From 624ece086d026da9150cd35b2404874ccf607b07 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 21:56:51 +0000
Subject: Created compose_rqtl_command and generate_rqtl_command to create the
 actual command to be run from the command line; used the same pattern as for
 GEMMA for consistency

---
 gn3/computations/rqtl.py | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)
 create mode 100644 gn3/computations/rqtl.py

(limited to 'gn3/computations')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
new file mode 100644
index 0000000..087a99f
--- /dev/null
+++ b/gn3/computations/rqtl.py
@@ -0,0 +1,25 @@
+"""Procedures related rqtl computations"""
+import os
+
+from typing import Dict
+from gn3.commands import compose_rqtl_cmd
+from gn3.fs_helpers import get_hash_of_files
+
+def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
+                      output_dir: str,
+                      rqtl_wrapper_kwargs: Dict) -> Dict:
+
+    _hash = get_hash_of_files(
+        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p", "addcovar",
+                                                    "model", "method",
+                                                    "interval", "nperm",
+                                                    "scale", "control"]])
+
+    _output_filename = f"{_hash}-output.json"
+    return {
+        "output_file":
+        _output_filename,
+        "rqtl_cmd":
+        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+    }
\ No newline at end of file
-- 
cgit v1.2.3


From 0a8754a582f057bd335441eab15da3f629df9ad7 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 17 May 2021 23:56:10 +0000
Subject: Fixed variety of issues detected by pylint

---
 gn3/api/rqtl.py          | 13 ++++++-------
 gn3/computations/rqtl.py | 50 ++++++++++++++++++++++++------------------------
 2 files changed, 31 insertions(+), 32 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 82cf34f..7756310 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -1,5 +1,4 @@
-import os
-
+"""Endpoints for running the rqtl cmd"""
 from flask import Blueprint
 from flask import current_app
 from flask import jsonify
@@ -12,8 +11,10 @@ rqtl = Blueprint("rqtl", __name__)
 
 @rqtl.route("/compute", methods=["POST"])
 def compute():
-    working_dir = os.path.join(current_app.config.get("TMPDIR"))
+    """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']
 
@@ -28,10 +29,8 @@ def compute():
             rqtl_kwargs[kwarg] = request.form[kwarg]
 
     results = generate_rqtl_cmd(
-        rqtl_wrapper_cmd = current_app.config.get("RQTL_WRAPPER_CMD"),
-        output_dir = current_app.config.get('TMPDIR'),
-        rqtl_wrapper_kwargs = rqtl_kwargs
+        rqtl_wrapper_cmd=current_app.config.get("RQTL_WRAPPER_CMD"),
+        rqtl_wrapper_kwargs=rqtl_kwargs
     )
 
     return jsonify(results)
-
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 087a99f..0e8cd1f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,25 +1,25 @@
-"""Procedures related rqtl computations"""
-import os
-
-from typing import Dict
-from gn3.commands import compose_rqtl_cmd
-from gn3.fs_helpers import get_hash_of_files
-
-def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
-                      output_dir: str,
-                      rqtl_wrapper_kwargs: Dict) -> Dict:
-
-    _hash = get_hash_of_files(
-        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p", "addcovar",
-                                                    "model", "method",
-                                                    "interval", "nperm",
-                                                    "scale", "control"]])
-
-    _output_filename = f"{_hash}-output.json"
-    return {
-        "output_file":
-        _output_filename,
-        "rqtl_cmd":
-        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
-                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
-    }
\ No newline at end of file
+"""Procedures related rqtl computations"""
+
+from typing import Dict
+from gn3.commands import compose_rqtl_cmd
+from gn3.fs_helpers import get_hash_of_files
+
+def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
+                      rqtl_wrapper_kwargs: Dict) -> Dict:
+    """Given the base rqtl_wrapper command and
+dict of keyword arguments, return the full rqtl_wrapper command and an
+output filename generated from a hash of the genotype and phenotype files
+
+    """
+
+    _hash = get_hash_of_files(
+        [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
+
+    _output_filename = f"{_hash}-output.json"
+    return {
+        "output_file":
+        _output_filename,
+        "rqtl_cmd":
+        compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+    }
-- 
cgit v1.2.3


From 74bc179807e80c1ee0f89cd98953263f68a05661 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 18 May 2021 19:40:46 +0000
Subject: Fixed generate_rqtl_cmd to make the kwarg hash from a combination of
 keywords and arguments + account for boolean kwargs without values (like
 --interval or --covar)

---
 gn3/computations/rqtl.py | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 0e8cd1f..855a819 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -2,24 +2,36 @@
 
 from typing import Dict
 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
 
 def generate_rqtl_cmd(rqtl_wrapper_cmd: str,
-                      rqtl_wrapper_kwargs: Dict) -> Dict:
+                      rqtl_wrapper_kwargs: Dict,
+                      rqtl_wrapper_bool_kwargs: list) -> Dict:
     """Given the base rqtl_wrapper command and
 dict of keyword arguments, return the full rqtl_wrapper command and an
 output filename generated from a hash of the genotype and phenotype files
 
     """
 
+    # Generate a hash from contents of the genotype and phenotype files
     _hash = get_hash_of_files(
         [v for k, v in rqtl_wrapper_kwargs.items() if k in ["g", "p"]])
 
+    # Append to hash a hash of keyword arguments
+    _hash += generate_hash_of_string(
+        ",".join([f"{k}:{v}" for k, v in rqtl_wrapper_kwargs.items() if k not in ["g", "p"]]))
+
+    # Append to hash a hash of boolean keyword arguments
+    _hash += generate_hash_of_string(
+        ",".join(rqtl_wrapper_bool_kwargs))
+
     _output_filename = f"{_hash}-output.json"
     return {
         "output_file":
         _output_filename,
         "rqtl_cmd":
         compose_rqtl_cmd(rqtl_wrapper_cmd=rqtl_wrapper_cmd,
-                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs)
+                         rqtl_wrapper_kwargs=rqtl_wrapper_kwargs,
+                         rqtl_wrapper_bool_kwargs=rqtl_wrapper_bool_kwargs)
     }
-- 
cgit v1.2.3


From e29a349b46d932411879a810fb0be3a0042bf540 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 19 May 2021 20:03:01 +0000
Subject: Temporarily replace forward-slashes with underscores, since they can
 be included in the hashes used for filenames

---
 gn3/computations/rqtl.py | 3 +++
 1 file changed, 3 insertions(+)

(limited to 'gn3/computations')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 855a819..605e0e1 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -26,6 +26,9 @@ output filename generated from a hash of the genotype and phenotype files
     _hash += generate_hash_of_string(
         ",".join(rqtl_wrapper_bool_kwargs))
 
+    # Temporarily substitute forward-slashes in hash with underscores
+    _hash = _hash.replace("/", "_")
+
     _output_filename = f"{_hash}-output.json"
     return {
         "output_file":
-- 
cgit v1.2.3


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/computations')

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
-- 
cgit v1.2.3


From 07464f44f48895cc31ba2b088d6125e7777e1073 Mon Sep 17 00:00:00 2001
From: Alexander Kabui
Date: Sun, 30 May 2021 13:26:15 +0300
Subject: fix index error (#16)

---
 gn3/computations/correlations.py            | 2 +-
 tests/unit/computations/test_correlation.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index 25dd26d..f0ce502 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -247,7 +247,7 @@ def fetch_lit_correlation_data(
             cursor.execute(query_formatter(query,
                                            *tuple(reversed(query_values))))
             lit_corr_results = cursor.fetchone()
-        lit_results = (gene_id, lit_corr_results[1])\
+        lit_results = (gene_id, lit_corr_results[0])\
             if lit_corr_results else (gene_id, 0)
         return lit_results
     return (gene_id, 0)
diff --git a/tests/unit/computations/test_correlation.py b/tests/unit/computations/test_correlation.py
index d264738..5746adf 100644
--- a/tests/unit/computations/test_correlation.py
+++ b/tests/unit/computations/test_correlation.py
@@ -276,7 +276,7 @@ class TestCorrelation(TestCase):
          input trait mouse gene id and mouse gene id
         """
 
-        expected_db_results = [("val", x*0.1)
+        expected_db_results = [[x*0.1]
                                for x in range(1, 4)]
         conn = DataBase(expected_results=expected_db_results)
         expected_results = ("1", 0.1)
-- 
cgit v1.2.3


From cd921a4778d141b6dbbf9f60c178a4f681d47860 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 16 Jun 2021 19:40:03 +0000
Subject: Fixed spelling of coeffient to coefficient

---
 gn3/computations/correlations.py | 26 +++++++++++++-------------
 1 file changed, 13 insertions(+), 13 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/correlations.py b/gn3/computations/correlations.py
index f0ce502..0fe46ab 100644
--- a/gn3/computations/correlations.py
+++ b/gn3/computations/correlations.py
@@ -68,8 +68,8 @@ pearson,spearman and biweight mid correlation return value is rho and p_value
         "spearman": scipy.stats.spearmanr
     }
     use_corr_method = corr_mapping.get(corr_method, "spearman")
-    corr_coeffient, p_val = use_corr_method(primary_values, target_values)
-    return (corr_coeffient, p_val)
+    corr_coefficient, p_val = use_corr_method(primary_values, target_values)
+    return (corr_coefficient, p_val)
 
 
 def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
@@ -84,13 +84,13 @@ def compute_sample_r_correlation(trait_name, corr_method, trait_vals,
 
     if num_overlap > 5:
 
-        (corr_coeffient, p_value) =\
+        (corr_coefficient, p_value) =\
             compute_corr_coeff_p_value(primary_values=sanitized_traits_vals,
                                        target_values=sanitized_target_vals,
                                        corr_method=corr_method)
 
-        if corr_coeffient is not None:
-            return (trait_name, corr_coeffient, p_value, num_overlap)
+        if corr_coefficient is not None:
+            return (trait_name, corr_coefficient, p_value, num_overlap)
     return None
 
 
@@ -140,10 +140,10 @@ def compute_all_sample_correlation(this_trait,
 
         for sample_correlation in results:
             if sample_correlation is not None:
-                (trait_name, corr_coeffient, p_value,
+                (trait_name, corr_coefficient, p_value,
                  num_overlap) = sample_correlation
                 corr_result = {
-                    "corr_coeffient": corr_coeffient,
+                    "corr_coefficient": corr_coefficient,
                     "p_value": p_value,
                     "num_overlap": num_overlap
                 }
@@ -151,7 +151,7 @@ def compute_all_sample_correlation(this_trait,
                 corr_results.append({trait_name: corr_result})
     return sorted(
         corr_results,
-        key=lambda trait_name: -abs(list(trait_name.values())[0]["corr_coeffient"]))
+        key=lambda trait_name: -abs(list(trait_name.values())[0]["corr_coefficient"]))
 
 
 def benchmark_compute_all_sample(this_trait,
@@ -174,12 +174,12 @@ def benchmark_compute_all_sample(this_trait,
             trait_vals=this_vals,
             target_samples_vals=target_vals)
         if sample_correlation is not None:
-            (trait_name, corr_coeffient,
+            (trait_name, corr_coefficient,
              p_value, num_overlap) = sample_correlation
         else:
             continue
         corr_result = {
-            "corr_coeffient": corr_coeffient,
+            "corr_coefficient": corr_coefficient,
             "p_value": p_value,
             "num_overlap": num_overlap
         }
@@ -195,20 +195,20 @@ def tissue_correlation_for_trait(
         compute_corr_p_value: Callable = compute_corr_coeff_p_value) -> dict:
     """Given a primary tissue values for a trait and the target tissues values
     compute the correlation_cooeff and p value the input required are arrays
-    output -> List containing Dicts with corr_coefficient value,P_value and
+    output -> List containing Dicts with corr_coefficient value, P_value and
     also the tissue numbers is len(primary) == len(target)
 
     """
 
     # ax :todo assertion that length one one target tissue ==primary_tissue
 
-    (tissue_corr_coeffient,
+    (tissue_corr_coefficient,
      p_value) = compute_corr_p_value(primary_values=primary_tissue_vals,
                                      target_values=target_tissues_values,
                                      corr_method=corr_method)
 
     tiss_corr_result = {trait_id: {
-        "tissue_corr": tissue_corr_coeffient,
+        "tissue_corr": tissue_corr_coefficient,
         "tissue_number": len(primary_tissue_vals),
         "tissue_p_val": p_value}}
 
-- 
cgit v1.2.3


From 476b146562070cee6a55c55c03c37ef3e19a1474 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 20:54:18 +0000
Subject: Resolve mypy errors in computations/rqtl.py

---
 gn3/computations/rqtl.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 22d9faf..7b1a35c 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,8 +1,7 @@
 """Procedures related rqtl computations"""
 import os
 import numpy as np
-from typing import Dict
-from typing import List
+from typing import Dict, List, Union
 
 from flask import current_app
 
@@ -55,7 +54,7 @@ def process_rqtl_output(file_name: str) -> List:
     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:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "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:
@@ -63,6 +62,7 @@ def process_rqtl_output(file_name: str) -> List:
                 continue
             else:
                 # Convert chr to int if possible
+                the_chr: Union[int, str]
                 try:
                     the_chr = int(line_items[1][1:-1])
                 except:
@@ -85,7 +85,7 @@ def process_perm_output(file_name: str):
 
     """
     perm_results = []
-    with open(os.path.join(current_app.config.get("TMPDIR"), "output", "PERM_" + file_name), "r") as the_file:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", "PERM_" + file_name), "r") as the_file:
         for i, line in enumerate(the_file):
             if i == 0:
                 # Skip header line
-- 
cgit v1.2.3


From d42b85ae5fcea1b71a7165fd6e64745a228c48f9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 18 Jun 2021 21:13:03 +0000
Subject: Fixed pylint issues

---
 gn3/api/rqtl.py          |  7 ++++---
 gn3/computations/rqtl.py | 45 ++++++++++++++++++++++++---------------------
 2 files changed, 28 insertions(+), 24 deletions(-)

(limited to 'gn3/computations')

diff --git a/gn3/api/rqtl.py b/gn3/api/rqtl.py
index 38f4c1e..ebb746c 100644
--- a/gn3/api/rqtl.py
+++ b/gn3/api/rqtl.py
@@ -6,7 +6,6 @@ from flask import current_app
 from flask import jsonify
 from flask import request
 
-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
 
@@ -45,13 +44,15 @@ run the rqtl_wrapper script and return the results as JSON
     )
 
     rqtl_output = {}
-    if not os.path.isfile(os.path.join(current_app.config.get("TMPDIR"), "output", rqtl_cmd.get('output_file'))):
+    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'))
+        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 7b1a35c..0433b3f 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,8 +1,9 @@
 """Procedures related rqtl computations"""
 import os
-import numpy as np
 from typing import Dict, List, Union
 
+import numpy as np
+
 from flask import current_app
 
 from gn3.commands import compose_rqtl_cmd
@@ -54,27 +55,28 @@ def process_rqtl_output(file_name: str) -> List:
     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", "/tmp"), "output", file_name), "r") as the_file:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+                           "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
-                the_chr: Union[int, str]
-                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)
+
+            # Convert chr to int if possible
+            the_chr: Union[int, str]
+            try:
+                the_chr = int(line_items[1][1:-1])
+            except ValueError:
+                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
 
@@ -85,14 +87,15 @@ def process_perm_output(file_name: str):
 
     """
     perm_results = []
-    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"), "output", "PERM_" + file_name), "r") as the_file:
+    with open(os.path.join(current_app.config.get("TMPDIR", "/tmp"),
+                           "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]))
+
+            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)
-- 
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