diff options
| -rw-r--r-- | gn3/computations/heatmap.py | 7 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 27 | ||||
| -rw-r--r-- | gn3/db/traits.py | 5 | ||||
| -rw-r--r-- | gn3/heatmaps/heatmaps.py | 25 | ||||
| -rw-r--r-- | gn3/random.py | 11 | ||||
| -rw-r--r-- | tests/unit/computations/test_qtlreaper.py | 5 |
6 files changed, 55 insertions, 25 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() diff --git a/gn3/db/traits.py b/gn3/db/traits.py index ccb101a..bfe887e 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,6 +1,8 @@ """This class contains functions relating to trait data manipulation""" -from gn3.settings import TMPDIR +import os from typing import Any, Dict, Union, Sequence +from gn3.settings import TMPDIR +from gn3.random import random_string from gn3.function_helpers import compose from gn3.db.datasets import retrieve_trait_dataset @@ -669,5 +671,6 @@ def retrieve_trait_data(trait: dict, conn: Any, strainlist: Sequence[str] = tupl return {} def generate_traits_filename(base_path: str = TMPDIR): + """Generate a unique filename for use with generated traits files.""" return "{}/traits_test_file_{}.txt".format( os.path.abspath(base_path), random_string(10)) diff --git a/gn3/heatmaps/heatmaps.py b/gn3/heatmaps/heatmaps.py index 3bf7917..88f546d 100644 --- a/gn3/heatmaps/heatmaps.py +++ b/gn3/heatmaps/heatmaps.py @@ -14,6 +14,19 @@ def generate_random_data(data_stop: float = 2, width: int = 10, height: int = 30 return [[random.uniform(0,data_stop) for i in range(0, width)] for j in range(0, height)] +def generate_random_data2(data_stop: float = 2, width: int = 10, height: int = 30): + """ + This is mostly a utility function to be used to generate random data, useful + for development of the heatmap generation code, without access to the actual + database data. + """ + return [ + [{ + "value": item, + "category": random.choice(["C57BL/6J +", "DBA/2J +"])} + for item in axis] + for axis in generate_random_data(data_stop, width, height)] + def heatmap_x_axis_names(): return [ "UCLA_BXDBXH_CARTILAGE_V2::ILM103710672", @@ -30,13 +43,14 @@ def heatmap_x_axis_names(): # Grey + Blue + Red def generate_heatmap(): - rows = 20 - data = generate_random_data(height=rows) - y = (["%s"%x for x in range(1, rows+1)][:-1] + ["X"]) #replace last item with x for now + cols = 20 + y_axis = (["%s"%x for x in range(1, cols+1)][:-1] + ["X"]) #replace last item with x for now + x_axis = heatmap_x_axis_names() + data = generate_random_data(height=cols, width=len(x_axis)) fig = px.imshow( data, - x=heatmap_x_axis_names(), - y=y, + x=x_axis, + y=y_axis, width=500) fig.update_traces(xtype="array") fig.update_traces(ytype="array") @@ -49,6 +63,5 @@ def generate_heatmap(): coloraxis_colorscale=[ [0.0, '#3B3B3B'], [0.4999999999999999, '#ABABAB'], [0.5, '#F5DE11'], [1.0, '#FF0D00']]) - fig.write_html("%s/%s"%(heatmap_dir, "test_image.html")) return fig diff --git a/gn3/random.py b/gn3/random.py new file mode 100644 index 0000000..f0ba574 --- /dev/null +++ b/gn3/random.py @@ -0,0 +1,11 @@ +""" +Functions to generate complex random data. +""" +import random +import string + +def random_string(length): + """Generate a random string of length `length`.""" + return "".join( + random.choices( + string.ascii_letters + string.digits, k=length)) diff --git a/tests/unit/computations/test_qtlreaper.py b/tests/unit/computations/test_qtlreaper.py index ec23664..6c3b64d 100644 --- a/tests/unit/computations/test_qtlreaper.py +++ b/tests/unit/computations/test_qtlreaper.py @@ -1,5 +1,4 @@ """Module contains tests for gn3.computations.qtlreaper""" -import os from unittest import TestCase from gn3.computations.qtlreaper import ( parse_reaper_main_results, parse_reaper_permutation_results) @@ -8,6 +7,7 @@ class TestQTLReaper(TestCase): """Class for testing qtlreaper interface functions.""" def test_parse_reaper_main_results(self): + """Test that the main results file is parsed correctly.""" self.assertEqual( parse_reaper_main_results( "tests/unit/computations/data/qtlreaper/main_output_sample.txt"), @@ -65,9 +65,10 @@ class TestQTLReaper(TestCase): ]) def test_parse_reaper_permutation_results(self): + """Test that the permutations results file is parsed correctly.""" self.assertEqual( parse_reaper_permutation_results( - "tests/unit/computations/data/qtlreaper/permu_output_sample.txt"), + "tests/unit/computations/data/qtlreaper/permu_output_sample.txt"), [4.44174, 5.03825, 5.08167, 5.18119, 5.18578, 5.24563, 5.24619, 5.24619, 5.27961, 5.28228, 5.43903, 5.50188, 5.51694, 5.56830, 5.63874, 5.71346, 5.71936, 5.74275, 5.76764, 5.79815, 5.81671, |