Closed mgalardini closed 2 years ago
Running this command line test:
$ python ../pyseer-runner.py --vcf variants.vcf.gz --phenotypes subset.pheno --wg enet --lineage-clusters lineage_clusters.txt --sequence-reweighting --alpha 1 --cor-filter 0.25 [...] Finding and printing selected variants variant af filter-pvalue lrt-pvalue beta notes FM211187_184_G_A 4.00E-02 2.01E-01 3.40E-01 NA bad-chisq FM211187_293_G_A 2.00E-02 2.54E-01 -6.69E-01 NA bad-chisq FM211187_869_C_T 1.00E-01 7.84E-03 -1.63E+00 NA bad-chisq FM211187_926_G_A 2.00E-02 2.54E-01 -8.91E-05 NA bad-chisq FM211187_1981_G_A 9.40E-01 1.13E-01 2.66E-02 NA bad-chisq FM211187_2032_C_A 2.00E-02 2.54E-01 -6.78E-01 NA bad-chisq FM211187_2865_C_T 2.00E-02 2.54E-01 -4.09E-05 NA bad-chisq FM211187_2943_T_C 1.20E-01 2.06E-02 1.44E+00 NA bad-chisq FM211187_3982_C_A 4.00E-02 2.01E-01 1.39E-01 NA bad-chisq FM211187_6054_C_T 6.00E-02 1.13E-01 4.74E-03 NA bad-chisq FM211187_6139_A_G 2.00E-02 2.54E-01 -4.40E-02 NA bad-chisq FM211187_7799_C_T 4.00E-02 2.01E-01 2.46E-04 NA bad-chisq FM211187_8872_A_G 2.40E-01 2.51E-01 -1.29E-02 NA FM211187_10838_C_T 5.20E-01 1.64E-01 -4.50E-01 NA FM211187_11527_T_C 4.80E-01 1.64E-01 -2.77E-01 NA FM211187_11559_T_G 4.00E-02 2.01E-01 8.47E-05 NA bad-chisq FM211187_11633_A_G 2.00E-02 2.54E-01 -2.81E-03 NA bad-chisq FM211187_11762_G_T 6.00E-02 1.13E-01 3.16E-03 NA bad-chisq FM211187_12304_C_CTTATA 2.00E-02 3.71E-01 7.90E-01 NA bad-chisq FM211187_13550_G_A 4.00E-02 2.01E-01 9.41E-06 NA bad-chisq FM211187_13781_C_T 2.00E-02 2.54E-01 -1.02E-04 NA bad-chisq FM211187_14044_G_A 3.00E-01 1.06E-01 5.63E-01 NA [...]
The NAs are due to the way we figure out whether to print the lineage information (i.e. the lineage_dict must be non-empty: https://github.com/mgalardini/pyseer/blob/badea9104e390fb64e695e57dae1802ea2f8b9f5/pyseer/utils.py#L94), while the header is added if the --lineage option is used. Will make a patch shortly.
lineage_dict
--lineage
Running this command line test:
The NAs are due to the way we figure out whether to print the lineage information (i.e. the
lineage_dictmust be non-empty: https://github.com/mgalardini/pyseer/blob/badea9104e390fb64e695e57dae1802ea2f8b9f5/pyseer/utils.py#L94), while the header is added if the--lineageoption is used. Will make a patch shortly.