Feature/add drv type

Dockerfile

@@ -50,6 +50,7 @@ ENV PATH="$VIRTUAL_ENV/bin:$PATH"
 
 COPY annotate/ annotate/
 COPY README.md setup.py requirements.txt requirements_dev.txt run_tests.sh ./
+RUN pip install setuptools==57.5.0
 RUN pip install --no-cache-dir -r requirements_dev.txt
 COPY tests/ tests/
 #COPY .coveragerc .

README.md

@@ -22,31 +22,34 @@ This project hosts scripts to annotate VCF files using user defined driver genes
 
 ## Design
 
-Uses [bcftools], [tabix] and [bgzip] in user's path , these are part of [htslib] or can be installed separately
+Uses [bcftools], [tabix] and [bgzip] in user's path, which are part of
+[htslib] and [bcftools], and can be installed separately.
 
 ## Tools
 
 `annotateVcf` has multiple command line options, listed with `annotateVcf --help`.
 
 ### annotateVcf
-Takes vcf file as input along with driver gene information, and optional unmatched normal panel vcf and outputs VCF with added  DRV INFO field.
+
+Takes vcf file as input along with driver gene information, and optional
+unmatched normal panel vcf and outputs VCF with added  DRV INFO field.
 
 Various exceptions can occur for malformed input files.
 
 ### inputFormat
 
- * ```input_vcf.gz```  snv or indel vcf file annotated using [VAGrENT]
- * ```normal_panel.vcf.gz```  normal panel to tag germline variants
- * ```lof_genes.txt ``` list of known loss of function [LoF] genes along with previous gene symbols ( to make sure all gene synonyms were matched with input vcf)
- * ```cpg_variants.tsv.gz``` list of variants in cancer predisposition genes to tag germline predisposition variants
- * ```filters.json``` filters to be applied during driver annotations ( see default file ```filters.josn``` in config  folder)
- * ```driver_mutations.tsv.gz``` tab separated driver mutations along with consequence type 
- * ```info.header``` vcf header INFO line showing driver and cancer predisposition annotations...
+ * `input_vcf.gz`  snv or indel vcf file annotated using [VAGrENT]
+ * `normal_panel.vcf.gz`  normal panel to tag germline variants
+ * `lof_genes.txt ` list of known loss of function [LoF] genes along with previous gene symbols (to make sure all gene synonyms were matched with input vcf)
+ * `cpg_variants.tsv.gz` list of variants in cancer predisposition genes to tag germline predisposition variants
+ * `filters.json` filters to be applied during driver annotations ( see default file `filters.josn` in config  folder)
+ * `driver_mutations.tsv.gz` tab separated driver mutations along with consequence type
+ * `info.header` vcf header INFO line showing driver and cancer predisposition annotations...
 
 ### outputFormat
 
- * ```<input>_drv.vcf.gz ``` output vcf file with DRV info field and consequence type if known, LoF in case annotated using LoF gene list, 
-CPV info field is added if variants in cancer predisposition genes are provided.
+ * `<input>_drv.vcf.gz` output vcf file with DRV info field and type of driver
+   instance (germline and/or somatic) overlapping with variant location.
 
 ## INSTALL
 Installing via `pip install`. Simply execute with the path to the compiled 'whl' found on the [release page][annotateVcf-releases]:
@@ -55,25 +58,26 @@ Installing via `pip install`. Simply execute with the path to the compiled 'whl'
 pip install annotateVcf.X.X.X-py3-none-any.whl
 ```
 
-Release `.whl` files are generated as part of the release process and can be found on the [release page][annotateVcf-releases]
+Release `.whl` files are generated as part of the release process and can be
+found on the [release page][annotateVcf-releases]
 
 ## Development environment
 
-This project uses git pre-commit hooks.  As these will execute on your system it
-is entirely up to you if you activate them.
+This project uses git pre-commit hooks.  As these will execute on your system
+it is entirely up to you if you activate them.
 
-If you want tests, coverage reports and lint-ing to automatically execute before
-a commit you can activate them by running:
+If you want tests, coverage reports and lint-ing to automatically execute
+before a commit you can activate them by running:
 
 ```
 git config core.hooksPath git-hooks
 ```
 
-Only a test failure will block a commit, lint-ing is not enforced (but please consider
-following the guidance).
+Only a test failure will block a commit, lint-ing is not enforced (but please
+consider following the guidance).
 
-You can run the same checks manually without a commit by executing the following
-in the base of the clone:
+You can run the same checks manually without a commit by executing the
+following in the base of the clone:
 
 ```bash
 ./run_tests.sh
@@ -102,6 +106,7 @@ source env/bin/activate # if not already in env
 pip install pytest
 pip install radon
 pip install pytest-cov
+pip install pyvcf3
 ```
 
 __Also see__ [Package Dependancies](#package-dependancies)
@@ -132,8 +137,9 @@ pip install --find-links=~/wheels annotateVcf
 <!--refs-->
  [htslib]: https://github.com/samtools/htslib
  [bcftools]: https://github.com/samtools/bcftools
+ [pyvcf3]: https://github.com/dridk/PyVCF3
  [tabix]: https://github.com/samtools/tabix
- [VAGrENT]: https://github.com/cancerit/VAGrENT 
+ [VAGrENT]: https://github.com/cancerit/VAGrENT
  [travis-master-badge]: https://travis-ci.org/cancerit/annotateVCF.svg?branch=master
  [travis-develop-badge]: https://travis-ci.org/cancerit/annotateVCF.svg?branch=develop
  [travis-repo]: https://travis-ci.org/cancerit/annotateVCF

annotate/commandline.py

@@ -49,8 +49,6 @@
 
 
 def main():
-    usage = "\n %prog [options] -vcf input.vcf [-filter -np -gt -g -m -lof -hl -o ]"
-
     optParser = argparse.ArgumentParser(prog='annotateVcf',
                                         formatter_class=argparse.ArgumentDefaultsHelpFormatter)
     optional = optParser._action_groups.pop()
@@ -90,14 +88,12 @@ def main():
     optional.add_argument("-q", "--quiet", action="store_false", dest="verbose", required=False, default=True)
 
     optParser._action_groups.append(optional)
-    if len(sys.argv) == 0:
-        optParser.print_help()
-        sys.exit(1)
     opts = optParser.parse_args()
     if not opts.vcf_file:
-        sys.exit('\nERROR Arguments required\n\tPlease run: annotateVcf --help\n')
-    print("Annotating VCF file")
+        optParser.print_help()
+        sys.exit('\nMissing ivcf/--vcf_file argument\n')
 
+    print("Annotating VCF file")
     # vars function returns __dict__ of Namespace instance
     my_formatter = formatter.IO_Formatter(**vars(opts))
     outdir_path = my_formatter.format(['outdir'])

annotate/config/filters.json

@@ -9,9 +9,11 @@
       "INFO": "INFO/VC=\"stop_lost,start_lost,ess_splice,frameshift,nonsense\"",
       "INFO_FLAG_GERMLINE": "NPGL"
     },
-
+    "driver_type": {
+      "DRV": "somatic",
+      "CPV": "germline"
+    },
     "exclude": {
       "None": null
     }
-}
-
+}

annotate/config/info.header

@@ -1,2 +1,2 @@
-##INFO=<ID=DRV,Number=., Type=String, Description="Driver Variant Class">
-##INFO=<ID=CPV,Number=., Type=String, Description="Cancer Predisposition Variant">
+##INFO=<ID=DRV,Number=., Type=String, Description="Driver Class (germline:cancer predisposition variant, somatic:somatic driver variant)">
+##INFO=<ID=CPV,Number=., Type=String, Description="Cancer Predisposition Variant(intermediate field, not used in annotated VCF)">

annotate/io_formatter.py

@@ -84,6 +84,8 @@ def _get_formatter(self, input_type):
             return self._check_input
         elif input_type == 'vcf_filters':
             return self._get_filters
+        elif input_type == 'drv_type':
+            return self._get_driver_type
         else:
             raise ValueError(input_type)
 
@@ -94,7 +96,7 @@ def _check_input(self):
         """
         input_status = check_inputs({'vcf_file': self.vcf_file, 'normal_panel': self.np_vcf,
                                      'mutations': self.muts_file, 'lof_genes': self.genes_file,
-                        'cancer_predisposition': self.cpv_file})
+                                     'cancer_predisposition': self.cpv_file})
         if input_status['vcf_file'] is None:
             sys.exit("Please provide input vcf file")
         return input_status
@@ -106,10 +108,17 @@ def _get_filters(self):
         """
           load parameters from json config file
         """
-        inc_filters = ['FORMAT', 'FILTER', 'INFO', 'INFO_FLAG_GERMLINE']
-        formatted_filters = parse_filters(self.json_file, 'include', inc_filters)
+        formatted_filters = parse_filters(self.json_file, 'include')
         return formatted_filters
 
+    def _get_driver_type(self):
+        """
+        get driver types from user provided json file
+        :return: driver type dictionary
+        """
+        driver_type = parse_filters(self.json_file, 'driver_type')
+        return driver_type
+
     def _get_outdir_path(self):
         """
          formatter function: add default output directory
@@ -119,8 +128,6 @@ def _get_outdir_path(self):
         os.makedirs(outputPath, exist_ok=True)
         return outputPath
 
-    # generic functions ....
-
 
 def check_inputs(file_dict):
     """
@@ -150,7 +157,7 @@ def get_file_metadata(full_file_name):
     return file_metadata
 
 
-def parse_filters(json_file, filter_type, filters):
+def parse_filters(json_file, filter_type):
     """
       load filtering parameters from json config file
     """
@@ -160,7 +167,7 @@ def parse_filters(json_file, filter_type, filters):
             sys.exit('Json configuration file must be provided')
         with open(json_file, 'r') as cfgfile:
             filter_cfg = json.load(cfgfile)
-            for filter in filters:
+            for filter in filter_cfg[filter_type]:
                 filter_param_dict[filter] = filter_cfg[filter_type][filter]
     except json.JSONDecodeError as jde:
         sys.exit('json error:{}'.format(jde.args[0]))