def processReportFile (reportFile, statusLabel, keyIndex, norelease, species):
hash = {}
f = open(reportFile, "r")
for line in f:
line = line.rstrip()
if line.startswith('Project'):
continue
splitArray = line.split('\t')
keyLabel = splitArray[keyIndex]
status = splitArray[8]
assembly = splitArray[9]
if status == 'revoked' or status == 'replaced':
continue
if norelease == 1 and status == 'released':
continue
if keyIndex == 5:
keyLabel=encodeReportLib.parseFreezeLabel(keyLabel)
if species == 'all':
pass
else:
if species == 'human' and assembly.startswith('hg'):
pass
elif species == 'mouse' and assembly.startswith('mm'):
pass
elif species == assembly:
pass
else:
continue
if not keyLabel in hash:
hash[keyLabel] = {}
for i in statusLabel:
hash[keyLabel][i] = 0
hash[keyLabel][status] += 1
f.close()
if keyIndex == 5:
sortKey = encodeReportLib.orderFreezeDateLabels(hash.keys())
else:
sortKey = sorted(hash)
# Populate dataArray with the contents of the matrix
dataArray = []
for labKey in sortKey:
array = []
array.append(labKey)
for statusKey in statusLabel:
array.append(hash[labKey][statusKey])
dataArray.append(array)
return dataArray
def processReportFile (reportFile, keyIndex):
hash = {}
labelHash = {}
f = open(reportFile, "r")
for line in f:
line = line.rstrip()
if line.startswith('Project'):
continue
splitArray = line.split('\t')
keyLabel = splitArray[keyIndex]
startDate = splitArray[6]
endDate = splitArray[7]
status = splitArray[8]
if keyIndex == 8 and (status == 'revoked' or status == 'replaced'):
continue
if keyIndex == 5:
keyLabel = encodeReportLib.parseFreezeLabel(keyLabel)
# Convert dates into ints
submitDate = encodeReportLib.convertDate(startDate)
releaseDate = encodeReportLib.convertDate(endDate)
if status == 'released':
if not isinstance(submitDate, int) or not isinstance(releaseDate, int):
print >> sys.stderr, "Error: Invalid date: %s" % line
else:
if not keyLabel in labelHash:
labelHash[keyLabel] = 0
labelHash[keyLabel] += 1
deltaTime = encodeReportLib.dateIntToObj(releaseDate) - encodeReportLib.dateIntToObj(submitDate)
days = deltaTime.days
if (days == 0):
days = 1
weeks = days / 7
if (days % 7 != 0):
# Adjust by one except when number of days is exactly divisible by 7
weeks += 1
if not weeks in hash:
hash[weeks] = {}
if not keyLabel in hash[weeks]:
hash[weeks][keyLabel] = 0
hash[weeks][keyLabel] += 1
f.close()
if keyIndex == 5:
labels = encodeReportLib.orderFreezeDateLabels(labelHash.keys())
else:
tmpLabels = sorted(labelHash.iteritems(), key=operator.itemgetter(1),
reverse=True)
labels = []
for i in tmpLabels:
labels.append(i[0])
maxWeek = max(hash)
for i in xrange(1, maxWeek+1):
if not i in hash:
hash[i] = {}
for label in labels:
if not label in hash[i]:
hash[i][label] = 0
# Populate dataArray with the contents of the matrix
dataArray = []
for key in sorted(hash):
array = []
array.append(key)
for label in labels:
array.append(hash[key][label])
dataArray.append(array)
return dataArray, labels
