Merge pull request #271 from jodyphelan/dev

Dev

tb-profiler

@@ -485,6 +485,7 @@ parser_sub.add_argument('--lofreq_sample_name',help='Sample name to use if VCF h
 parser_sub.add_argument('--suspect',action="store_true",help="Use the suspect suite of tools to add ML predictions")
 parser_sub.add_argument('--txt',action="store_true",help="Add text output")
 parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
+parser_sub.add_argument('--docx',help="Add docx output. This requires docxtpl to be installed")
 parser_sub.add_argument('--add_columns',default=None,type=str,help="Add additional columns found in the mutation database to the text and csv results")
 parser_sub.add_argument('--verbose',default=0, choices=[0,1,2],help="Verbosity increases from 0 to 2",type=int)
 parser_sub.add_argument('--delly_vcf',help=argparse.SUPPRESS)
@@ -504,6 +505,7 @@ parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (
 parser_sub.add_argument('--suspect',action="store_true",help="Use the suspect suite of tools to add ML predictions")
 parser_sub.add_argument('--txt',action="store_true",help="Add text output")
 parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
+parser_sub.add_argument('--docx',help="Add docx output. This requires docxtpl to be installed")
 parser_sub.add_argument('--add_columns',default=None,type=str,help="Add additional columns found in the mutation database to the text and csv results")
 parser_sub.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
 parser_sub.add_argument('--verbose',default=0, choices=[0,1,2],help="Verbosity increases from 0 to 2",type=int)
@@ -519,6 +521,7 @@ parser_sub.add_argument('--bam','-a',required=True, help='BAM file. Make sure it
 parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix')
 parser_sub.add_argument('--txt',action="store_true",help="Add text output")
 parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
+parser_sub.add_argument('--docx',help="Add docx output. This requires docxtpl to be installed")
 parser_sub.add_argument('--snps',action="store_true",help='Sample prefix')
 parser_sub.add_argument('--caller',default='freebayes',choices=["bcftools","freebayes","gatk"],type=str,help="Variant caller")
 parser_sub.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
@@ -542,6 +545,7 @@ group.add_argument('--fasta','-f',help='Fasta file')
 parser_sub.add_argument('--prefix','-p',default="tbprofiler",help='Sample prefix')
 parser_sub.add_argument('--txt',action="store_true",help="Add text output")
 parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
+parser_sub.add_argument('--docx',help="Add docx output. This requires docxtpl to be installed")
 parser_sub.add_argument('--output_template',type=str,help='Jinja2 formatted template for output')
 parser_sub.add_argument('--kmer_counter',default='kmc',choices=["kmc","dsk"],type=str,help="Kmer counter")
 parser_sub.add_argument('--platform','-m',choices=["illumina","nanopore","pacbio"],default="illumina",help='NGS Platform used to generate data')
@@ -591,6 +595,7 @@ parser_sub = subparsers.add_parser('reformat', help='Reformat json results into
 parser_sub.add_argument('json',default="tbprofiler",help='Sample prefix')
 parser_sub.add_argument('--txt',action="store_true",help="Add text output")
 parser_sub.add_argument('--csv',action="store_true",help="Add CSV output")
+parser_sub.add_argument('--docx',help="Add docx output. This requires docxtpl to be installed")
 parser_sub.add_argument('--output_template',type=str,help='Jinja2 formatted template for output')
 parser_sub.add_argument('--db',default='tbdb',help='Mutation panel name')
 parser_sub.add_argument('--external_db',type=str,help='Path to db files prefix (overrides "--db" parameter)')

tbprofiler/__init__.py

@@ -7,4 +7,4 @@
 from .output import *
 from .snp_dists import *
 
-__version__ = "4.4.1"
+__version__ = "4.4.2"

tbprofiler/docx.py

@@ -33,7 +33,8 @@ def write_docx(json_results,conf,outfile,template_file,reporting_af = 0.0):
         'sensitive': True if data['drtype'] == "Sensitive" else False,
         'mdr': True if data['drtype'] in ("MDR-TB","Pre-XDR-TB") else False,
         'xdr': True if data['drtype'] in "XDR-TB" else False,
-        'resistant': True if data['drtype'] in ("Other","RR-TB","HR-TB") else False
+        'resistant': True if data['drtype'] in ("Other","RR-TB","HR-TB") else False,
+        'drtype': data['drtype'],
     }
 
     for d in conf['drugs']: