Included acmg verdict in annotated vcf

README.md

@@ -2,7 +2,7 @@
 
 ## A basic API client implementation for [api.varsome.com](https://api.varsome.com)
 
-This tool contains examples for the Varsome API usage. It can be used against either the production server ([api.varsome.com](https://api.varsome.com)) or the staging server ( ([staging-api.varsome.com](https://staging-api.varsome.com)))
+This tool contains examples for the Varsome API usage. It can be used against the production server ([api.varsome.com](https://api.varsome.com)), the staging server ([staging-api.varsome.com](https://staging-api.varsome.com)) or the stable api server ([stable-api.varsome.com](https://stable-api.varsome.com))
 
 ### Staging-api environment
 
@@ -69,6 +69,13 @@ Notice, however, that not all available annotations will be present in the `anno
 of the returned annotations will be available when running this script. See the "Using the client in your code" 
 section below for how to annotate a VCF file with the annotations that are of interest to you. 
 
+*Warning*: varsome_api_annotate_vcf.py can only deal with:
+
+- SNPs
+- small indels (up to 200bp)
+
+If you want to use this script please remove any variant from your VCF that does not meet the above criteria.
+
 ### Using the client in your code
 
 Using the API client is quite straightforward. Just install the API client package and use the following in your code:
@@ -77,7 +84,7 @@ Using the API client is quite straightforward. Just install the API client packa
 from varsome_api.client import VarSomeAPIClient
 # API key is not required for single variant lookups
 api_key = 'Your token'
-api = VarSomeAPIClient(api_key)
+api = VarSomeAPIClient(api_key, api_url="https://stable-api.varsome.com")
 # fetch information about a variant into a dictionary
 result = api.lookup('chr7-140453136-A-T', params={'add-source-databases': 'gnomad-exomes,refseq-transcripts'}, ref_genome='hg19')
 # access results e.g. the transcripts of the variant
@@ -105,7 +112,7 @@ except VarSomeAPIException as e:
 
 To view available request parameters (used by the `params` method parameter), refer to an example at [api.varsome.com](https://api.varsome.com).
 
-To understand how annotation properties are included in the JSON response, please refer to the relevant [schema](https://api.varsome.com/lookup/schema).
+To understand how annotation properties are included in the JSON response, please refer to the relevant [schema](https://api.varsome.com/docs/variants/).
 
 #### JSON response wrapper
 
@@ -171,7 +178,7 @@ To annotate the VCF file with the annotations that you are interested in, you ne
 
 ```python
 from varsome_api.vcf import VCFAnnotator
-from vcf.parser import _Info
+from vcf.parser import _Info, _encode_type
 class MyVCFAnnotator(VCFAnnotator):
 
     def annotate_record(self, record, variant_result):
@@ -192,8 +199,9 @@ class MyVCFAnnotator(VCFAnnotator):
         :param vcf_template: vcf reader object
         :return:
         """
-        vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', '.', 'Integer',
-                                                             'GnomAD exomes allele number value', None, None)
+        vcf_template.infos['gnomad_exomes_AN'] = _Info('gnomad_exomes_AN', 1, 'Integer',
+                                                       'GnomAD exomes allele number value', 
+                                                       None, None, _encode_type("Integer"),)
         # if you wish to also include the default headers
         # super().add_vcf_header_info(vcf_template)
 
@@ -217,9 +225,9 @@ To obtain an API key please [contact us](mailto:support@saphetor.com).
 
 Clone the repository, after creating a virtual environment, and run:
 
-    python setup.py test
+    pip install tox
+    tox
 
-Running the tests will install [nose](https://nose.readthedocs.io/en/latest/) in your virtual environment.
 To run the tests, set the `VARSOME_API_KEY` environment variable to your API token. Otherwise,
 tests will fail because the API will return a 401 (not authenticated) error.
 Be advised as well that running the tests will count towards your account request limit depending on the

scripts/varsome_api_annotate_vcf.py

@@ -15,42 +15,78 @@
 # limitations under the License.
 
 import argparse
-import sys
 
 from varsome_api.vcf import VCFAnnotator
 
-__author__ = 'ckopanos'
 
-
-def annotate_vcf(argv):
-    parser = argparse.ArgumentParser(description='VCF Annotator command line')
-    parser.add_argument('-k', help='Your key to the API', type=str, metavar='API Key', required=True)
-    parser.add_argument('-g', help='Reference genome either hg19 or hg38', type=str, metavar='Reference Genome',
-                        required=False, default='hg19')
-    parser.add_argument('-i',
-                        help='Path to vcf file',
-                        type=str, metavar='Input VCF File', required=True)
-    parser.add_argument('-o',
-                        help='Path to output vcf file',
-                        type=str, metavar='Output VCF File', required=False)
-    parser.add_argument('-p',
-                        help='Request parameters e.g. add-all-data=1 expand-pubmed-articles=0',
-                        type=str, metavar='Request Params', required=False, nargs='+')
-    parser.add_argument('-t', help='Run vcf annotator using x threads', type=int, default=3, required=False,
-                        metavar='Number of threads')
+def annotate_vcf():
+    parser = argparse.ArgumentParser(description="VCF Annotator command line")
+    parser.add_argument(
+        "-k", help="Your key to the API", type=str, metavar="API Key", required=True
+    )
+    parser.add_argument(
+        "-g",
+        help="Reference genome either hg19 or hg38",
+        type=str,
+        metavar="Reference Genome",
+        required=False,
+        default="hg19",
+    )
+    parser.add_argument(
+        "-i", help="Path to vcf file", type=str, metavar="Input VCF File", required=True
+    )
+    parser.add_argument(
+        "-o",
+        help="Path to output vcf file",
+        type=str,
+        metavar="Output VCF File",
+        required=False,
+    )
+    parser.add_argument(
+        "-p",
+        help="Request parameters e.g. add-all-data=1 add-ACMG-annotation=1",
+        type=str,
+        metavar="Request Params",
+        required=False,
+        nargs="+",
+    )
+    parser.add_argument(
+        "-t",
+        help="Run vcf annotator using x threads",
+        type=int,
+        default=3,
+        required=False,
+        metavar="Number of threads",
+    )
+    parser.add_argument(
+        "-u",
+        help="Use specific VarSome API host url "
+        "(e.g. https://api.varsome.com or https://stable-api.varsome.com",
+        type=str,
+        required=False,
+        metavar="VarSome API host url",
+    )
     args = parser.parse_args()
     api_key = args.k
     vcf_file = args.i
     output_vcf_file = args.o
     ref_genome = args.g
     num_threads = args.t
+    api_url = args.u
     request_parameters = None
     if args.p:
-        request_parameters = {param[0]: param[1] for param in [param.split("=") for param in args.p]}
-    vcf_annotator = VCFAnnotator(api_key=api_key, ref_genome=ref_genome, get_parameters=request_parameters,
-                                 max_threads=num_threads)
+        request_parameters = {
+            param[0]: param[1] for param in [param.split("=") for param in args.p]
+        }
+    vcf_annotator = VCFAnnotator(
+        api_key=api_key,
+        api_url=api_url,
+        ref_genome=ref_genome,
+        get_parameters=request_parameters,
+        max_threads=num_threads,
+    )
     vcf_annotator.annotate(vcf_file, output_vcf_file)
 
 
 if __name__ == "__main__":
-    annotate_vcf(sys.argv[1:])
+    annotate_vcf()