Merge pull request #1184 from fls-bioinformatics-core/qc-pipeline-update-organism-name-normalisation

Update organism name normalisation function and apply more consistently

Author: pjbriggs

auto_process_ngs/qc/pipeline.py

@@ -36,12 +36,8 @@
 import tempfile
 import shutil
 import random
-from bcftbx.JobRunner import SimpleJobRunner
 from bcftbx.FASTQFile import FastqIterator
-from bcftbx.TabFile import TabFile
 from bcftbx.utils import mkdir
-from bcftbx.utils import mkdirs
-from bcftbx.utils import find_program
 from bcftbx.ngsutils import getreads
 from bcftbx.ngsutils import getreads_subset
 from ..analysis import AnalysisFastq
@@ -57,10 +53,8 @@
 from ..pipeliner import PipelineParam as Param
 from ..pipeliner import ListParam
 from ..pipeliner import PipelineFailure
-from ..tenx.cellplex import CellrangerMultiConfigCsv
 from ..tenx.multiome import MultiomeLibraries
-from ..tenx.utils import add_cellranger_args
-from ..utils import get_organism_list
+from ..utils import normalise_organism_name
 from .modules.cellranger_atac_count import CellrangerAtacCount
 from .modules.cellranger_arc_count import CellrangerArcCount
 from .modules.cellranger_count import CellrangerCount
@@ -74,8 +68,6 @@
 from .modules.rseqc_infer_experiment import RseqcInferExperiment
 from .modules.sequence_lengths import SequenceLengths
 from .modules.strandedness import Strandedness
-from .protocols import determine_qc_protocol
-from .protocols import fetch_protocol_definition
 from .protocols import parse_qc_module_spec
 from .reporting import report as reportqc
 from .utils import get_bam_basename
@@ -286,10 +278,7 @@ def add_project(self,project,protocol,qc_dir=None,organism=None,
             organism = project.info.organism
 
         # Sanitised organism name
-        organism_name = str(organism).\
-                        strip().\
-                        lower().\
-                        replace(' ','_')
+        organism_name = normalise_organism_name(organism)
 
         # Report details
         self.report("-- Protocol   : %s" % protocol.name)

auto_process_ngs/test/test_utils.py

@@ -1386,6 +1386,7 @@ def test_normalise_organism_name(self):
                          "mus_musculus")
         self.assertEqual(normalise_organism_name(" Mus  musculus "),
                          "mus_musculus")
+        self.assertEqual(normalise_organism_name("C. elegans"), "c_elegans")
 
 class TestSplitUserHostDir(unittest.TestCase):
     """Tests for the split_user_host_dir function

auto_process_ngs/utils.py

@@ -1100,9 +1100,9 @@ def normalise_organism_name(name):
       String: normalised organism name
     """
     # Make lowercase, split on commas and replace whitespace
-    # with single underscore, then strip leading/trailing
-    # underscores
-    return re.sub(r'\s+','_',str(name).lower()).strip('_')
+    # and other non-alphanumeric characters with single underscore,
+    # finally strip leading/trailing underscores
+    return re.sub(r'\W+','_',str(name).lower()).strip('_')
 
 def split_user_host_dir(location):
     # Split a location of the form [[user@]host:]dir into its