first commit

longevity2reporter.md

@@ -0,0 +1,10 @@
+# Longevity2 reporter (pre alpha version) display your genome analysis related to longevity and disease risks
+
+It consist now of 3 parts:
+* Longevitymap report, show your longevity-related rsid and their influence.
+* Cancer report, show cancer risks.
+* Drug report, show how your genome influences drug effects.
+* Coranary disease report, lists snps that influence on chanses to have coranary disease.
+* Prs report, have poligenic risk scores.
+
+It deppends on annotators: dbsnp, clinvar, omim, ncbigene, pubmed, gnomad, vcfinfo.

longevity2reporter.py

@@ -0,0 +1,91 @@
+import json
+
+from cravat.cravat_report import CravatReport
+import sys
+import datetime
+import re
+import csv
+import zipfile
+from pathlib import Path
+import sqlite3
+from mako.template import Template
+
+class Reporter(CravatReport):
+
+    def __init__(self, args):
+        super().__init__(args)
+        self.savepath = args['savepath']
+
+
+    async def run(self):
+        self.setup()
+        self.write_data()
+        self.end()
+        pass
+
+
+    def setup(self):
+        self.input_database_path = f'{self.savepath}_longevity.sqlite'
+        self.db_conn = sqlite3.connect(self.input_database_path)
+        self.db_cursor = self.db_conn.cursor()
+        outpath = f'{self.savepath}.longevity2.html'
+        self.outfile = open(outpath, 'w', encoding='utf-8')
+        cur_path = str(Path(__file__).parent)
+        self.template = Template(filename=str(Path(__file__).parent)+"/template.html")
+
+
+    def write_table(self, name, json_fields = [], sort_field = "", sort_revers = False):
+        try:
+            sort_sql = ""
+            if sort_field != "":
+                sort_sql = " ORDER BY " + sort_field
+                if sort_revers:
+                    sort_sql = sort_sql+" DESC"
+                else:
+                    sort_sql = sort_sql+" ASC"
+
+            self.db_cursor.execute("SELECT * FROM "+name+sort_sql)
+            rows = self.db_cursor.fetchall()
+            res = []
+
+            for row in rows:
+                tmp = {}
+                for i, item in enumerate(self.db_cursor.description):
+                    if item[0] in json_fields:
+                        lst = json.loads(row[i])
+                        if len(lst) == 0:
+                            tmp[item[0]] = ""
+                        else:
+                            tmp[item[0]] = lst[0]
+                    else:
+                        tmp[item[0]] = row[i]
+                res.append(tmp)
+            self.data[name] = res
+        except Exception as e:
+            print("Warning:", e)
+
+
+    def write_data(self):
+        # self.data = {"test1":[1,2,3], "test2":["aa", "bbb", "cccc"]}
+        self.data = {}
+        self.write_table("prs", [], "id", True)
+        self.write_table("longevitymap", ["conflicted_rows", "description"], "weight", False)
+        self.write_table("cancer", [], "id", True)
+        self.write_table("coronary", [], "weight", False)
+        self.write_table("drugs", [], "id", True)
+
+
+    def end(self):
+        self.outfile.write(self.template.render(data=self.data))
+        self.outfile.close()
+        return Path(self.outfile.name).resolve()
+
+
+### Don't edit anything below here ###
+def main():
+    reporter = Reporter(sys.argv)
+    reporter.run()
+
+
+if __name__ == '__main__':
+    main()

longevity2reporter.yml

@@ -0,0 +1,32 @@
+title: Longevity2
+version: 0.3.0
+type: reporter
+description: Create report with longevity ralated information (pre alpha version). It deppends on postagregators .
+output_filename_schema:
+- '{run_name}.longevity2.html'
+developer:
+  name: DNA-seq
+  organization: DNA-seq
+  email: karmazinalex@gmail.com
+  website: https://github.com/dna-seq/opencravat-longevity
+  citation: ''
+requires:
+  - just_cancer
+  - just_coronary
+  - just_drugs
+  - just_longevitymap
+  - just_prs
+tags:
+- input/output
+- reporters
+- longevity
+data_version: 0.1.3
+release_note:
+0.1.0: initial version
+0.1.1: added prs support
+0.1.2: bugfix rsid for prs, template improved
+0.1.3: added Coronary arthery disease sub reporter, fixed bugs in prs sub report
+0.1.4: in coranary sub report added color signaling and sorted by weight results
+0.1.5: fixed bug in column acces for new version of oakvar
+0.2.0: changed to fit new oakvar, not compatible with previuse versions of oak var
+0.3.0: rebuilded reporter for new version of oakvar and postagregators