From 971c5f1342770b999c62e345a9ebf942a0410758 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 26 Jul 2021 20:47:37 +0000
Subject: Added pairscan boolean kwarg and process_rqtl_pairscan function for
 reading in pairscan results + renamed process_rqtl_output to
 process_rqtl_mapping to distinguish between that and pairscan

---
 gn3/api/rqtl.py          |  8 +++++---
 gn3/computations/rqtl.py | 17 ++++++++++++++++-
 2 files changed, 21 insertions(+), 4 deletions(-)

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index ebb746c..ff76356 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -25,7 +25,7 @@ run the rqtl_wrapper script and return the results as JSON
 
     # 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"]
+    boolean_kwargs = ["addcovar", "interval", "pstrata", "pairscan"]
     all_kwargs = kwargs + boolean_kwargs
 
     rqtl_kwargs = {"geno": genofile, "pheno": phenofile}
@@ -48,9 +48,11 @@ run the rqtl_wrapper script and return the results as JSON
                                        "output", rqtl_cmd.get('output_file'))):
         os.system(rqtl_cmd.get('rqtl_cmd'))
 
-    rqtl_output['results'] = process_rqtl_output(rqtl_cmd.get('output_file'))
+    if "pairscan" in boolean_kwargs:
+        rqtl_output['results'] = process_rqtl_pairscan(rqtl_cmd.get('output_file'))
+    else:
+        rqtl_output['results'] = process_rqtl_mapping(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'))
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 0433b3f..405b743 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -47,7 +47,7 @@ output filename generated from a hash of the genotype and phenotype files
     }
 
 
-def process_rqtl_output(file_name: str) -> List:
+def process_rqtl_mapping(file_name: str) -> List:
     """Given an output file name, read in R/qtl results and return
     a List of marker objects
 
@@ -80,6 +80,21 @@ def process_rqtl_output(file_name: str) -> List:
 
     return marker_obs
 
+def process_rqtl_pairscan(file_name: str) -> List:
+    """Given an output file name, read in R/qtl pair-scan results and return
+    a List of Lists representing the matrix of results
+
+    """
+    results = []
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+                           "output", file_name), "r") as the_file:
+        for i, line in enumerate(the_file):
+            if i == 0: # Skip first line
+                continue
+            line_items = line.split(",")
+            results.append(line_items[1:]) # Append all but first item in line
+
+    return results
 
 def process_perm_output(file_name: str):
     """Given base filename, read in R/qtl permutation output and calculate
-- 
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