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path: root/Code/make_parameter_dapseq2.py
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import sys, glob, os, operator
from geneid2name import make_gene_name_AGI_map_dict

DAPSEQ_DIR = '../Data/C/Mapped/dapseq/peaks'

GENE_ID_TO_GENE_NAME = '../Data/information/AGI-to-gene-names_v2.txt'


def make_dapseq_dictionary(dirname):

    d = {}

    files = glob.glob(os.path.join(dirname, '*/*/*/*.narrowPeak'))

    for f in files:
        lst = f.split('/')
        tf_name = lst[-3]
        if not tf_name in d:
            d[tf_name] = f
        else:
            print('ERROR: transcription factor name not unique.')
            sys.exit()

    return d


d = make_dapseq_dictionary(DAPSEQ_DIR)
agi2name_dict = make_gene_name_AGI_map_dict(GENE_ID_TO_GENE_NAME)


count = 1
for k, v in sorted(d.items(), key=operator.itemgetter(0)):
    cid = 'C0002%09d' % (count)
    count += 1
    print('@%s' % (cid))
    g = k.split('_')[0]
    g = g.upper()


    if g.startswith('AT'):
        print('PROTEIN_ID:%s' % (g))
    elif g in agi2name_dict and g != agi2name_dict[g]:
        print('PROTEIN_ID:%s' % (agi2name_dict[g]))
    else:
        print('PROTEIN_ID:%s' % (g))

    if g.startswith('AT') and g in agi2name_dict and g != agi2name_dict[g]:
        print('PROTEIN_NAME:%s' % (agi2name_dict[g]))
    else:
        print('PROTEIN_NAME:%s' % (g))

    print('DATA_NAME:%s' % (k))
    print('DATA_FORMAT:%s' % ('narrowPeak'))
    print('DESCRIPTION:dapseq')    
    print('LOCATION:%s' % (v))
    print('NOTE:')
    print('')