From d3a4146fd38fc1d372091cecadfcf7c8fb377f3b Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 25 May 2021 20:27:05 +0000
Subject: Include code that processes rqtl output files and returns actual
 results instead of just the output filename

---
 gn3/api/rqtl.py          | 16 +++++++++---
 gn3/computations/rqtl.py | 64 ++++++++++++++++++++++++++++++++++++++++++++++--
 2 files changed, 75 insertions(+), 5 deletions(-)

(limited to 'gn3')

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index de620f7..0194b6f 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -1,10 +1,13 @@
 """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
+from gn3.commands import run_cmd
+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__)
@@ -35,10 +38,17 @@ run the rqtl_wrapper script and return the results as JSON
             if kwarg in boolean_kwargs:
                 rqtl_bool_kwargs.append(kwarg)
 
-    results = generate_rqtl_cmd(
+    rqtl_cmd = generate_rqtl_cmd(
         rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
         rqtl_wrapper_kwargs=rqtl_kwargs,
         rqtl_wrapper_bool_kwargs=boolean_kwargs
     )
 
-    return jsonify(results)
+    os.system(rqtl_cmd.get('rqtl_cmd'))
+
+    rqtl_output = {}
+    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)
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 605e0e1..22d9faf 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,6 +1,11 @@
 """Procedures related rqtl computations"""
-
+import os
+import numpy as np
 from typing import Dict
+from typing import List
+
+from flask import current_app
+
 from gn3.commands import compose_rqtl_cmd
 from gn3.computations.gemma import generate_hash_of_string
 from gn3.fs_helpers import get_hash_of_files
@@ -29,7 +34,9 @@ output filename generated from a hash of the genotype and phenotype files
     # Temporarily substitute forward-slashes in hash with underscores
     _hash = _hash.replace("/", "_")
 
-    _output_filename = f"{_hash}-output.json"
+    _output_filename = f"{_hash}-output.csv"
+    rqtl_wrapper_kwargs["filename"] = _output_filename
+
     return {
         "output_file":
         _output_filename,
@@ -38,3 +45,56 @@ output filename generated from a hash of the genotype and phenotype files
                          rqtl_wrapper_kwargs=rqtl_wrapper_kwargs,
                          rqtl_wrapper_bool_kwargs=rqtl_wrapper_bool_kwargs)
     }
+
+
+def process_rqtl_output(file_name: str) -> List:
+    """Given an output file name, read in R/qtl results and return
+    a List of marker objects
+
+    """
+    marker_obs = []
+    # Later I should probably redo this using csv.read to avoid the
+    # awkwardness with removing quotes with [1:-1]
+    with open(os.path.join(current_app.config.get("TMPDIR"), "output", file_name), "r") as the_file:
+        for line in the_file:
+            line_items = line.split(",")
+            if line_items[1][1:-1] == "chr" or not line_items:
+                # Skip header line
+                continue
+            else:
+                # Convert chr to int if possible
+                try:
+                    the_chr = int(line_items[1][1:-1])
+                except:
+                    the_chr = line_items[1][1:-1]
+                this_marker = {
+                    "name": line_items[0][1:-1],
+                    "chr": the_chr,
+                    "cM": float(line_items[2]),
+                    "Mb": float(line_items[2]),
+                    "lod_score": float(line_items[3])
+                }
+                marker_obs.append(this_marker)
+
+    return marker_obs
+
+
+def process_perm_output(file_name: str):
+    """Given base filename, read in R/qtl permutation output and calculate
+    suggestive and significant thresholds
+
+    """
+    perm_results = []
+    with open(os.path.join(current_app.config.get("TMPDIR"), "output", "PERM_" + file_name), "r") as the_file:
+        for i, line in enumerate(the_file):
+            if i == 0:
+                # Skip header line
+                continue
+            else:
+                line_items = line.split(",")
+                perm_results.append(float(line_items[1]))
+
+    suggestive = np.percentile(np.array(perm_results), 67)
+    significant = np.percentile(np.array(perm_results), 95)
+
+    return perm_results, suggestive, significant
-- 
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