TST: the two tests that can be run pass now. The OTU table had an und…

…efined pH for one of the samples, which is invalid for the hdf5 formatter, issue biocore/biom-format#609

picrust_test_data/predict_metagenomes/otu_table_for_custom_trait_table.biom

@@ -1 +1 @@
-{"rows": [{"id": "A", "metadata": null}, {"id": "B", "metadata": null}, {"id": "C", "metadata": null}], "format": "Biological Observation Matrix v0.9", "data": [[0, 0, 1.0], [0, 1, 2.0], [0, 2, 3.0], [0, 3, 5.0], [1, 0, 5.0], [1, 1, 1.0], [1, 3, 2.0], [2, 2, 1.0], [2, 3, 4.0]], "columns": [{"id": "Sample1", "metadata": {"pH":7.0}}, {"id": "Sample2", "metadata": {"pH":8.0}}, {"id": "Sample3", "metadata": {"pH":7.0}}, {"id": "Sample4", "metadata": null}],"generated_by": "QIIME 1.4.0-dev, svn revision 2753", "matrix_type": "sparse", "shape": [3, 4], "format_url": "http://www.qiime.org/svn_documentation/documentation/biom_format.html", "date": "2012-02-22T20:50:05.024661", "type": "OTU table", "id": null, "matrix_element_type": "float"}
+{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "picrust","date": "2015-03-07T11:40:42.151151","type": "OTU table","matrix_element_type": "float","shape": [3, 4],"data": [[0,0,1.0],[0,1,2.0],[0,2,3.0],[0,3,5.0],[1,0,5.0],[1,1,1.0],[1,3,2.0],[2,2,1.0],[2,3,4.0]],"rows": [{"id": "A", "metadata": null},{"id": "B", "metadata": null},{"id": "C", "metadata": null}],"columns": [{"id": "Sample1", "metadata": {"pH": 7.0}},{"id": "Sample2", "metadata": {"pH": 8.0}},{"id": "Sample3", "metadata": {"pH": 7.0}},{"id": "Sample4", "metadata": {"pH": NaN}}]}

scripts/predict_metagenomes.py

@@ -26,15 +26,16 @@
 script_info = {}
 script_info['brief_description'] = "This script produces the actual metagenome functional predictions for a given OTU table."
 script_info['script_description'] = ""
-script_info['script_usage'] = [("","Predict KO abundances for a given OTU table picked against the newest version of GreenGenes.",\
-                                    "%prog -i normalized_otus.biom -o predicted_metagenomes.biom"),
+script_info['script_usage'] = [
+                               ("","Predict KO abundances for a given OTU table picked against the newest version of GreenGenes.", "%prog -i normalized_otus.biom -o predicted_metagenomes.biom"),
                                ("","Change output format to plain tab-delimited:","%prog -f -i normalized_otus.biom -o predicted_metagenomes.txt"),
                                ("","Predict COG abundances for a given OTU table.","%prog -i normalized_otus.biom -t cog -o cog_predicted_metagenomes.biom"),\
                                ("","Predict RFAM abundances for a given OTU table.","%prog -i normalized_otus.biom -t rfam -o rfam_predicted_metagenomes.biom"),\
                                ("","Output confidence intervals for each prediction.","%prog -i normalized_otus.biom -o predicted_metagenomes.biom --with_confidence"),\
                                ("","Predict metagenomes using a custom trait table in tab-delimited format.","%prog -i otu_table_for_custom_trait_table.biom -c custom_trait_table.tab -o output_metagenome_from_custom_trait_table.biom"),\
                                ("","Predict metagenomes,variances,and 95% confidence intervals for each gene category using a custom trait table in tab-delimited format.","%prog -i otu_table_for_custom_trait_table.biom --input_variance_table custom_trait_table_variances.tab -c custom_trait_table.tab -o output_metagenome_from_custom_trait_table.biom --with_confidence"),\
-                                   ("","Change the version of GG used to pick OTUs","%prog -i normalized_otus.biom -g 18may2012 -o predicted_metagenomes.biom")]
+                               ("","Change the version of GG used to pick OTUs","%prog -i normalized_otus.biom -g 18may2012 -o predicted_metagenomes.biom")
+                                ]
 script_info['output_description']= "Output is a table of function counts (e.g. KEGG KOs) by sample ids."
 script_info['required_options'] = [
  make_option('-i','--input_otu_table',type='existing_filepath',help='the input otu table in biom format'),
@@ -150,7 +151,7 @@ def main():
         print "Loading OTU table: ",opts.input_otu_table
 
     otu_table = load_table(opts.input_otu_table)
-    ids_to_load = otu_table.ids(axis='observation')
+    ids_to_load = otu_table.ids(axis='observation').tolist()
 
     if opts.verbose:
         print "Done loading OTU table containing %i samples and %i OTUs." \