diff --git a/test/tiles/bedarcsdb.py b/test/tiles/bedarcsdb.py index 64ff032b..79c18734 100644 --- a/test/tiles/bedarcsdb.py +++ b/test/tiles/bedarcsdb.py @@ -10,7 +10,7 @@ def get_counts(filename, zoom, pos): for i, d in enumerate(data[0][1][pos]): chr1, chr2 = sorted([d['fields'][0], d['fields'][3]]) - #print('d:', d) + # print('d:', d) counts[(chr1, chr2)] += 1 return counts @@ -18,27 +18,29 @@ def get_counts(filename, zoom, pos): def test_bedarcsdb_tiles1(): filename = op.join( - 'data', '9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa.pcawg_consensus_1.6.161022.somatic.sv.bedpe.multires.db') + 'data', + '9ae0744a-9bc1-4cd7-b7cf-c6569ed9e4aa' + '.pcawg_consensus_1.6.161022.somatic.sv.bedpe.multires.db') tiles_to_get = [(2, 2)] for ttg in tiles_to_get: - counts = get_counts(filename, *ttg) + get_counts(filename, *ttg) # print(*ttg, counts) - #counts1 = get_counts(filename, 0,0) - #counts1 = get_counts(filename, 1,1) + # counts1 = get_counts(filename, 0,0) + # counts1 = get_counts(filename, 1,1) # counts2 = get_counts(filename, 2,2) # counts3 = get_counts(filename, 2,3) - #print('1,1', counts1) - #print('2,2', counts2) + # print('1,1', counts1) + # print('2,2', counts2) # print('2,3', counts3) - #print('1', counts1[('21', 'X')]) - #print('2', counts1[('21', 'X')]) + # print('1', counts1[('21', 'X')]) + # print('2', counts1[('21', 'X')]) - #print("1,1", get_counts(filename, 1,1)) - #print('2,2', get_counts(filename, 2,2)) + # print("1,1", get_counts(filename, 1,1)) + # print('2,2', get_counts(filename, 2,2)) ''' data = hgbad.tiles(filename, ["b.0.0"]) @@ -85,6 +87,6 @@ def test_bedarcsdb_tiles(): filename = op.join('data', 'arrowhead_domains_short.txt.multires.db') pos = 2 - data = hgbad.tiles(filename, ["b.2.{}".format(pos)]) + hgbad.tiles(filename, ["b.2.{}".format(pos)]) - pass + # TODO: Do something with the data we get back? diff --git a/test/tiles/beddb_test.py b/test/tiles/beddb_test.py index ceccb4d0..35d36e22 100644 --- a/test/tiles/beddb_test.py +++ b/test/tiles/beddb_test.py @@ -1,16 +1,16 @@ import clodius.tiles.beddb as hgbe -import json import os.path as op def test_get_tiles(): filename = op.join('data', 'corrected.geneListwithStrand.bed.multires') - ret = hgbe.tiles(filename, ['x.1.0', 'x.1.1']) + hgbe.tiles(filename, ['x.1.0', 'x.1.1']) + # TODO: Do something with the return value def test_list_items(): filename = op.join('data', 'gene_annotations.short.db') - ret = hgbe.list_items(filename, 0, 100000000, max_entries=100) - # print('ret:', ret) + hgbe.list_items(filename, 0, 100000000, max_entries=100) + # TODO: Do something with the return value diff --git a/test/tiles/bigwig_test.py b/test/tiles/bigwig_test.py index 1dbaae74..ed275812 100644 --- a/test/tiles/bigwig_test.py +++ b/test/tiles/bigwig_test.py @@ -96,12 +96,15 @@ def test_natsorted(): 'expected': ['1', '2', '3', '4', 'x', 'y', 'm'] }, { - 'input': ['chr1', 'chr4', 'chr5', 'chr2', 'chr3', 'chrMT', 'chrY', 'chrX'], - 'expected': ['chr1', 'chr2', 'chr3', 'chr4', 'chr5', 'chrX', 'chrY', 'chrMT'] + 'input': ['chr1', 'chr4', 'chr5', 'chr2', + 'chr3', 'chrMT', 'chrY', 'chrX'], + 'expected': ['chr1', 'chr2', 'chr3', 'chr4', + 'chr5', 'chrX', 'chrY', 'chrMT'] } ] for test in chromname_tests: sorted_output = hgbi.natsorted(test['input']) - assert sorted_output == test['expected'], 'Sorted output was %s\nExpected: %s' % ( - sorted_output, test['expected']) + assert sorted_output == test['expected'],\ + 'Sorted output was %s\nExpected: %s' \ + % (sorted_output, test['expected']) diff --git a/test/tiles/cooler_test.py b/test/tiles/cooler_test.py index 7b7fb55f..9d26a219 100644 --- a/test/tiles/cooler_test.py +++ b/test/tiles/cooler_test.py @@ -1,18 +1,18 @@ import clodius.tiles.cooler as hgco -import json import numpy as np import os.path as op +import base64 def test_cooler_info(): filename = op.join( 'data', 'Dixon2012-J1-NcoI-R1-filtered.100kb.multires.cool') - info = hgco.tileset_info(filename) + hgco.tileset_info(filename) + # TODO: Make assertion about info returned. tiles = hgco.generate_tiles(filename, ['a.0.0.0']) - import base64 r = base64.decodestring(tiles[0][1]['dense'].encode('utf-8')) q = np.frombuffer(r, dtype=np.float32) diff --git a/test/tiles/density_test.py b/test/tiles/density_test.py index 4e319e44..34b56702 100644 --- a/test/tiles/density_test.py +++ b/test/tiles/density_test.py @@ -6,7 +6,7 @@ def test_bundled_tiles(): filename = 'data/points_density.h5' - tiles = hgut.bundled_tiles_wrapper_2d(['c.2.0.0', 'c.2.1.1', 'c.2.0.1', 'c.2.1.0'], - ft.partial(hgde.tiles, filename)) + tiles = hgut.bundled_tiles_wrapper_2d( + ['c.2.0.0', 'c.2.1.1', 'c.2.0.1', 'c.2.1.0'], + ft.partial(hgde.tiles, filename)) assert(len(tiles) == 4) - return diff --git a/test/tiles/hitile_test.py b/test/tiles/hitile_test.py index b980db44..2eea8d41 100644 --- a/test/tiles/hitile_test.py +++ b/test/tiles/hitile_test.py @@ -1,11 +1,8 @@ import dask.array as da import h5py import clodius.tiles.hitile as hghi -import math import numpy as np import os.path as op -import random -import sys import tempfile diff --git a/test/tiles/multivec_test.py b/test/tiles/multivec_test.py index de4a7f3d..07fc6876 100644 --- a/test/tiles/multivec_test.py +++ b/test/tiles/multivec_test.py @@ -5,5 +5,5 @@ def test_multivec(): filename = op.join('data', 'all.KL.bed.multires.mv5') - tsinfo = hgmu.tileset_info(filename) - # print(hgmu.tileset_info(filename)) + hgmu.tileset_info(filename) + # TODO: Make assertions about info returned. diff --git a/test/tiles/npvector_test.py b/test/tiles/npvector_test.py index 67a7fe9c..be4fb2b8 100644 --- a/test/tiles/npvector_test.py +++ b/test/tiles/npvector_test.py @@ -7,4 +7,5 @@ def test_npvector(): # print('ts:', hgnv.tileset_info(array)) assert('max_width' in hgnv.tileset_info(array)) - tile = hgnv.tiles(array, 0, 0) + hgnv.tiles(array, 0, 0) + # TODO: Make assertions about tile returned. diff --git a/test/tiles/time_interval_test.py b/test/tiles/time_interval_test.py index fd4b966c..589c613c 100644 --- a/test/tiles/time_interval_test.py +++ b/test/tiles/time_interval_test.py @@ -5,5 +5,5 @@ def test_tileset_info(): filename = op.join('data', 'sample_htime.json') - tsinfo = hgti.tileset_info(filename) - # print(hgti.tileset_info(filename)) + hgti.tileset_info(filename) + # TODO: Make assertions about info returned. diff --git a/travis_test.sh b/travis_test.sh index f80c8d66..4c7bf061 100755 --- a/travis_test.sh +++ b/travis_test.sh @@ -13,10 +13,7 @@ flake8 --config=.flake8-ignore # TODO: Add more files to this list: flake8 test/tsv_to_mrmatrix_test.py \ scripts/tsv_to_mrmatrix.py \ - test/*.py -# TODO: When everything is covered, -# just lint the whole directory once, -# instead of listing special cases. + test/*/*.py end flake8 start download