Merge pull request #336 from jodyphelan/dev

Dev

tb-profiler

@@ -8,7 +8,6 @@ import json
 import tbprofiler as tbp
 import os
 import csv
-from datetime import datetime
 from uuid import uuid4
 import glob
 import atexit
@@ -198,9 +197,6 @@ def main_update_tbdb(args):
         pp.run_cmd(f"git checkout {args.commit}")
 
     if args.prefix==None:
-        if args.branch == "master":
-            args.prefix = "tbdb"
-        else:
             args.prefix = args.branch
 
 
@@ -517,7 +513,7 @@ parser_sub.set_defaults(func=main_load_library)
 parser_sub = subparsers.add_parser('update_tbdb', help='Pull the latest tbdb library and load', formatter_class=ArgumentDefaultsRichHelpFormatter)
 parser_sub.add_argument('--prefix','-p',help='Database name')
 parser_sub.add_argument('--repo','-r',default="https://github.com/jodyphelan/tbdb.git",help='Repository to pull from')
-parser_sub.add_argument('--branch','-b',default="master",help='Branch to pull from')
+parser_sub.add_argument('--branch','-b',default="tbdb",help='Branch to pull from')
 parser_sub.add_argument('--commit','-c',help='Git commit hash to checkout (default: latest)')
 parser_sub.add_argument('--match_ref',type=str,help='The prefix for all output files')
 parser_sub.add_argument('--dir','-d',default=".",help='Storage directory')

tbprofiler/__init__.py

@@ -7,4 +7,4 @@
 from .snp_dists import *
 from .phylo import *
 
-__version__ = "6.1.0"
+__version__ = "6.2.0"

tbprofiler/docx.py

@@ -1,7 +1,6 @@
 import sys
 from docxtpl import DocxTemplate
 from collections import defaultdict
-import datetime
 
 
 def sanitize(d):

tbprofiler/models.py

@@ -111,7 +111,7 @@ def get_qc(self):
         else:
             text = "Not available for VCF input"
         return text
-    
+
     def get_missing_pos(self,sep="\t"):
         if isinstance(self.qc, (BamQC,)):
             text = dict_list2text(self.qc.missing_positions,mappings={"pos":"Genome Position","annotation.gene":"Gene","annotation.variant":"Variant", "depth":"Depth"},sep=sep)

tbprofiler/phylo.py

@@ -9,7 +9,7 @@
 import argparse
 
 def usher_add_sample(args: argparse.Namespace) -> None:
-    logging.info(f"Adding sample to phylogeny")
+    logging.info("Adding sample to phylogeny")
 
 
     if args.vcf:
@@ -54,7 +54,7 @@ def generate_low_dp_mask(bam: str,ref: str,outfile: str,min_dp: int = 10) -> Non
         for p in range(length):
             if (chrom,p) not in ok_positions:
                 missing_positions.append((chrom,p))
-    
+
     # write missing positions to bed file
     with open(outfile,"w") as O:
         for x in missing_positions:

tbprofiler/reformat.py

@@ -225,7 +225,7 @@ def create_resistance_result(
     main_lineage, sub_lineage = get_main_lineage(lineage)
     drtype = get_drtypes(dr_variants)
     pipeline = Pipeline(
-        software_version=args.version, 
+        software_version=args.version,
         db_version=args.conf['version'],
         software=[{'process':k,'software':v} for k,v in shared_dict.items()]
     )