PFGI/next_generation_sequencing.py at master · lyotvincent/PFGI · 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
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
import preprocessing
import annotation
# import denovo
import os

class NextGenerationSequencing:

    input_file = None
    input_file_1 = None
    input_file_2 = None
    # input_file_12 = None
    result_dir = None
    conf = None

    preprocessing_output = None
    preprocessing_output_1 = None
    preprocessing_output_2 = None

    def __init__(self, result_dir, conf, input_file=None, input_file_1=None, input_file_2=None):
        self.result_dir = result_dir
        self.conf = conf
        self.input_file = input_file
        self.input_file_1 = input_file_1
        self.input_file_2 = input_file_2
        # self.input_file_12 = input_file_12

    def run_single(self):
        if self.conf['preprocessing']['enable'] != False:
            os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing')
            preprocessing_obj = preprocessing.Preprocessing(self.result_dir, self.conf, input_file=self.input_file)

            if self.conf['preprocessing']['fastp']['enable'] != False:
                preprocessing_obj.fastp_single_end()
                self.preprocessing_output = self.result_dir+'/preprocessing/fastp_output.fastq'
            else:
                if self.conf['preprocessing']['fastqc']['enable'] != False:
                    os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_before_filtering')
                    preprocessing_obj.fastqc_single_end('fastqc_before_filtering')
                if self.conf['preprocessing']['trimmomatic']['enable'] != False:
                    preprocessing_obj.trimmomatic_single_end()
                    self.preprocessing_output = self.result_dir+'/preprocessing/trimmomatic_output.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file = self.preprocessing_output
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_single_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['cutadapt']['enable'] != False:
                    preprocessing_obj.cutadapt_single_end()
                    self.preprocessing_output = self.result_dir+'/preprocessing/cutadapt_output.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file = self.preprocessing_output
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_single_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['sickle']['enable'] != False:
                    preprocessing_obj.sickle_single_end()
                    self.preprocessing_output = self.result_dir+'/preprocessing/sickle_output.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file = self.preprocessing_output
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_single_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['SOAPnuke']['enable'] != False:
                    preprocessing_obj.soapnuke_single_end()
                    self.preprocessing_output = self.result_dir+'/preprocessing/SOAPnuke_output.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file = self.preprocessing_output
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_single_end('fastqc_after_filtering')
                else:
                    self.preprocessing_output = self.input_file
            temp_file = open(os.path.abspath('.') + '/' + self.result_dir+'/Summary_of_results.html', 'a+')
            temp_file.write('<ul>\n')
            temp_file.write('<li>preprocessing result is in %s</li>\n' % './preprocessing')
            temp_file.write('<li><a href="%s">click to report</a></li>\n' % ('./preprocessing/'))
            temp_file.write('</ul>\n')
            temp_file.close()
        else:
            self.preprocessing_output = self.input_file

        if self.conf['identification']['enable'] != False:
            os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'identification')
            resequencing_obj = annotation.Resequencing(self.result_dir, self.conf, self.preprocessing_output)
            resequencing_obj.run()
        # if self.conf['denovo']['enable'] != False:
        #     os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'denovo')
        #     denovo_obj = denovo.Denovo(self.result_dir, self.conf, input_file=self.preprocessing_output)
        #     denovo_obj.run_single()

    def run_paired(self):
        if self.conf['preprocessing']['enable'] != False:
            os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing')
            preprocessing_obj = preprocessing.Preprocessing(self.result_dir, self.conf, input_file_1=self.input_file_1, input_file_2=self.input_file_2)

            if self.conf['preprocessing']['fastp']['enable'] != False:
                preprocessing_obj.fastp_paired_end()
                self.preprocessing_output_1 = self.result_dir+'/preprocessing/fastp_output_1.fastq'
                self.preprocessing_output_2 = self.result_dir+'/preprocessing/fastp_output_2.fastq'
            else:
                if self.conf['preprocessing']['fastqc']['enable'] != False:
                    os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_before_filtering')
                    preprocessing_obj.fastqc_paired_end('fastqc_before_filtering')
                if self.conf['preprocessing']['trimmomatic']['enable'] != False:
                    preprocessing_obj.trimmomatic_paired_end()
                    self.preprocessing_output_1 = self.result_dir+'/preprocessing/paired_output_1.fastq'
                    self.preprocessing_output_2 = self.result_dir+'/preprocessing/paired_output_2.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file_1 = self.preprocessing_output_1
                        preprocessing_obj.input_file_2 = self.preprocessing_output_2
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_paired_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['cutadapt']['enable'] != False:
                    preprocessing_obj.cutadapt_paired_end()
                    self.preprocessing_output_1 = self.result_dir+'/preprocessing/cutadapt_output_1.fastq'
                    self.preprocessing_output_2 = self.result_dir+'/preprocessing/cutadapt_output_2.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file_1 = self.preprocessing_output_1
                        preprocessing_obj.input_file_2 = self.preprocessing_output_2
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_paired_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['sickle']['enable'] != False:
                    preprocessing_obj.sickle_paired_end()
                    self.preprocessing_output_1 = self.result_dir+'/preprocessing/sickle_output_1.fastq'
                    self.preprocessing_output_2 = self.result_dir+'/preprocessing/sickle_output_2.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file_1 = self.preprocessing_output_1
                        preprocessing_obj.input_file_2 = self.preprocessing_output_2
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_paired_end('fastqc_after_filtering')
                elif self.conf['preprocessing']['SOAPnuke']['enable'] != False:
                    preprocessing_obj.soapnuke_paired_end()
                    self.preprocessing_output_1 = self.result_dir+'/preprocessing/SOAPnuke_output_1.fastq'
                    self.preprocessing_output_2 = self.result_dir+'/preprocessing/SOAPnuke_output_2.fastq'
                    if self.conf['preprocessing']['fastqc']['enable'] != False:
                        preprocessing_obj.input_file_1 = self.preprocessing_output_1
                        preprocessing_obj.input_file_2 = self.preprocessing_output_2
                        os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing/fastqc_after_filtering')
                        preprocessing_obj.fastqc_paired_end('fastqc_after_filtering')
                else:
                    self.preprocessing_output_1 = self.input_file_1
                    self.preprocessing_output_2 = self.input_file_2
            temp_file = open(os.path.abspath('.') + '/' + self.result_dir+'/Summary_of_results.html', 'a+')
            temp_file.write('<ul>\n')
            temp_file.write('<li>preprocessing result is in %s</li>\n' % './preprocessing')
            temp_file.write('<li><a href="%s">click to report</a></li>\n' % ('./preprocessing/'))
            temp_file.write('</ul>\n')
            temp_file.close()
        else:
            self.preprocessing_output_1 = self.input_file_1
            self.preprocessing_output_2 = self.input_file_2

        print('preprocessing_output_1='+str(self.preprocessing_output_1))
        print('preprocessing_output_2='+str(self.preprocessing_output_2))

        if self.conf['identification']['enable'] != False:
            os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'identification')
            resequencing_obj = annotation.Resequencing(self.result_dir, self.conf, self.preprocessing_output_1, self.preprocessing_output_2)
            resequencing_obj.run()
        # if self.conf['denovo']['enable'] != False:
        #     os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'denovo')
        #     denovo_obj = denovo.Denovo(self.result_dir, self.conf, input_file_1=self.preprocessing_output_1, input_file_2=self.preprocessing_output_2)
        #     denovo_obj.run_paired()

    # def run_interleaved(self):
    #     if self.conf['preprocessing']['enable'] != False:
    #         os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'preprocessing')
    #         preprocessing_obj = preprocessing.Preprocessing(self.result_dir, self.conf, input_file=self.input_file_12)
    #         if self.conf['preprocessing']['fastqc']['enable'] != False:
    #             preprocessing_obj.fastqc_single_end()
    #             if self.conf['preprocessing']['trimmomatic']['enable'] != False:
    #                 preprocessing_obj.trimmomatic_single_end()
    #                 self.preprocessing_output = self.result_dir+'/preprocessing/trimmomatic_output.fastq'
    #             elif self.conf['preprocessing']['cutadapt']['enable'] != False:
    #                 preprocessing_obj.cutadapt_single_end()
    #                 self.preprocessing_output = self.result_dir+'/preprocessing/cutadapt_output.fastq'
    #             elif self.conf['preprocessing']['fastp']['enable'] != False:
    #                 preprocessing_obj.fastp_single_end()
    #                 self.preprocessing_output = self.result_dir+'/preprocessing/fastp_output.fastq'
    #             else:
    #                 self.preprocessing_output = self.input_file
    #         elif self.conf['preprocessing']['fastp']['enable'] != False:
    #             preprocessing_obj.fastp_single_end()
    #             self.preprocessing_output = self.result_dir+'/preprocessing/fastp_output.fastq'
    #         else:
    #             self.preprocessing_output = self.input_file_12
    #     else:
    #         self.preprocessing_output = self.input_file_12

    #     if self.conf['identification']['enable'] != False:
    #         os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'resequencing')
    #         resequencing_obj = resequencing.Resequencing(self.result_dir, self.conf, self.preprocessing_output)
    #         resequencing_obj.run()
    #     if self.conf['denovo']['enable'] != False:
    #         os.mkdir(os.path.abspath('.') + '/' + self.result_dir + '/' + 'denovo')
    #         denovo_obj = denovo.Denovo(self.result_dir, self.conf, input_file_12=self.preprocessing_output)
    #         denovo_obj.run_interleaved()