2
3 BED_PATHS = {}
4
5 - def __init__(self, service, query, ucsc_compatible=True):
14
16 return "\n".join(self._header)
17
19 params = self.query.to_query_params()
20 if not self.ucsc_compatible:
21 params["ucscCompatible"] = "no"
22 try:
23 path = self.query.bed_path
24 except:
25 path = self.path
26 i = self.service.get_results(path, params, "tsv", self.query.views)
27 return i
28
30 lines = [line for line in self]
31 return "\n".join(self._header + lines)
32
35
37 line = self.it.next()
38 while line and line.startswith("#") or line.startswith("track"):
39 self._header.append(line)
40 line = self.it.next()
41 if line:
42 return line
43 raise StopIteration
44
46
47 GFF3_PATHS = {}
48
57
59 return "\n".join(self._header)
60
62 params = self.query.to_query_params()
63 try:
64 path = self.query.gff3_path
65 except:
66 path = self.path
67 i = self.service.get_results(path, params, "tsv", self.query.views)
68 return i
69
71 lines = [line for line in self]
72 return "\n".join(self._header + lines)
73
76
78 line = self.it.next()
79 while line and line.startswith("#"):
80 self._header.append(line)
81 line = self.it.next()
82 if line:
83 return line
84 raise StopIteration
85
87
88 FASTA_PATHS = {}
89
98
100 params = self.query.to_query_params()
101 try:
102 path = self.query.fasta_path
103 except:
104 path = self.path
105 i = self.service.get_results(path, params, "tsv", self.query.views)
106 return i
107
109 records = [rec for rec in self]
110 return "\n".join(records)
111
114
116 lines = []
117 if self._holdover is not None:
118 lines.append(self._holdover)
119 self._holdover = None
120 else:
121 try:
122 lines.append(self.it.next())
123 except StopIteration:
124 pass
125
126 try:
127 while True:
128 line = self.it.next()
129 if line.startswith(">"):
130 self._holdover = line
131 break
132 lines.append(line)
133 except StopIteration:
134 pass
135
136 if len(lines):
137 return "\n".join(lines)
138
139 if self._holdover:
140 ret = self._holdover
141 self._holdover = None
142 return self._holdover
143
144 raise StopIteration
145