本文整理汇总了Python中BCBio.GFF.GFFParser.parse_simple方法的典型用法代码示例。如果您正苦于以下问题：Python GFFParser.parse_simple方法的具体用法？Python GFFParser.parse_simple怎么用？Python GFFParser.parse_simple使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类BCBio.GFF.GFFParser的用法示例。
在下文中一共展示了GFFParser.parse_simple方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: t_simple_parsing
# 需要导入模块: from BCBio.GFF import GFFParser [as 别名]
# 或者: from BCBio.GFF.GFFParser import parse_simple [as 别名]
def t_simple_parsing(self):
"""Parse GFF into a simple line by line dictionary without nesting.
"""
parser = GFFParser()
num_lines = 0
for line_info in parser.parse_simple(self._test_gff_file):
num_lines += 1
assert num_lines == 177, num_lines
line_info = line_info['child'][0]
assert line_info['quals']['confirmed_est'] == \
['yk1055g06.5', 'OSTF085G5_1']
assert line_info['location'] == [4582718, 4583189]示例2: simpleGFF2PygrSQLite
# 需要导入模块: from BCBio.GFF import GFFParser [as 别名]
# 或者: from BCBio.GFF.GFFParser import parse_simple [as 别名]
class simpleGFF2PygrSQLite(object):
def __init__(self,liteserver):
"""Uses BCBio.GFF.GFFparser.parse_simple() to initiate and populate SQLite tables.
No 'nested' Parent:Child relationships are used, but P:C info can be accessed in parse_simple
results. For NOW, only essential data for pygrSliceObj is recorded.
Returns: I THINK nothing --> external liteserver should be populated after loop?
"""
self._parser = GFFParser()
self.srvrInfo = liteserver
self.tables = {} # <-- should add func to populate this on init if any already exist in serverInfo
def _newRow(self, sliceObj):
'''Creates new row in correct table. Creates new table if need be.
'''
# Do we have to make a new table?
if sliceObj.featureType in self.tables:
# Get next k integer
k = len(self.tables[sliceObj.featureType]) # works bc k starts w/ 0
self.tables[sliceObj.featureType].new(k = k,
seq_id = sliceObj.seq_id,
start = sliceObj.start,
stop = sliceObj.stop,
orientation = sliceObj.orientation,
featureType = sliceObj.featureType,
gffKind = sliceObj.gffKind,
coordReference = sliceObj.coordReference,
Parent = sliceObj.Parent,
description = sliceObj.description)
else:
self._newTable(sliceObj)
def _newTable(self,sliceObj):
'''Convert parsed GFF data to correct sql CREATE command, and add
tableObj and keyName to self.tables.
'''
sqlCmd = 'CREATE TABLE %s (k INTEGER PRIMARY KEY, seq_id TEXT, start INT, stop INT, orientation INT, featureType TEXT, gffKind TEXT, coordReference TEXT, Parent TEXT, description TEXT,);'
self.tables[sliceObj.featureType] = sqlgraph.SQLTable(sliceObj.featureType,
serverInfo=self.srvrInfo,
writeable=True,
createTable=sqlCmd)
self.tables[sliceObj.featureType].new(k = 0,
seq_id = sliceObj.seq_id,
start = sliceObj.start,
stop = sliceObj.stop,
orientation = sliceObj.orientation,
featureType = sliceObj.featureType,
gffKind = sliceObj.gffKind,
coordReference = sliceObj.coordReference,
Parent = sliceObj.Parent,
description = sliceObj.description)
def update(self,gffPath):
gff = open(gffFullPath)
gffPrsr = self._parser.parse_simple(gff)
for rec in gffPrsr:
# If rec == 'directive' Move on.
if rec.keys()[0] == 'directive':
continue
# else: create/add to correct table
else:
self.newRow(sGFFrow2SliceObj(gffRec)) # calls newTable if needed
self.srvrInfo.commit()
def getTableNames(self):
srvrInfo.commit()
cur = self.srvrInfo.cursor()
x = cur.execute('SELECT * FROM sqlite_master;')
return [x[1] for x in x]