def _composeDataLine(self, ge, hbColumns, dataLineCount, lastGE):
cols = []
for hbColName in hbColumns:
if hbColName == "start":
cols.append(self._formatStart(ge.start))
elif hbColName == "end":
cols.append(self._formatEnd(ge.end))
elif hbColName == "strand":
cols.append(getStringFromStrand(ge.strand))
elif hbColName == "val":
cols.append(self._formatValue(ge.val))
elif hbColName == "edges":
cols.append(self._formatEdges(ge.edges, ge.weights))
elif hbColName == "weights":
pass
else:
cols.append(
self._formatPhraseWithCorrectChrUsage(
str(getattr(ge, hbColName)), useUrlEncoding=True, notAllowedChars="#\t"
)
)
if self._headerDict["fixed-size data lines"]:
assert len(cols) == 1
return cols[0] + (os.linesep if (dataLineCount * len(cols[0])) % 60 < len(cols[0]) or lastGE else "")
else:
return "\t".join(cols) + os.linesep
def _compose(self, out):
trackName = self._geSource.getTrackName()
if trackName is not None:
name = ':'.join(self._geSource.getTrackName()).replace(' ','_')
print >>out, 'track' + ' name=' + name
numCols = self._findNumCols()
bedColumnsList = list(self._bedColumnsDict.iteritems())
for ge in self._geSource:
cols = ['']*numCols
for i in range(numCols):
colNames, colInfo = bedColumnsList[i]
for colName in (colNames if type(colNames) == tuple else (colNames,)):
try:
value = getattr(ge, colName)
except AttributeError:
value = None
if colName == 'end':
value = self._handleEnd(ge, value)
elif colName == 'val':
value = self._handleVal(value)
elif colName == 'strand':
value = getStringFromStrand(value)
if isinstance(value, str) and colName not in ('name', 'id'):
if '|' in value or any('|' in getattr(ge, col) \
for col in colInfo.checkExtra if hasattr(ge,col)):
cols[i] = colInfo.defaultVal
else:
cols[i] = value
else:
cols[i] = value if value is not None else colInfo.defaultVal
if colName == 'id' and value is not None:
break
print >>out, '\t'.join([str(x) for x in cols])
def _compose(self, out):
print >>out, '##gff-version 3'
gffColumnsList = list(self._gffColumnsDict.iteritems())
numCols = 9
for ge in self._geSource:
cols = [''] * numCols
for i in range(numCols):
colName, colInfo = gffColumnsList[i]
try:
value = getattr(ge, colName)
except AttributeError:
value = None
if colName == 'source':
if value is not None and '\t' in value: #from old source memmaps
value = '.'
if colName == 'start':
value = value + 1
elif colName == 'val':
value = self._commonFormatNumberVal(value)
elif colName == 'strand':
value = getStringFromStrand(value)
elif colName == 'attributes':
if value is None:
attrs = ''
if ge.id is not None:
attrs += 'ID=%s;' % quote(ge.id, safe=' |')
if hasattr(ge, 'name'):
attrs += 'Name=%s;' % quote(ge.name, safe=' |')
if attrs != '':
value = attrs
cols[i] = value if value is not None else colInfo.defaultVal
print >>out, '\t'.join([str(x) for x in cols])
