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added test for y-str filtering
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rnmitchell committed Aug 14, 2024
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42 changes: 42 additions & 0 deletions lusSTR/tests/data/powerseq_example_evidence_ngs.csv
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Locus,CE Allele,Allele Seq,Reads
DYS19,13.0,TAGATAGATAGATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,1326
DYS19,14.0,TAGATAGATAGATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13539
DYS385A-B,13.0,AAGGAAGGAAGGAAGGAGAAAGAAAGTAAAAAAGAAAGAAAGAGAAAAAGAGAAAAAGAAAGAAAGAGAAGAAAGAGAAAGAGGAAAGAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAA,4446
DYS385A-B,16.0,AAGGAAGGAAGGAAGGAGAAAGAAAGTAAAAAAGAAAGAAAGAGAAAAAGAGAAAAAGAAAGAAAGAGAAGAAAGAGAAAGAGGAAAGAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGGGAAAGAAATAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAA,3932
DYS389II,30.0,TCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATTATACCTACTTCTGTATCCAACTCTCATCTGTATTATCTATGTATCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,288
DYS389II,31.0,TCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATTATACCTACTTCTGTATCCAACTCTCATCTGTATTATCTATGTATCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,2593
DYS390,23.0,TCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTATCTATCTATCTA,658
DYS390,24.0,TCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTATCTATCTATCTA,9090
DYS391,9.0,TGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTG,1086
DYS391,10.0,TGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTG,12298
DYS392,12.0,TATTATTATTATTATTATTATTATTATTATTATTAT,2565
DYS392,13.0,TATTATTATTATTATTATTATTATTATTATTATTATTAT,15505
DYS393,12.0,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATGTATGTCTTTTCTATGAGACATA,1946
DYS393,13.0,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATGTATGTCTTTTCTATGAGACATA,19034
DYS437,13.0,TCTATCTATCTATCTATCTATCTATCTATCTGTCTGTCTATCTATCTATCTA,522
DYS437,14.0,TCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTGTCTATCTATCTATCTA,9559
DYS438,8.0,TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC,411
DYS438,9.0,TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC,15233
DYS439,11.0,AAATAGAAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,2052
DYS439,12.0,AAATAGAAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,25067
DYS448,19.0,AGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATATAGAGATAGAGAGATAGAGATAGAGATAGATAGATAGAGAAAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGAT,2823
DYS456,16.0,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATTCCATTAGTTCTGTCCCTCTAGAGAACCCTAATACATCAGTTTAAGAA,1834
DYS456,17.0,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATTCCATTAGTTCTGTCCCTCTAGAGAACCCTAATACATCAGTTTAAGAA,11109
DYS458,16.0,GAAAGAAAGAAAAGGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGGGTGGGCGTGGTGGCTCATGCTTGTAATGCCAGAACTTTGGGAGGCCGAGGTGG,1660
DYS458,17.0,GAAAGAAAGAAAAGGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGGGTGGGCGTGGTGGCTCATGCTTGTAATGCCAGAACTTTGGGAGGCCGAGGTGG,10541
DYS481,21.0,CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT,2848
DYS481,22.0,CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT,12071
DYS533,11.0,TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC,735
DYS533,12.0,TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC,8598
DYS549,12.0,GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,1559
DYS549,13.0,GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,17735
DYS570,16.0,TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC,1561
DYS570,17.0,TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC,14991
DYS576,17.0,AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG,1530
DYS576,18.0,AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG,9658
DYS635,20.0,TCTATCTATCTATCTATGTATGTATCTATCTATGTATGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,1399
DYS635,21.0,TCTATCTATCTATCTATGTATGTATCTATCTATGTATGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,14753
DYS643,9.0,CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCTTTT,287
DYS643,10.0,CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCTTTT,9866
Y-GATA-H4,10.0,AGATAGATAGATAGATCTATAGATAGATAGGTAGGTAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,662
Y-GATA-H4,11.0,AGATAGATAGATAGATCTATAGATAGATAGGTAGGTAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,8052
43 changes: 43 additions & 0 deletions lusSTR/tests/data/powerseq_example_sexloci_sequence_info.csv
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SampleID,Locus,UAS_Output_Sequence,CE_Allele,UAS_Output_Bracketed_Notation,Reads,allele_type,parent_allele1,parent_allele2,allele1_ref_reads,allele2_ref_reads,perc_noise,perc_stutter
powerseq_example,DYS19,TAGATAGATAGATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,14.0,[TAGA]3 TAGG [TAGA]11,13539,real_allele,,,,,,
powerseq_example,DYS19,TAGATAGATAGATAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,13.0,[TAGA]3 TAGG [TAGA]10,1326,-1_stutter,[TAGA]3 TAGG [TAGA]11,,13539.0,,,0.098
powerseq_example,DYS385A-B,AAGGAAGGAAGGAAGGAGAAAGAAAGTAAAAAAGAAAGAAAGAGAAAAAGAGAAAAAGAAAGAAAGAGAAGAAAGAGAAAGAGGAAAGAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGGGAAAGAAATAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAA,16.0,AAG [GAAG]3 GAGA AAGA AAGT AAAA [AAGA]3 GAAA AAGA GAAA [AAGA]3 GAAG AAAG AGAA AGAG GAAA GAGA AAGA [AAGG]6 [GAAA]2 TAAA [GAAA]13 GAGA AAAA,3932,real_allele,,,,,,
powerseq_example,DYS385A-B,AAGGAAGGAAGGAAGGAGAAAGAAAGTAAAAAAGAAAGAAAGAGAAAAAGAGAAAAAGAAAGAAAGAGAAGAAAGAGAAAGAGGAAAGAGAAAGAAAGGAAGGAAGGAAGGAAGGAAGGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAGAAAAA,13.0,AAG [GAAG]3 GAGA AAGA AAGT AAAA [AAGA]3 GAAA AAGA GAAA [AAGA]3 GAAG AAAG AGAA AGAG GAAA GAGA AAGA [AAGG]6 [GAAA]13 GAGA AAAA,4446,real_allele,,,,,,
powerseq_example,DYS389II,TCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATTATACCTACTTCTGTATCCAACTCTCATCTGTATTATCTATGTATCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,31.0,[TCTG]4 [TCTA]13 TCAT TATA CCTA CTTC TGTA TCCA ACTC TCAT CTGT ATTA TCTA TGTA [TCTG]3 [TCTA]11,2593,real_allele,,,,,,
powerseq_example,DYS389II,TCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCATTATACCTACTTCTGTATCCAACTCTCATCTGTATTATCTATGTATCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,30.0,[TCTG]4 [TCTA]13 TCAT TATA CCTA CTTC TGTA TCCA ACTC TCAT CTGT ATTA TCTA TGTA [TCTG]3 [TCTA]10,288,-1_stutter,[TCTG]4 [TCTA]13 TCAT TATA CCTA CTTC TGTA TCCA ACTC TCAT CTGT ATTA TCTA TGTA [TCTG]3 [TCTA]11,,2593.0,,,0.111
powerseq_example,DYS390,TCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTATCTATCTATCTA,24.0,[TCTA]2 [TCTG]8 [TCTA]11 TCTG [TCTA]4,9090,real_allele,,,,,,
powerseq_example,DYS390,TCTATCTATCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTATCTATCTATCTA,23.0,[TCTA]2 [TCTG]8 [TCTA]10 TCTG [TCTA]4,658,-1_stutter,[TCTA]2 [TCTG]8 [TCTA]11 TCTG [TCTA]4,,9090.0,,,0.072
powerseq_example,DYS391,TGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTG,10.0,TG TCTG [TCTA]10 TCTG,12298,real_allele,,,,,,
powerseq_example,DYS391,TGTCTGTCTATCTATCTATCTATCTATCTATCTATCTATCTATCTG,9.0,TG TCTG [TCTA]9 TCTG,1086,-1_stutter,TG TCTG [TCTA]10 TCTG,,12298.0,,,0.088
powerseq_example,DYS392,TATTATTATTATTATTATTATTATTATTATTATTATTAT,13.0,[TAT]13,15505,real_allele,,,,,,
powerseq_example,DYS392,TATTATTATTATTATTATTATTATTATTATTATTAT,12.0,[TAT]12,2565,-1_stutter,[TAT]13,,15505.0,,,0.165
powerseq_example,DYS393,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATGTATGTCTTTTCTATGAGACATA,13.0,[AGAT]13 [ATGT]2 CTTT TCTA TGAG ACAT A,19034,real_allele,,,,,,
powerseq_example,DYS393,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATGTATGTCTTTTCTATGAGACATA,12.0,[AGAT]12 [ATGT]2 CTTT TCTA TGAG ACAT A,1946,-1_stutter,[AGAT]13 [ATGT]2 CTTT TCTA TGAG ACAT A,,19034.0,,,0.102
powerseq_example,DYS437,TCTATCTATCTATCTATCTATCTATCTATCTATCTGTCTGTCTATCTATCTATCTA,14.0,[TCTA]8 [TCTG]2 [TCTA]4,9559,real_allele,,,,,,
powerseq_example,DYS437,TCTATCTATCTATCTATCTATCTATCTATCTGTCTGTCTATCTATCTATCTA,13.0,[TCTA]7 [TCTG]2 [TCTA]4,522,-1_stutter,[TCTA]8 [TCTG]2 [TCTA]4,,9559.0,,,0.055
powerseq_example,DYS438,TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC,9.0,[TTTTC]9,15233,real_allele,,,,,,
powerseq_example,DYS438,TTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTC,8.0,[TTTTC]8,411,-1_stutter,[TTTTC]9,,15233.0,,,0.027
powerseq_example,DYS439,AAATAGAAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,12.0,AAAT AGAA [GATA]12,25067,real_allele,,,,,,
powerseq_example,DYS439,AAATAGAAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,11.0,AAAT AGAA [GATA]11,2052,-1_stutter,AAAT AGAA [GATA]12,,25067.0,,,0.082
powerseq_example,DYS448,AGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATATAGAGATAGAGAGATAGAGATAGAGATAGATAGATAGAGAAAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGAT,19.0,[AGAGAT]11 [ATAGAG]2 [AGATAG]3 ATAGAT AGAGAA [AGAGAT]8,2823,real_allele,,,,,,
powerseq_example,DYS448,AGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATATAGAGATAGAGAGATAGAGATAGAGATAGAGAGATAGAGAAAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGATAGAGAT,19.0,[AGAGAT]11 [ATAGAG]2 [AGATAG]3 AGAGAT AGAGAA [AGAGAT]8,88,BelowAT,,,,,0.03,
powerseq_example,DYS456,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATTCCATTAGTTCTGTCCCTCTAGAGAACCCTAATACATCAGTTTAAGAA,17.0,[AGAT]17 ATTC CATT AGTT CTGT CCCT CTAG AGAA CCCT AATA CATC AGTT TAAG AA,11109,real_allele,,,,,,
powerseq_example,DYS456,AGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATATTCCATTAGTTCTGTCCCTCTAGAGAACCCTAATACATCAGTTTAAGAA,16.0,[AGAT]16 ATTC CATT AGTT CTGT CCCT CTAG AGAA CCCT AATA CATC AGTT TAAG AA,1834,real_allele,,,,,,
powerseq_example,DYS458,GAAAGAAAGAAAAGGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGGGTGGGCGTGGTGGCTCATGCTTGTAATGCCAGAACTTTGGGAGGCCGAGGTGG,17.0,[GAAA]3 AG GAAG [GAAA]17 GGAG GGTG GGCG TGGT GGCT CATG CTTG TAAT GCCA GAAC TTTG GGAG GCCG AGGT GG,10541,real_allele,,,,,,
powerseq_example,DYS458,GAAAGAAAGAAAAGGAAGGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGGGTGGGCGTGGTGGCTCATGCTTGTAATGCCAGAACTTTGGGAGGCCGAGGTGG,16.0,[GAAA]3 AG GAAG [GAAA]16 GGAG GGTG GGCG TGGT GGCT CATG CTTG TAAT GCCA GAAC TTTG GGAG GCCG AGGT GG,1660,real_allele,,,,,,
powerseq_example,DYS481,CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT,22.0,[CTT]22,12071,real_allele,,,,,,
powerseq_example,DYS481,CTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTTCTT,21.0,[CTT]21,2848,-1_stutter,[CTT]22,,12071.0,,,0.236
powerseq_example,DYS533,TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC,12.0,[TATC]12,8598,real_allele,,,,,,
powerseq_example,DYS533,TATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATC,11.0,[TATC]11,735,-1_stutter,[TATC]12,,8598.0,,,0.085
powerseq_example,DYS549,GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,13.0,[GATA]13,17735,real_allele,,,,,,
powerseq_example,DYS549,GATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATA,12.0,[GATA]12,1559,-1_stutter,[GATA]13,,17735.0,,,0.088
powerseq_example,DYS570,TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC,17.0,[TTTC]17,14991,real_allele,,,,,,
powerseq_example,DYS570,TTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC,16.0,[TTTC]16,1561,-1_stutter,[TTTC]17,,14991.0,,,0.104
powerseq_example,DYS576,AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG,18.0,[AAAG]18,9658,real_allele,,,,,,
powerseq_example,DYS576,AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAG,17.0,[AAAG]17,1530,real_allele,,,,,,
powerseq_example,DYS635,TCTATCTATCTATCTATGTATGTATCTATCTATGTATGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,21.0,[TCTA]4 [TGTA]2 [TCTA]2 [TGTA]2 [TCTA]11,14753,real_allele,,,,,,
powerseq_example,DYS635,TCTATCTATCTATCTATGTATGTATCTATCTATGTATGTATCTATCTATCTATCTATCTATCTATCTATCTATCTATCTA,20.0,[TCTA]4 [TGTA]2 [TCTA]2 [TGTA]2 [TCTA]10,1399,-1_stutter,[TCTA]4 [TGTA]2 [TCTA]2 [TGTA]2 [TCTA]11,,14753.0,,,0.095
powerseq_example,DYS643,CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCTTTT,10.0,[CTTTT]10 CTTTC TTTT,9866,real_allele,,,,,,
powerseq_example,DYS643,CTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTTCTTTCTTTT,9.0,[CTTTT]9 CTTTC TTTT,287,-1_stutter,[CTTTT]10 CTTTC TTTT,,9866.0,,,0.029
powerseq_example,Y-GATA-H4,AGATAGATAGATAGATCTATAGATAGATAGGTAGGTAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,11.0,AGA [TAGA]3 TCTA [TAGA]2 [TAGG]3 [TAGA]11,8052,real_allele,,,,,,
powerseq_example,Y-GATA-H4,AGATAGATAGATAGATCTATAGATAGATAGGTAGGTAGGTAGATAGATAGATAGATAGATAGATAGATAGATAGATAGA,10.0,AGA [TAGA]3 TCTA [TAGA]2 [TAGG]3 [TAGA]10,662,-1_stutter,AGA [TAGA]3 TCTA [TAGA]2 [TAGG]3 [TAGA]11,,8052.0,,,0.082
30 changes: 30 additions & 0 deletions lusSTR/tests/test_filters.py
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Original file line number Diff line number Diff line change
Expand Up @@ -441,3 +441,33 @@ def test_lusplus_sequence_info(tmp_path):
all_arglist = ["strs", "all", "-w", str_path]
lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(all_arglist))
assert filecmp.cmp(exp_out, obs_out) is True


def test_filtering_ystrs(tmp_path):
str_path = str(tmp_path / "WD")
inputfile = data_file("powerseq_flanking_convert_test.csv")
inputfile_sex = data_file("powerseq_flanking_convert_test_sexloci.csv")
exp_out = data_file("powerseq_example_evidence_ngs.csv")
exp_info_out = data_file("powerseq_example_sexloci_sequence_info.csv")
obs_out = str(tmp_path / f"WD/lusstr_output/ystrs/powerseq_example_evidence_ngs.csv")
obs_info_out = str(
tmp_path / f"WD/lusstr_output/ystrs/lusstr_output_sexloci_sequence_info.csv"
)
arglist = [
"config",
"-w",
str_path,
"--input",
str(inputfile),
"--sex",
"--analysis-software",
"straitrazor",
"--powerseq",
]
lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(arglist))
shutil.copyfile(inputfile, os.path.join(str_path, "lusstr_output.csv"))
shutil.copyfile(inputfile_sex, os.path.join(str_path, "lusstr_output_sexloci.csv"))
all_arglist = ["strs", "all", "-w", str_path]
lusSTR.cli.main(lusSTR.cli.get_parser().parse_args(all_arglist))
assert filecmp.cmp(exp_out, obs_out) is True
assert filecmp.cmp(exp_info_out, obs_info_out) is True

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