Initial commit

Author: furkanmtorun

gnomad_python_api.py

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+# gnomAD Python API by @furkanmtorun 
+# [[email protected]](mailto:[email protected]) 
+# | GitHub: [@furkanmtorun](https://github.com/furkanmtorun)  
+# | [Google Scholar](https://scholar.google.com/citations?user=d5ZyOZ4AAAAJ) 
+# | [Personal Website](https://furkanmtorun.github.io/)
+
+# Import required libraries and packages
+from pandas.io.json import json_normalize as json_normalize
+from tqdm import tqdm
+import pandas as pd
+import requests
+import argparse
+import json
+import os
+
+# Create a folder for outputs in the current directory
+if not os.path.exists('outputs/'):
+    os.mkdir('outputs/')
+
+# Argument parsing
+def arg_parser():
+    global filter_by
+    global search_by
+    global dataset
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-filter_by", type=str, required=True, default="gene_name", help="Get your variants according to: gene_name, gene_id or transcript_id ")
+    parser.add_argument("-search_by", type=str, required=True, default="TP53", help="Type the Ensembl Gene ID or Gene Name or the file name (e.g: myGenes.txt) containing genes")
+    parser.add_argument("-dataset", type=str, required=True, default="gnomad_r2_1", help="Select your dataset: exac, gnomad_r2_1, gnomad_r3, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed")
+    args = parser.parse_args()
+    if args.dataset not in ["exac", "gnomad_r2_1", "gnomad_r3", "gnomad_r2_1_controls", "gnomad_r2_1_non_neuro", "gnomad_r2_1_non_cancer", "gnomad_r2_1_non_topmed"]:
+        print("! Select a proper gnomAD data set:\n\texac, gnomad_r2_1, gnomad_r3, gnomad_r2_1_controls, gnomad_r2_1_non_neuro, gnomad_r2_1_non_cancer, gnomad_r2_1_non_topmed")
+    if args.filter_by not in ["gene_name", "gene_id", "transcript_id"]:
+        print("! Select a proper filter type :\n\tgene_name, gene_id or transcript_id")
+    filter_by = args.filter_by
+    search_by = args.search_by
+    dataset = args.dataset
+
+# gnomAD Parameters and API Function
+end_point = "https://gnomad.broadinstitute.org/api/"
+
+def get_variants_by(filter_by, search_term, dataset, timeout=None):
+    query = """
+    {
+      %s(%s: "%s") {
+        variants(dataset: %s) {
+          gene_id
+          gene_symbol
+          chrom
+          pos
+          rsid
+          ref
+          alt
+          consequence
+          genome {
+            genome_af:af
+            genome_ac:ac
+            genome_an:an
+            genome_ac_hemi:ac_hemi
+            genome_ac_hom:ac_hom
+          }
+          exome {
+            exome_af:af
+            exome_ac:ac
+            exome_an:an
+            exome_ac_hemi:ac_hemi
+            exome_ac_hom:ac_hom
+          }
+          flags
+          lof
+          consequence_in_canonical_transcript
+          gene_symbol
+          hgvsc
+          lof_filter
+          lof_flags
+          hgvsc
+          hgvsp
+          reference_genome
+          variant_id: variantId
+        }
+      }
+    }
+    """
+    if filter_by == "transcript_id":
+        query = query % ("transcript", filter_by, search_term, dataset)
+    else:
+        query = query % ("gene", filter_by, search_term, dataset)
+    response = requests.post(end_point, data={'query': query}, timeout=timeout)
+    if response.status_code == 200:
+        try:
+            if filter_by == "transcript_id":
+                data = json_normalize(response.json()["data"]["transcript"]["variants"])
+            else:
+                data = json_normalize(response.json()["data"]["gene"]["variants"])
+            data.columns = data.columns.map(lambda x: x.split(".")[-1])
+            data.to_csv("outputs/" + search_term + ".tsv", sep="\t", index=False) 
+            # return data
+        except (KeyError, TypeError):
+            print(str(response["error"]))
+        except (ConnectionError, ConnectionAbortedError, ConnectionRefusedError, ConnectionResetError):
+            print("An unknown error occured regarding the internet connection!")
+    elif response.status_code == 404:
+        print('API is not accessible right now. Check the end point out!')
+
+# Action
+if __name__ == "__main__":
+    arg_parser()
+    if "." in search_by.upper():
+        try:
+            with open(search_by, "r") as f:
+                gene_list = [line.rstrip() for line in f]
+                for tmp_gene in tqdm(gene_list):
+                    get_variants_by(filter_by, tmp_gene.upper(), dataset)
+        except:
+            print("A problem occured while reading the file namely {} or the type {} you selected is wrong!"\
+                  .format(search_by, filter_by))
+        finally:
+            f.close()
+    elif "." not in search_by.upper():
+        get_variants_by(filter_by, search_by.upper(), dataset)

requirements.txt

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+pandas
+requests
+tqdm
+argparse