0.0266666666667 0.027397260274 0.0134228187919 0.0134228187919 0.0136054421769 0.0469798657718 0.02
+Root;k__Bacteria;p__Actinobacteria 0.00675675675676 0.00671140939597 0.0 0.00684931506849 0.0 0.0 0.0 0.0201342281879 0.02
+Root;k__Bacteria;p__Bacteroidetes 0.695945945946 0.523489932886 0.193333333333 0.143835616438 0.0738255033557 0.389261744966 0.285714285714 0.275167785235 0.653333333333
+Root;k__Bacteria;p__Deferribacteres 0.0472972972973 0.0134228187919 0.0 0.0 0.0 0.0 0.0 0.0201342281879 0.0333333333333
+Root;k__Bacteria;p__Firmicutes 0.209459459459 0.395973154362 0.773333333333 0.787671232877 0.89932885906 0.41610738255 0.700680272109 0.456375838926 0.22
+Root;k__Bacteria;p__Proteobacteria 0.00675675675676 0.00671140939597 0.0 0.0 0.0 0.0335570469799 0.0 0.0201342281879 0.0133333333333
+Root;k__Bacteria;p__TM7 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0133333333333
+Root;k__Bacteria;p__Tenericutes 0.0135135135135 0.00671140939597 0.00666666666667 0.0342465753425 0.0134228187919 0.147651006711 0.0 0.161073825503 0.0266666666667

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