From: Brandon King <kingb@caltech.edu>
Date: Sat, 17 Nov 2007 02:09:29 +0000 (+0000)
Subject: [project @ Species and build to valid genome dir mapper!]
X-Git-Tag: 0.1.0~63
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=249f6a9bd2464f10a0f87c9952fc72bc7713b9ce

[project @ Species and build to valid genome dir mapper!]
 * Config generator returns genome dir with %(species|build)s
 * This module contains a dictionary generator which given
   a genome base dir, will generate a dictionary whos key is
   species|build and whos value is the valid genome dir
 * requires a file in each genome dir called _metainfo_
   * containing: species|build
---

diff --git a/bin/genome_mapper.py b/bin/genome_mapper.py
new file mode 100644
index 0000000..aacc068
--- /dev/null
+++ b/bin/genome_mapper.py
@@ -0,0 +1,94 @@
+#!/usr/bin/python
+import glob
+import sys
+import os
+
+import logging
+
+class DuplicateGenome(Exception): pass
+
+
+def _has_metainfo(genome_dir):
+  metapath = os.path.join(genome_dir, '_metainfo_')
+  if os.path.isfile(metapath):
+    return True
+  else:
+    return False
+
+def getAvailableGenomes(genome_base_dir):
+  """
+  raises IOError (on genome_base_dir not found)
+  raises DuplicateGenome on duplicate genomes found.
+  
+  returns a double dictionary (i.e. d[species][build] = path)
+  """
+
+  # Need valid directory
+  if not os.path.exists(genome_base_dir):
+    msg = "Directory does not exist: %s" % (genome_base_dir)
+    raise IOError, msg
+
+  # Find all subdirectories
+  filepath_list = glob.glob(os.path.join(genome_base_dir, '*'))
+  potential_genome_dirs = \
+    [ filepath for filepath in filepath_list if os.path.isdir(filepath)]
+
+  # Get list of metadata files
+  genome_dir_list = \
+    [ dirpath \
+      for dirpath in potential_genome_dirs \
+      if _has_metainfo(dirpath) ]
+
+  # Genome double dictionary
+  d = {}
+
+  for genome_dir in genome_dir_list:
+    line = open(os.path.join(genome_dir, '_metainfo_'), 'r').readline().strip()
+
+    # Get species, build... log and skip on failure
+    try:
+      species, build = line.split('|')
+    except:
+      logging.warning('Skipping: Invalid metafile (%s) line: %s' \
+                      % (metafile, line))
+      continue
+
+    build_dict = d.setdefault(species, {})
+    if build in build_dict:
+      msg = "Duplicate genome for %s|%s" % (species, build)
+      raise DuplicateGenome, msg
+
+    build_dict[build] = genome_dir
+
+  return d
+  
+
+def constructMapperDict(genome_dict):
+  """
+  Creates a dictionary which can map the genome
+  in the eland config generator output to a local
+  genome path
+
+  ie. 'Homo sapiens|hg18' -> <genome_dir>
+  """
+  mapper_dict = {}
+  for species in genome_dict.keys():
+    for build in genome_dict[species]:
+      mapper_dict[species+'|'+build] = genome_dict[species][build]
+
+  return mapper_dict
+
+
+if __name__ == '__main__':
+
+  if len(sys.argv) != 2:
+    print 'useage: %s <base_genome_dir>' % (sys.argv[0])
+    sys.exit(1)
+
+  d = getAvailableGenomes(sys.argv[1])
+  d2 = constructMapperDict(d)
+
+  for k,v in d2.items():
+    print '%s: %s' % (k,v)
+  
+