aading a new file to address caporaso-lab-graveyard#13

biom_to_core_diversity_analyses.py

@@ -0,0 +1,89 @@
+#!/usr/bin/env python
+from __future__ import division
+
+__author__ = "Giorgio Casaburi and Greg Caporaso"
+__copyright__ = "Copyright 2013, The miMAP project"
+__credits__ = "Giorgio Casaburi", "Greg Caporaso"
+__license__ = "GPL"
+__version__ = "0.0.0-dev"
+__maintainer__ = "Giorgio Casaburi"
+__email__ = "[email protected]"
+
+from shutil import rmtree
+from os.path import join, split, splitext, exists
+from glob import glob
+from tempfile import gettempdir
+from pyqi.util import pyqi_system_call, remove_files
+from pyqi.core.command import (Command, CommandIn, CommandOut,
+    ParameterCollection)
+
+class biomtocorediversityanalyses(Command):
+    BriefDescription = "This command allows to run core diversity analysis using as input a biom table (i.e. output from fasta_to_closed_reference_otu_picking.py script)"
+    LongDescription = "A command for running core diversity analysis using in Qiime in order to obtain alpha and beta diversity using a miRNAs biom table. Alpha diversity id performed with obsrved specied metric while the beta diversity with bray-curtis. THIS CODE IS CURRENTLY UNTESTED. YOU SHOULD NOT USE THIS VERSION OF THE CODE. THIS MESSAGE WILL BE REMOVED WHEN TESTS ARE ADDED."
+
+    CommandIns = ParameterCollection([
+        CommandIn(Name='input_file', DataType=str,
+                  Description='directory containing the input biom table', Required=True),
+        CommandIn(Name='output_dir', DataType=str,
+                  Description='the path where the output of core diversity analysis should be written', Required=True),
+        CommandIn(Name='sampling_depth', DataType=int,
+                  Description='Sequencing depth to use for even sub-sampling and maximum rarefaction depth. You should review the output of print_biom_table_summary.py on the miRNAs biom table to decide on this value', Required=True),
+        CommandIn(Name='jobs_to_start', DataType=int,
+                  Description='the number of jobs you want to run in parallel', Default=1)
+
+        ])
+
+    CommandOuts = ParameterCollection([
+        CommandOut(Name='status', DataType=str,
+                  Description='the final result'),
+        CommandOut(Name='error', DataType=str,
+                  Description='the error result')
+
+    ])
+
+# Qiime is required to be installed by the User so that every scripts can be called in the command line within the User $HOME.
+
+    # Scripts included in Qiime
+    core_diversity_analyses_path = "core_diversity_analyses.py"
+
+
+
+    # Temporary folder to store the files:
+    temp_dir = gettempdir()
+    verbose = True
+
+    def run(self, **kwargs):
+
+        input_fp = kwargs['input_file']
+
+        output_dir = kwargs['output_dir']
+
+
+        #Mapping file
+        mapping_file_fp = kwargs['mapping_file_fp']
+        input_mapping_file_pattern = join(mapping_file_fp,'mapping_file.txt')
+
+
+        temp_files_to_remove = []
+        temp_dirs_to_remove = []
+        input_filename = split(input_fp)[1]
+        input_basename = splitext(input_filename)[0]
+
+        #Create and call the core_diversity_analysis.py command and run it using a miRNAs biom table
+        command = "%s -i %s -m %s -e %s -o %s -O %s --suppress_otu_category_significance --nonphylogenetic_diversity" % (self.core_diversity_analyses_path, input_fp, mapping_file_fp, int(kwargs["sampling_depth"]), output_dir, int(kwargs["jobs_to_start"]))
+        if self.verbose:
+                print command
+        stdout, stderr, ret_val = pyqi_system_call(command)
+        if ret_val != 0:
+
+                return {"status":ret_val,
+                        "error":stderr}
+
+
+
+
+
+            # clean up (to do)
+
+
+CommandConstructor = biomtocorediversityanalyses