From 337a20a45fa568490700edb043994ed98d9070ce Mon Sep 17 00:00:00 2001 From: kedhammar Date: Tue, 2 Jul 2024 10:13:22 +0000 Subject: [PATCH] limit scope of tests https://github.com/remiolsen/anglerfish/pull/85#discussion_r1654331636 --- .../test_anglerfish/test_demux/test_demux.py | 21 +------------------ 1 file changed, 1 insertion(+), 20 deletions(-) diff --git a/tests/test_anglerfish/test_demux/test_demux.py b/tests/test_anglerfish/test_demux/test_demux.py index 902a73f..ed8124b 100644 --- a/tests/test_anglerfish/test_demux/test_demux.py +++ b/tests/test_anglerfish/test_demux/test_demux.py @@ -88,6 +88,7 @@ def fixture(): def test_run_minimap2(fixture): + """Check that the function runs successfully, not the output.""" # Test alignment on single read to_test.run_minimap2( fastq_in=fixture["testdata_single"], @@ -97,10 +98,6 @@ def test_run_minimap2(fixture): minimap_b=1, ) - expected = "0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t302\t374\t+\ttruseq_i7\t67\t0\t67\t51\t64\t25\tNM:i:23\tms:i:275\tAS:i:266\tnn:i:10\ttp:A:P\tcm:i:5\ts1:i:29\ts2:i:0\tde:f:0.2388\trl:i:0\tcg:Z:11M2D33M7I21M\tcs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17\n0ad8bdb6-e009-43c5-95b1-d381e699f983\t418\t45\t110\t+\ttruseq_i5\t58\t0\t58\t56\t66\t38\tNM:i:10\tms:i:313\tAS:i:305\tnn:i:0\ttp:A:P\tcm:i:10\ts1:i:37\ts2:i:0\tde:f:0.0667\trl:i:0\tcg:Z:15M1D6M7I3M1I33M\tcs:Z::15-a*cg:5+tcccgat:3+g:33\n" - received = open(fixture["paf_single"]).read() - assert expected == received - # Create aligntment from multiple reads to_test.run_minimap2( fastq_in=fixture["testdata_multiple"], @@ -118,28 +115,12 @@ def test_map_reads_to_alns(fixture): assert read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983" for aln in alns: if aln.adapter_name == "truseq_i7": - assert aln.read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983" - assert aln.adapter_name == "truseq_i7" - assert aln.read_len == 418 - assert aln.read_start == 302 - assert aln.read_end == 374 - assert aln.read_strand == "+" - assert aln.cg == "cg:Z:11M2D33M7I21M" assert ( aln.cs == "cs:Z::11-ca:6*tg:13*nt*na*na*nc*nt*nt*ng*ng*nt*nc:1*ta:1+ctagaaa:2*gt*tg:17" ) - assert aln.q == 25 else: - assert aln.read_name == "0ad8bdb6-e009-43c5-95b1-d381e699f983" - assert aln.adapter_name == "truseq_i5" - assert aln.read_len == 418 - assert aln.read_start == 45 - assert aln.read_end == 110 - assert aln.read_strand == "+" - assert aln.cg == "cg:Z:15M1D6M7I3M1I33M" assert aln.cs == "cs:Z::15-a*cg:5+tcccgat:3+g:33" - assert aln.q == 38 def test_parse_cs(fixture):