Finalised mash reference genome parsing

Author: adamkoziol

OLCspades/OLCspades.py

@@ -142,6 +142,7 @@ def __init__(self, args, pipelinecommit, startingtime, scriptpath):
         import reporter
         import compress
         import multiprocessing
+        printtime('Welcome to the CFIA de novo bacterial assembly pipeline {}'.format(pipelinecommit), startingtime)
         # Define variables from the arguments - there may be a more streamlined way to do this
         self.args = args
         self.path = os.path.join(args.path, '')
@@ -213,7 +214,9 @@ def __init__(self, args, pipelinecommit, startingtime, scriptpath):
     homepath = os.path.split(os.path.abspath(__file__))[0]
     # Find the commit of the script by running a command to change to the directory containing the script and run
     # a git command to return the short version of the commit hash
-    commit = subprocess.Popen('cd {} && git rev-parse --short HEAD'.format(homepath),
+    # commit = subprocess.Popen('cd {} && git rev-parse --short HEAD'.format(homepath),
+    #                           shell=True, stdout=subprocess.PIPE).communicate()[0].rstrip()
+    commit = subprocess.Popen('cd {} && git tag'.format(homepath),
                               shell=True, stdout=subprocess.PIPE).communicate()[0].rstrip()
     from argparse import ArgumentParser
     # Parser for arguments

OLCspades/mash.py

@@ -86,12 +86,6 @@ def mash(self):
 
     def parse(self):
         import re
-        from csv import DictReader
-        from glob import glob
-        # Set the name of the refseq profile
-        refseqprofile = glob('{}{}/*.txt'.format(self.referencefilepath, self.analysistype))[0]
-        # Open the refseq profile file as a dictionary
-        profile = DictReader(open(refseqprofile), dialect='excel-tab')
         printtime('Determining closest refseq genome', self.starttime)
         for sample in self.metadata:
             if sample.general.bestassemblyfile != 'NA':