def __init__(self, bowtieOutputFile, alignedReadsFile):
self.numberRegularExpression = re.compile("\d+")
self.bowtieOutputFile = safeOpenFile(
bowtieOutputFile, "r",
"Error: no bowtie output file for translation found. Terminated.")
self.alignedReadsFile = safeOpenFile(
alignedReadsFile, "w",
"Error: file can not be created. Terminated.")
def __init__(self, originalReadsFile, alignedReadsFile, correctedReadsFile, failedToAlignReadsFile, reportFile):
# #overall reads counts (might be slow)
# self.alignedReadsCount = fileLinesCount(alignedReadsFile) / 4
# self.failedToAlignReadsCount = fileLinesCount(failedToAlignReadsFile) / 4
# self.originalReadsCount = fileLinesCount(originalReadsFile) / 4
# file handlers
self.originalReadsFile = safeOpenFile(
originalReadsFile, "Comparator error: no file with original reads found. Terminated."
)
self.alignedReadsFile = safeOpenFile(
alignedReadsFile, "Comparator error: no file with aligned reads found. Terminated."
)
self.correctedReadsFile = safeOpenFile(
correctedReadsFile, "Comparator error: no file with corrected reads found. Terminated."
)
self.failedToAlignReadsFile = safeOpenFile(
failedToAlignReadsFile, "Comparator error: no file with reads failed to align found. Terminated."
)
self.reportFile = open(reportFile, "w")
# constants
self.readLength = self.defineReadLength()
# temporary
self.alignedReadsCache = {}
self.failedToAlignReadsCache = {}
# report
self.notAlignedReadsCount = 0
self.notFoundInAlignedReadsCount = 0
self.notFoundInOriginalReadsCount = 0
self.processedReadsCount = 0
self.correctedAndTrimmedReadsCount = 0 # corrected and trimmed
self.correctedOnlyReadsCount = 0
self.trimmedOnlyReadsCount = 0
self.wronglyCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
self.wronglyUncorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
self.finelyCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
self.shouldNotHaveBeenCorrectedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
self.wronglyTrimmedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
self.finelyTrimmedNucleotidesQualities = numpy.zeros((127,), dtype=numpy.int32)
def __init__(self, originalReadsFile, alignedReadsFile, correctedReadsFile,
failedToAlignReadsFile, reportDir, reportTotal,
noSmartGraphics):
if reportDir[-1] == "/":
self.reportDir = reportDir
else:
self.reportDir = reportDir + "/"
if reportTotal:
#overall reads counts (might be slow)
self.alignedReadsCount = fileLinesCount(alignedReadsFile) / 4
self.failedToAlignReadsCount = fileLinesCount(
failedToAlignReadsFile) / 4
self.originalReadsCount = fileLinesCount(originalReadsFile) / 4
self.noSmartGraphics = noSmartGraphics
#file handlers
self.originalReadsFile = safeOpenFile(
originalReadsFile, "r",
"Comparator error: no file with original reads found. Terminated.")
self.alignedReadsFile = safeOpenFile(
alignedReadsFile, "r",
"Comparator error: no file with aligned reads found. Terminated.")
self.correctedReadsFile = safeOpenFile(
correctedReadsFile, "r",
"Comparator error: no file with corrected reads found. Terminated."
)
self.failedToAlignReadsFile = safeOpenFile(
failedToAlignReadsFile, "r",
"Comparator error: no file with reads failed to align found. Terminated."
)
self.reportFile = safeOpenFile(
self.reportDir + "report", "w",
"Error: file can not be created. Terminated.")
#constants
self.readLength = self.defineReadLength()
#temporary
self.alignedReadsCache = {}
self.failedToAlignReadsCache = {}
#report
self.notAlignedReadsCount = 0
self.notFoundInAlignedReadsCount = 0
self.notFoundInOriginalReadsCount = 0
self.processedReadsCount = 0
self.correctedAndTrimmedReadsCount = 0 #corrected and trimmed
self.correctedOnlyReadsCount = 0
self.trimmedOnlyReadsCount = 0
self.wronglyCorrectedNucleotidesQualities = numpy.zeros(
(127, ), dtype=numpy.int32)
self.wronglyUncorrectedNucleotidesQualities = numpy.zeros(
(127, ), dtype=numpy.int32)
self.finelyCorrectedNucleotidesQualities = numpy.zeros(
(127, ), dtype=numpy.int32)
self.shouldNotHaveBeenCorrectedNucleotidesQualities = numpy.zeros(
(127, ), dtype=numpy.int32)
self.wronglyTrimmedNucleotidesQualities = numpy.zeros(
(127, ), dtype=numpy.int32)
self.finelyTrimmedNucleotidesQualities = numpy.zeros((127, ),
dtype=numpy.int32)
def __init__(self, rawAlignedReadsFile, alignedReadsFile):
self.numberRegularExpression = re.compile("\d+")
self.inputFile = safeOpenFile(
rawAlignedReadsFile, "Translator error: no input file for translation found. Terminated."
)
self.outputFile = open(alignedReadsFile, "w")
