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 i = self.service.get_results(self.path, params, "tsv", self.query.views)
23 return i
24
26 lines = [line for line in self]
27 return "\n".join(self._header + lines)
28
31
33 line = self.it.next()
34 while line and line.startswith("#") or line.startswith("track"):
35 self._header.append(line)
36 line = self.it.next()
37 if line:
38 return line
39 raise StopIteration
40
42
43 GFF3_PATHS = {}
44
53
55 return "\n".join(self._header)
56
58 params = self.query.to_query_params()
59 i = self.service.get_results(self.path, params, "tsv", self.query.views)
60 return i
61
63 lines = [line for line in self]
64 return "\n".join(self._header + lines)
65
68
70 line = self.it.next()
71 while line and line.startswith("#"):
72 self._header.append(line)
73 line = self.it.next()
74 if line:
75 return line
76 raise StopIteration
77
79
80 FASTA_PATHS = {}
81
90
92 params = self.query.to_query_params()
93 i = self.service.get_results(self.path, params, "tsv", self.query.views)
94 return i
95
97 records = [rec for rec in self]
98 return "\n".join(records)
99
102
104 lines = []
105 if self._holdover is not None:
106 lines.append(self._holdover)
107 self._holdover = None
108 else:
109 try:
110 lines.append(self.it.next())
111 except StopIteration:
112 pass
113
114 try:
115 while True:
116 line = self.it.next()
117 if line.startswith(">"):
118 self._holdover = line
119 break
120 lines.append(line)
121 except StopIteration:
122 pass
123
124 if len(lines):
125 return "\n".join(lines)
126
127 if self._holdover:
128 ret = self._holdover
129 self._holdover = None
130 return self._holdover
131
132 raise StopIteration
133