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authorAlexander Kabui2021-06-20 09:11:03 +0300
committerAlexander Kabui2021-06-20 09:11:03 +0300
commit123ad47af288d6b94f0354a0abd5bc669bc988d4 (patch)
tree999eb41c1fab3d443215c0e4a8533abecf64f9af /gn3/api/rqtl.py
parent75801d83c8302b48051d413490e6ce2a0b8ff01f (diff)
parentd653a635d0efd2291754c18f51d31f91a1c0a25c (diff)
downloadgenenetwork3-123ad47af288d6b94f0354a0abd5bc669bc988d4.tar.gz
merge main
Diffstat (limited to 'gn3/api/rqtl.py')
-rw-r--r--gn3/api/rqtl.py58
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diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
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+++ b/gn3/api/rqtl.py
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+"""Endpoints for running the rqtl cmd"""
+import os
+
+from flask import Blueprint
+from flask import current_app
+from flask import jsonify
+from flask import request
+
+from gn3.computations.rqtl import generate_rqtl_cmd, process_rqtl_output, process_perm_output
+from gn3.computations.gemma import do_paths_exist
+
+rqtl = Blueprint("rqtl", __name__)
+
+@rqtl.route("/compute", methods=["POST"])
+def compute():
+    """Given at least a geno_file and pheno_file, generate and
+run the rqtl_wrapper script and return the results as JSON
+
+    """
+    genofile = request.form['geno_file']
+    phenofile = request.form['pheno_file']
+
+    if not do_paths_exist([genofile, phenofile]):
+        raise FileNotFoundError
+
+    # Split kwargs by those with values and boolean ones that just convert to True/False
+    kwargs = ["model", "method", "nperm", "scale", "control_marker"]
+    boolean_kwargs = ["addcovar", "interval", "pstrata"]
+    all_kwargs = kwargs + boolean_kwargs
+
+    rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
+    rqtl_bool_kwargs = []
+    for kwarg in all_kwargs:
+        if kwarg in request.form:
+            if kwarg in kwargs:
+                rqtl_kwargs[kwarg] = request.form[kwarg]
+            if kwarg in boolean_kwargs:
+                rqtl_bool_kwargs.append(kwarg)
+
+    rqtl_cmd = generate_rqtl_cmd(
+        rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
+        rqtl_wrapper_kwargs=rqtl_kwargs,
+        rqtl_wrapper_bool_kwargs=rqtl_bool_kwargs
+    )
+
+    rqtl_output = {}
+    if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"),
+                                       "output", rqtl_cmd.get('output_file'))):
+        os.system(rqtl_cmd.get('rqtl_cmd'))
+
+    rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+
+    rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+    if int(rqtl_kwargs['nperm']) > 0:
+        rqtl_output['perm_results'], rqtl_output['suggestive'], rqtl_output['significant'] = \
+        process_perm_output(rqtl_cmd.get('output_file'))
+
+    return jsonify(rqtl_output)