Merge pull request #9 from trstickland/tweak_config_for_farm4

Tweak config for farm4

Author: trstickland

gffmunger-config.yml

@@ -40,14 +40,13 @@ annotated_feature_types :
 only_transfer_anot_to_mRNA : False
 
 # For use of genometools to validate GFF3 input.
-# gt_path                 : '/usr/bin/gt'
-gt_path                 : '/software/pathogen/external/apps/usr/local/genometools-1.5.9/bin/gt'
+gt_path                 : '/usr/bin/gt'
 gff3_validator_tool     : 'gff3validator'
 gff3_validation_timeout : 60
 
 # Working filenames; shouldn't need to edit these unless their location offends.
 # A UUID is substituted for <uid> to avoid clashes if there are concurrent gffmunder processes.
-gffutils_db_filename : 'gffutils.<uid>.db'
+gffutils_db_filename : '/tmp/gffutils.<uid>.db'
 temp_input_file      : '/tmp/gffmunger_input.<uid>.gff3'
 
 # Causes features in the input GFF3 to be read into a read_features_to_buffer.

gffmunger/tests/gff_tests.py

@@ -1,6 +1,7 @@
 import unittest
 import os
 import gffutils
+import uuid
 import warnings
 
 from gffmunger.GFFMunger import GFFMunger
@@ -9,7 +10,7 @@
 data_dir                = os.path.join(      test_modules_dir, 'data' )
 test_gff_file           = os.path.join(      data_dir,         'SMALL_SAMPLE.gff3.gz' )            # must be valid GFF3 with *no* FASTA
 test_gff_and_fasta_file = os.path.join(      data_dir,         'SMALL_SAMPLE_INCL_FASTA.gff3.gz' ) # must be valid GFF3 with FASTA
-test_gff_db_file        = os.path.join(      data_dir,         'gffutils_test.db' )
+test_gff_db_file        = '/tmp/gffutils_test.<uid>.db'
 
 #sample_gff_gene_id      = 'PF3D7_0100100' # use with SAMPLE.gff3
 sample_gff_gene_id      = '13J3.01' # use with SMALL_SAMPLE.gff3
@@ -31,7 +32,7 @@ def setUpClass(self):
          warnings.filterwarnings("ignore", "generator '_FileIterator\.",         PendingDeprecationWarning, "gffutils", 186 )
          warnings.filterwarnings("ignore", "unclosed file <_io\.TextIOWrapper",  ResourceWarning,           "gffutils", 668 )
          self.test_gff_db = gffutils.create_db( test_gff_file,
-                                                dbfn                    = test_gff_db_file,
+                                                dbfn                    = str(test_gff_db_file).replace('<uid>',uuid.uuid4().hex),
                                                 force                   = True,     # overwrite previous testing db file
                                                 merge_strategy          = 'error',
                                                 keep_order              = False,    # True doesn't appear to maintain attribute order :-/  (and turning this off may be faster)

gffmunger/tests/io_tests.py

@@ -72,7 +72,8 @@ def test_020_gff3_i0(self):
       self.assertEqual(expected_num_metadata_lines,      newmunger.extract_GFF3_components())
       self.assertEqual(expected_num_metadata_lines,      newmunger.extract_GFF3_components(test_gff_no_fasta))
       with warnings.catch_warnings():
-         warnings.filterwarnings("ignore", "unclosed file", ResourceWarning, "gffutils", 0 )
+         warnings.filterwarnings("ignore", "unclosed file <_io\.FileIO",   ResourceWarning, "six",      581 )
+         warnings.filterwarnings("ignore", "",                ResourceWarning, "gffutils", 0 )
          self.assertIsInstance(newmunger.import_fasta(), pyfaidx.Fasta)
          self.assertIsInstance(newmunger.import_fasta(test_fasta_file), pyfaidx.Fasta)
          try: