From 2fae966d58a3dc0c7fefea35f3c4b360930daff5 Mon Sep 17 00:00:00 2001
From: Giorgio Casaburi <casaburi@ceinge.unina.it>
Date: Tue, 12 Nov 2013 22:28:48 +0100
Subject: [PATCH] adding a new file to address #13

---
 biom_to_core_diversity_analysis.py | 85 ++++++++++++++++++++++++++++++
 1 file changed, 85 insertions(+)
 create mode 100755 biom_to_core_diversity_analysis.py

diff --git a/biom_to_core_diversity_analysis.py b/biom_to_core_diversity_analysis.py
new file mode 100755
index 0000000..49aa250
--- /dev/null
+++ b/biom_to_core_diversity_analysis.py
@@ -0,0 +1,85 @@
+#!/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__ = "casaburi@ceinge.unina.it"
+
+from shutil import rmtree
+from os.path import join, split, splitext, exists
+from glob import glob
+
+from pyqi.util import pyqi_system_call, remove_files
+from pyqi.core.command import Command, Parameter, ParameterCollection
+
+class biomtocorediversityanalysis(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."
+    Parameters = ParameterCollection([
+        Parameter(Name='input_dir', DataType=str,
+                  Description='directory containing the input biom table', Required=True),
+        Parameter(Name='output_dir', DataType=str,
+                  Description='the path where the output of core diversity analysis should be written', Required=True),
+        Parameter(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),
+        Parameter(Name='mapping_file', DataType=str,
+                  Description='the path to the mapping file associated with your samples', Required=True)
+    
+        ])
+
+# 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_anlysis_path = "core_diversity_analyses.py"
+    
+    
+    
+    # Temporary folder to store the files:
+    temp_dir = "/tmp/miMAP"
+    verbose = True
+
+    def run(self, **kwargs):
+        
+        input_dir = kwargs['input_dir']
+        input_biom_table_pattern = join(input_dir,'*.biom')
+        input_filepath = glob(input_biom_table_pattern)
+        
+        output_dir = kwargs['output_dir']
+        
+        sampling_depth = kwargs['sampling_depth']
+        
+        
+        
+        mapping_file = kwargs['mapping_file']
+        input_mapping_file_pattern = (mapping_file + 'mapping_file.txt')
+        
+
+        for input_filepath in input_filepath:
+            temp_files_to_remove = []
+            temp_dirs_to_remove = []
+            input_filename = split(input_filepath)[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  --suppress_otu_category_significance --nonphylogenetic_diversity" % (self.core_diversity_anlysis_path, input_filepath,  mapping_file, sampling_depth, output_dir)
+            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 = biomtocorediversityanalysis
+