Support for BICSeq2

[amcpherson]

It appears that the bicseq output has changed (perhaps from bicseq to bicseq2). As a result BICSeqToTHetA doesnt work with the most recent version of bicseq2. Is there any reason to not use bicseq2 as input to theta?

In case it is helpful, the following python code does most of what BICSeqToTHetA does, and is robust to column order:

import pandas as pd

segs = pd.read_csv(
    bicseq2_seg_filename, sep='\t',
    converters={'chrom': str, 'start': int, 'end': int})
segs['#ID'] = (
    'start_' + segs['chrom'] + '_' + segs['start'].astype(str) +
    'end_' + segs['chrom'] + '_' + segs['end'].astype(str))
segs['chrm'] = segs['chrom']
segs['tumorCount'] = segs['tumor']
segs['normalCount'] = segs['normal']
segs['length'] = segs['end'] - segs['start']

# Length filter (default 10Mb)
segs = segs[segs['length'] >= config.get('min_length', int(10e6))]

theta_seg_filename = os.path.join(tmp_directory, 'theta_input.seg')
cols = ['#ID', 'chrm', 'start', 'end', 'tumorCount', 'normalCount']
segs[cols].to_csv(theta_seg_filename, sep='\t', index=False)