diff options
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/heatmap.py | 7 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 27 |
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() |