In [1]:

    

%run ~/relmapping/annot/notebooks/__init__.ipynb


    

    




/mnt/home3/jj374/anaconda36/lib/python3.6/site-packages/statsmodels/compat/pandas.py:56: FutureWarning: The pandas.core.datetools module is deprecated and will be removed in a future version. Please use the pandas.tseries module instead.
  from pandas.core import datetools






    




os.getcwd(): /mnt/b2/scratch/ahringer/jj374/lab/relmapping

In [2]:

    

df_ = pd.concat([
    pd.read_csv('WS260_ce10/WS260_ce10.exon_first.bed', sep='\t', usecols=[0,1,2], names=yp.NAMES_BED3),
    pd.read_csv('WS260_ce10/WS260_ce10.exon_other.bed', sep='\t', usecols=[0,1,2], names=yp.NAMES_BED3),
]).sort_values(['chrom', 'start', 'end']).reset_index(drop=True)
df_ = BedTool.from_dataframe(df_).merge().to_dataframe()
df_['col'] = 1
df_.to_csv('WS260_ce10/WS260_ce10.exon_coverage_unstranded.bedGraph', sep='\t', index=False, header=False)

!bedGraphToBigWig \
    WS260_ce10/WS260_ce10.exon_coverage_unstranded.bedGraph \
    shared/ce10.chroms \
    WS260_ce10/WS260_ce10.exon_coverage_unstranded.bw

!rm WS260_ce10/WS260_ce10.exon_coverage_unstranded.bedGraph