Merge branch 'hotfix/1.1.4'

updated regex to lookup gene name with .search

CHANGES.md

@@ -1,3 +1,5 @@
+## 1.1.4
+* updated regex to get genename
 ## 1.1.3
 * fixed bug in gene name comparison with hyphen(-)
 * corrected typo in default directory name

Dockerfile

@@ -3,7 +3,7 @@ USER root
 
 MAINTAINER  [email protected]
 
-ENV ANNOTATEVCF_VER '1.1.3'
+ENV ANNOTATEVCF_VER '1.1.4'
 
 # install system tools
 RUN apt-get -yq update

annotate/commandline.py

@@ -17,7 +17,7 @@
 
 
 def main():
-    usage = "\n %prog [options] -vcf input.vcf [-drv_json test.json -drv_data test_dir] "
+    usage = "\n %prog [options] -vcf input.vcf [-filter -np -gt -g -m -lof -hl -o ]"
 
     optParser = argparse.ArgumentParser(prog='annotateVcf',
                                         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -27,7 +27,7 @@ def main():
     required.add_argument("-vcf", "--vcf_file", type=str, dest="vcf_file", required=True,
                           default=None, help="vcf_file to annotate")
 
-    required.add_argument("-filter", "--vcf_filter", type=str, dest="vcf_filter", nargs='+',
+    optional.add_argument("-filter", "--vcf_filter", type=str, dest="vcf_filter", nargs='+',
                           required=False, default=['PASS'], help="Include variant sites \
                           matching vcf FILTER flag(s), multiple flags can be specified \
                           with space separator")
@@ -36,7 +36,8 @@ def main():
                           default=None, help="normal panel file to flag germline variant sites")
 
     optional.add_argument("-gt", "--germline_tag", type=str, dest="germline_tag", required=False,
-                          default="NPGL", help="tag to mark normal panel filtered variants in vcf INFO field")
+                          default="NPGL", help="tag to mark normal panel filtered variants in \
+                          vcf INFO field, only applicable when -np is set")
 
     optional.add_argument("-g", "--lof_genes", type=str, dest="lof_genes", required=False,
                           default=None, help="LoF gene name file to use annotations")

annotate/vcf_annotator.py

@@ -133,8 +133,8 @@ def annotate_lof_genes(self, genes_file, lof_types):
         :param lof_types: lof consequences type string
         :return:
         """
-        get_gene = re.compile(r'.*;VD=(\w+)|.*')
         # create dummy genome locationo file to annoate LoF genes...
+        get_gene = re.compile(r'\bVD=([-\w]+)')
         genome_loc_file = self.outdir + '/genome.tab.gz'
         create_dummy_genome(self.vcf_path, genome_loc_file)
         genes_outfile = self.outfile_name.format('_genes.vcf')
@@ -150,9 +150,10 @@ def annotate_lof_genes(self, genes_file, lof_types):
                 if line.startswith('#'):
                     lof_fh.write(line)
                 else:
-                    gene = line.split('VD=')[1].split('|')[0]
+                    gene = get_gene.search(line)[1]
+                    # gene = _get_gene('VD', 0))
                     # write matching LoF genes....
-                    if gene in lof_gene_list:
+                    if gene.upper() in lof_gene_list:
                         lof_fh.write(line)
         self.merge_vcf_dict['b'] = compress_vcf(lof_outfile)
 
@@ -171,9 +172,19 @@ def concat_results(self):
 
 
 # generic methods ....
+def _get_gene(line, gene_field, field_loc):
+    # Not used ... kept for future implementation of different annotation fields....
+    # ANN=T|missense_variant|MODERATE|AGAP005273|AGAP005273| [ e.g. 'ANN', 3]
+    # VD=TP5-TEST1-TEST2|CCDS11118.1|r.276_277insa|c.86_87insA|p.N29fs*14| [ e.g. 'VD', 0 ]
+    info_list = line.split("\t")[7].split(';')
+    info_dict = dict(f.split('=') for f in info_list if '=' in f)
+    gene = info_dict[gene_field].split('|')[field_loc]
+    return gene.upper()
+
+
 def get_drv_gene_list(drv_genes):
     with open(drv_genes) as f_drv:
-        lof_gene_list = f_drv.read().splitlines()
+        lof_gene_list = [gene.upper() for gene in f_drv.read().splitlines()]
     return lof_gene_list
 
 

setup.py

@@ -3,7 +3,7 @@
 from setuptools import setup
 
 config = {
-    'version': '1.1.3',
+    'version': '1.1.4',
     'name': 'annotateVcf',
     'description': 'Tool to annotate and filter vcf files...',
     'author': 'Shriram Bhosle',