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-rw-r--r--gn3/computations/heatmap.py7
-rw-r--r--gn3/computations/qtlreaper.py27
2 files changed, 18 insertions, 16 deletions
diff --git a/gn3/computations/heatmap.py b/gn3/computations/heatmap.py
index 92014cf..1143450 100644
--- a/gn3/computations/heatmap.py
+++ b/gn3/computations/heatmap.py
@@ -6,6 +6,7 @@ generate various kinds of heatmaps.
from functools import reduce
from typing import Any, Dict, Sequence
from gn3.computations.slink import slink
+from gn3.computations.qtlreaper import generate_traits_file
from gn3.computations.correlations2 import compute_correlation
from gn3.db.genotypes import build_genotype_file, load_genotype_samples
from gn3.db.traits import (
@@ -155,14 +156,14 @@ def heatmap_data(traits_names, conn: Any):
for fullname in traits_names]
traits_list = tuple(x[0] for x in traits_details)
traits_data_list = [x[1] for x in traits_details]
- exported_traits_data_list = tuple(
- export_trait_data(td, strainlist) for td in traits_data_list)
genotype_filename = build_genotype_file(traits_list[0]["riset"])
strainlist = load_genotype_samples(genotype_filename)
+ exported_traits_data_list = tuple(
+ export_trait_data(td, strainlist) for td in traits_data_list)
slink_data = slink(cluster_traits(exported_traits_data_list))
ordering_data = compute_heatmap_order(slink_data)
strains_and_values = retrieve_strains_and_values(
- orders, strainlist, exported_traits_data_list)
+ ordering_data, strainlist, exported_traits_data_list)
strains_values = strains_and_values[0][1]
trait_values = [t[2] for t in strains_and_values]
traits_filename = generate_traits_filename()
diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py
index 3b8e4db..30c7051 100644
--- a/gn3/computations/qtlreaper.py
+++ b/gn3/computations/qtlreaper.py
@@ -3,17 +3,10 @@ This module contains functions to interact with the `qtlreaper` utility for
computation of QTLs.
"""
import os
-import random
-import string
import subprocess
+from gn3.random import random_string
from gn3.settings import TMPDIR, REAPER_COMMAND
-def random_string(length):
- """Generate a random string of length `length`."""
- return "".join(
- random.choices(
- string.ascii_letters + string.digits, k=length))
-
def generate_traits_file(strains, trait_values, traits_filename):
"""
Generate a traits file for use with `qtlreaper`.
@@ -25,11 +18,13 @@ def generate_traits_file(strains, trait_values, traits_filename):
computation of QTLs.
"""
header = "Trait\t{}\n".format("\t".join(strains))
- data = [header] + [
- "T{}\t{}\n".format(i+1, "\t".join([str(i) for i in t]))
- for i, t in enumerate(trait_values[:-1])] + [
- "T{}\t{}".format(len(trait_values), "\t".join([str(i) for i in t]))
- for t in trait_values[-1:]]
+ data = (
+ [header] +
+ ["T{}\t{}\n".format(i+1, "\t".join([str(i) for i in t]))
+ for i, t in enumerate(trait_values[:-1])] +
+ ["T{}\t{}".format(
+ len(trait_values), "\t".join([str(i) for i in t]))
+ for t in trait_values[-1:]])
with open(traits_filename, "w") as outfile:
outfile.writelines(data)
@@ -93,6 +88,9 @@ def run_reaper(
def parse_reaper_main_results(results_file):
+ """
+ Parse the results file of running QTLReaper into a list of dicts.
+ """
with open(results_file, "r") as infile:
lines = infile.readlines()
@@ -104,6 +102,9 @@ def parse_reaper_main_results(results_file):
return [dict(zip(header, __parse_line(line))) for line in lines[1:]]
def parse_reaper_permutation_results(results_file):
+ """
+ Parse the results QTLReaper permutations into a list of values.
+ """
with open(results_file, "r") as infile:
lines = infile.readlines()