DeepFilter/theory_process.py at master · Biocomputing-Research-Group/DeepFilter · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
import pandas as pd
import shutil
import sys


def generate_sipros_input(file, outfile1, outfile2, outfilefasta):
    f = open(file)
    size = len(f.readlines())
    f.close()
    f = open(file)
    peptide = []
    unique_id = []
    fidx = open(outfile1, 'w')
    fcharge = open(outfile2, 'w')
    fpep = open(outfilefasta, 'w')
    for line_id, line in enumerate(f):
        if line_id == 0:
            continue
        line = line.strip().split(',')
        string = line[0]
        string = string.split('_')
        '''
        file_id=str(int(string[1]))
        scannum=str(int(string[2]))
        charge_id=str(int(string[3]))
        rank=str(int(string[4]))
        '''
        file_id = str(int(string[6]))
        scannum = str(int(string[7]))
        charge_id = str(int(string[8]))
        rank = str(int(string[9]))

        fidx.write(str(file_id) + '_' + str(scannum) +
                   '_' + str(charge_id) + '_' + str(rank))
        if line_id < size - 1:
            fidx.write('\n')
        peptide = line[26]
        s = peptide.replace('[15.9949]', '~')
        r = s.split('.')[1]
        fpep.write(r)
        if line_id < size - 1:
            fpep.write('\n')
        charge = charge_id
        fcharge.write(str(charge))
        if line_id < size - 1:
            fcharge.write('\n')

    fidx.close()
    fcharge.close()
    fpep.close()


# need to change by filename
def FeatureLoader(file, outfile):
    f = open(outfile, 'w')
    fr = open(file)
    for line_id, line in enumerate(fr):
        if line_id == 0:
            continue
        line = line.strip().split(',')
        string = line[0]
        string = string.split('_')
        '''
        file_id=str(int(string[1]))
        scan_id=str(int(string[2]))
        charge_id=str(int(string[3]))
        rank=str(int(string[4]))
        '''
        file_id = str(int(string[6]))
        scan_id = str(int(string[7]))
        charge_id = str(int(string[8]))
        rank = str(int(string[9]))

        idx = file_id + '_' + scan_id + '_' + charge_id + '_' + rank
        pep_str = line[26].replace('[15.9949]', '~').split('.')[1]
        # 11 feature from comet output
        Xcorr = line[9]
        deltLCn = line[6]
        deltCn = line[7]
        Mass = line[12]
        PepLen = line[13]
        charge1 = line[14]
        charge2 = line[15]
        charge3 = line[16]
        enzInt = line[22]
        dM = line[24]
        absdM = str(abs(float(line[3]) - float(line[4])))

        f.write(idx + '\n' + pep_str + '\n')
        f.write(Xcorr + ' ' + deltLCn + ' ' + deltCn + ' ' + Mass + ' ' + PepLen + ' ' +
                charge1 + ' ' + charge2 + ' ' + charge3 + ' ' + enzInt + ' ' + dM + ' ' + absdM + '\n\n')

    f.close()


'''
def ExpGenerate(file,msfile):
    f=open(msfile)
    fw=open('expMz.txt','w')
    fname=f.name.replace('.ms2','')
    file_id=str(fname.split('_')[3].replace('Repl',''))
    reader=pd.read_csv(file,sep='\t')
    for line_id,line in enumerate(reader['Scan number']):
    file_id=str(reader['Raw file'][line_id].split('_')[3].replace('Repl',''))
        scan=str(line.strip())
        idx=file_id+'_'+scan
'''


def main(input_file, out_file1, out_file2, out_file3, out_file4):
    # 1. extract comet output into sipros, require: unique_id(fileid_scanid), charge state, peptide string
    generate_sipros_input(input_file, out_file1, out_file2, out_file3)
    # 2. run sipros programm (c++)
    # 3. additional features loader
    FeatureLoader(input_file, out_file4)


if __name__ == "__main__":
    input_file = sys.argv[1]  # comet pin format
    out_file1 = sys.argv[2]  # idx
    out_file2 = sys.argv[3]  # charge
    out_file3 = sys.argv[4]  # peptide
    out_file4 = sys.argv[5]  # 11 feature
    main(input_file, out_file1, out_file2, out_file3, out_file4)
    # runing sipros
    # sipros command -i1 out_file1 -i2 out_file2 -i3 out_file3 -i4 theoratic.txt