paf.py 6.77 KB
Newer Older
1
2
#!/usr/bin/env python3

Floreal Cabanettes's avatar
Floreal Cabanettes committed
3
4
from math import sqrt

5
6
7
8
9
10
11
12
13
14
15
16
17

class Paf:
    limit_idy = 0.5

    def __init__(self, paf, idx_q, idx_t):
        self.paf = paf
        self.idx_q = idx_q
        self.idx_t = idx_t

        self.len_q = None
        self.len_t = None
        self.min_idy = None
        self.max_idy = None
Floreal Cabanettes's avatar
Floreal Cabanettes committed
18
19
20
21
22
        self.lines = {}
        self.q_contigs = {}
        self.q_order = []
        self.t_contigs = {}
        self.t_order = []
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
        self.name_q = None
        self.name_t = None
        self.parsed = False
        self.error = False

        self.parse_paf()

    def parse_paf(self):
        len_q = 0
        len_t = 0
        min_idy = 10000000000
        max_idy = -10000000000
        name_q = None
        name_t = None
        lines = {
            "pos+": [],
            "pos-": [],
            "neg+": [],
            "neg-": []
        }
43
44
        q_abs_start = {}
        q_abs_current_start = 0
45
46
        try:
            with open(self.idx_q, "r") as idx_q_f:
47
                name_q = idx_q_f.readline().strip("\n")
48
49
50
51
52
53
54
                q_order = []
                q_contigs = {}
                for line in idx_q_f:
                    parts = line.strip("\n").split("\t")
                    id_c = parts[0]
                    len_c = int(parts[1])
                    q_order.append(id_c)
55
                    q_abs_start[id_c] = q_abs_current_start
56
                    q_contigs[id_c] = len_c
57
                    q_abs_current_start += len_c
58
59
60
61
        except IOError:
            self.error = "Index file does not exist for query!"
            return False

62
63
        t_abs_start = {}
        t_abs_current_start = 0
64
65
        try:
            with open(self.idx_t, "r") as idx_t_f:
66
                name_t = idx_t_f.readline().strip("\n")
67
68
69
70
71
72
73
                t_order = []
                t_contigs = {}
                for line in idx_t_f:
                    parts = line.strip("\n").split("\t")
                    id_c = parts[0]
                    len_c = int(parts[1])
                    t_order.append(id_c)
74
                    t_abs_start[id_c] = t_abs_current_start
75
                    t_contigs[id_c] = len_c
76
                    t_abs_current_start += len_c
77
78
79
80
        except IOError:
            self.error = "Index file does not exist for target!"
            return False

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
        len_q = q_abs_current_start
        len_t = t_abs_current_start

        try:
            with open(self.paf, "r") as paf_file:
                for line in paf_file:
                    parts = line.strip("\n").split("\t")
                    v1 = parts[0]
                    v6 = parts[5]
                    strand = 1 if parts[4] == "+" else -1
                    idy = int(parts[9]) / int(parts[10]) * strand
                    min_idy = min(min_idy, idy)
                    max_idy = max(max_idy, idy)
                    # x1, x2, y1, y2, idy
                    y1 = int(parts[2]) + q_abs_start[v1]
                    y2 = int(parts[3]) + q_abs_start[v1]
                    x1 = int(parts[7 if strand == 1 else 8]) + t_abs_start[v6]
                    x2 = int(parts[8 if strand == 1 else 7]) + t_abs_start[v6]
                    if idy < -self.limit_idy:
                        class_idy = "neg-"
                    elif idy < 0:
                        class_idy = "neg+"
                    elif idy < self.limit_idy:
                        class_idy = "pos-"
                    else:
                        class_idy = "pos+"
Floreal Cabanettes's avatar
Floreal Cabanettes committed
107
                    lines[class_idy].append([x1, x2, y1, y2, idy, v1, v6])
108
109
110
111
        except IOError:
            self.error = "PAF file does not exist!"
            return False

112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
        self.parsed = True
        self.len_q = len_q
        self.len_t = len_t
        self.min_idy = min_idy
        self.max_idy = max_idy
        self.lines = lines
        self.q_contigs = q_contigs
        self.q_order = q_order
        self.t_contigs = t_contigs
        self.t_order = t_order
        self.name_q = name_q
        self.name_t = name_t

    def get_d3js_data(self):
        return {
127
128
            'y_len': self.len_q,
            'x_len': self.len_t,
129
130
131
            'min_idy': self.min_idy,
            'max_idy': self.max_idy,
            'lines': self.lines,
132
133
134
135
136
137
            'y_contigs': self.q_contigs,
            'y_order': self.q_order,
            'x_contigs': self.t_contigs,
            'x_order': self.t_order,
            'name_y': self.name_q,
            'name_x': self.name_t,
138
139
140
141
142
143
144
145
146
147
148
            'limit_idy': self.limit_idy
        }

    def save_json(self, out):
        import json
        success, data = self.parse_paf()
        if success:
            with open(out, "w") as out_f:
                out_f.write(json.dumps(data))
        else:
            raise Exception(data)
Floreal Cabanettes's avatar
Floreal Cabanettes committed
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
194
195
196
197
198
199
200
201
202
203
204

    def sort(self):
        gravity_contig = {}
        lines_on_block = {}
        # Compute size of blocks (in term of how many big match they have), and save median of each match on each one
        # (for next step)
        for line in [j for i in list(self.lines.values()) for j in i]:
            x1 = int(line[0])
            x2 = int(line[1])
            y1 = int(line[2])
            y2 = int(line[3])
            idy = int(line[4])
            contig = line[5]
            chrm = line[6]
            block = (contig, chrm)
            med_q = x1 + (abs(x2 - x1) / 2)
            len_m = sqrt(pow(x2 - x1, 2) + pow(y2 - y1, 2))  # Pow of len
            len_m_2 = pow(1 + len_m, 2)
            if block not in lines_on_block:
                lines_on_block[block] = []
            lines_on_block[block].append((med_q, len_m_2))

            if contig not in gravity_contig:
                gravity_contig[contig] = {}
            if chrm not in gravity_contig[contig]:
                gravity_contig[contig][chrm] = 0
            gravity_contig[contig][chrm] += len_m_2

        # For each contig, find best block, and deduce gravity of contig:
        gravity_on_contig = {}
        for contig, chr_blocks in gravity_contig.items():
            # Find best block:
            max_number = 0
            max_chr = None
            for chrm, size in chr_blocks.items():
                if size > max_number:
                    max_number = size
                    max_chr = chrm

            # Compute gravity of contig:
            nb_items = 0
            sum_items = 0
            for med in lines_on_block[(contig, max_chr)]:
                sum_items += med[0] * med[1]
                nb_items += med[1]
            gravity_on_contig[contig] = sum_items / nb_items

        # Sort contigs:
        self.q_order.sort(key=lambda x: gravity_on_contig[x] if x in gravity_on_contig else self.len_q + 1000)

        with open(self.idx_q, "w") as idx_q_f:
            idx_q_f.write(self.name_q + "\n")
            for contig in self.q_order:
                idx_q_f.write("\t".join([contig, str(self.q_contigs[contig])]) + "\n")
        self.parsed = False
        self.parse_paf()