a hW@sFddlZddlZddlmZddlZedddZeedddZdS) N)Path)commandccsftjt|tjtjd}t|jjdD].}|r(| d}| drP|dd}|Vq(| VdS)N)stdoutstderrzutf-8 ) subprocessPopenshlexsplitPIPEDEVNULLiterrreadlinedecodeendswithwait)rplinerX/mounts/lovelace/software/anaconda3/envs/py39/lib/python3.9/site-packages/metaDMG/PMD.pyiterate_command s   r)bam_file metaDMG_cppc Cs|d|}d}g}g}tt|D]>\}}t|tr>|}q&|d\}} |||t| q&|dkr|td|t ||d} | S)zRun the PMD command from metaDMG-cpp and get a DataFrame with the results. Parameters ---------- bam_file Alignment file to compute the PMD scores on metaDMG_cpp The metaDMG binary to use z pmd z PMD:rzError running )readPMD) enumerater isinstanceintr appendfloat ExceptionpdZ DataFrame) rrr returncodeZreadsZPMDsirrrZdfrrr compute_PMDss   r') r r pathlibrZpandasr$strrr'rrrrs