def loadFile(self, fileName):
file = QFile(fileName)
if not file.open(QFile.ReadOnly):
mb = QMessageBox(self)
mb.setTextFormat(Qt.RichText)
mb.setText("<p style='font-size: 18pt'>File opening error</p>"
"<p style='font-size: 14pt; font-weight: normal'> Unable to open file <i>{}</i>.<br><br>File error was: \"{}\".</p>".format(fileName, file.errorString()))
mb.setIcon(QMessageBox.Warning)
mb.exec()
return
inf = QTextStream(file)
QApplication.setOverrideCursor(Qt.WaitCursor)
QApplication.processEvents()
Line1=inf.readLine()
if Line1.startswith(">"):
readOK=self.read_seq(fileName, "fasta")
elif Line1.upper().startswith("CLUSTAL"):
readOK=self.read_seq(fileName, "clustal")
elif Line1.upper().startswith("#NEXUS"):
readOK=self.read_seq(fileName, "nexus")
elif Line1.upper().find("STOCKHOLM") > -1:
readOK=self.read_seq(fileName, "stockholm")
elif Line1.upper().find("MULTIPLE_ALIGNMENT") > -1 or Line1.upper().find("PILEUP") > -1:
readOK=self.read_seq(fileName, "msf")
elif len([int(i) for i in Line1.split() if i.isdigit()]) == 2:
readOK=self.read_seq(fileName, "phylip-relaxed")
else:
QApplication.restoreOverrideCursor()
mb = QMessageBox(self)
mb.setTextFormat(Qt.RichText)
mb.setText("<p style='font-size: 18pt'>Alignment file error</p>"
"<p style='font-size: 14pt; font-weight: normal'> Sorry, I don't recognise the format of file:<br><i>{}</i></p>".format(fileName))
mb.setIcon(QMessageBox.Warning)
mb.exec()
file.close()
return
if not readOK: # If there was an error in read_seq, the cursor has already been reset
file.close()
return
self.seqs = np.array([list(rec.upper()) for rec in self.al], str, order="F")
self.seqnames = [rec.id for rec in self.al]
self.al = []
# release the memory used by the BioPython construct, not needed now.
# now that I know how big an alignment I have, I redefine the space taken up by the various arrays
self.no_seqs = self.seqs.shape[0]
self.maxseqlen = self.seqs.shape[1]
mbflag=False
if self.no_seqs*self.maxseqlen >50000:
mb = QMessageBox(self)
mb.setAttribute(Qt.WA_DeleteOnClose)
mb.setTextFormat(Qt.RichText)
mb.setText("<p style='font-size: 18pt'>Large file warning</p>"
"<p style='font-size: 14pt; font-weight: normal'> OK, that's a big alignment!<br>"
"Be aware that processing the alignment and preparing images/files will take more than a few seconds \U0001F609.<br>"
"Working.....</p>")
mb.setIcon(QMessageBox.Information)
mb.setStandardButtons(QMessageBox.NoButton)
mb.setWindowModality(Qt.NonModal)
mbflag=True
mb.show()
app.processEvents()
if system() == "Darwin":
BS.monofont.setPointSize(14)
else:
BS.monofont.setPointSize(12)
BS.monofont.setWeight(QFont.Normal)
self.textEdit.setFont(BS.monofont)
inf.seek(0)
self.textEdit.setPlainText(inf.readAll())
file.close()
self.cols = np.full(self.seqs.shape, 0, dtype=np.int32)
self.cons = np.full(self.maxseqlen, ' ', dtype=str)
self.conschar = np.copy(self.cons)
self.seqlens = np.full(self.no_seqs, self.maxseqlen, dtype=np.int32)
self.startnums = np.full(self.no_seqs, 1, dtype=np.int64) # a newly loaded file has all startnums set to 1 by default
#
#set consensus length = length of longest sequence (not counting dots,
#spaces, etc. at the "far" end. May be a problem here for some strange cases
self.consenslen = 0
for i in range(0,self.no_seqs):
while self.seqlens[i] and (self.seqs[i, self.seqlens[i] - 1] in [' ', '-', '.']):
self.seqlens[i] -= 1
if self.seqlens[i] > self.consenslen:
self.consenslen = self.seqlens[i]
self.setCurrentFile(fileName)
QApplication.restoreOverrideCursor()
self.process_seqs()
if mbflag:
mb.done(1)
self.statusBar().showMessage("File loaded", 2000)
return # from load_file
class LogsReadThread(QThread):
MAX_INITIAL_SIZE = 2*1024*1024 # 2Mb
updateLogs = pyqtSignal()
def __init__(self, parent):
QThread.__init__(self, parent)
self.fCloseNow = False
self.fPurgeLogs = False
self.fRealParent = parent
# -------------------------------------------------------------
# Take some values from Logs Window
self.LOG_FILE_JACK = LogsW.LOG_FILE_JACK
self.LOG_FILE_A2J = LogsW.LOG_FILE_A2J
self.LOG_FILE_LASH = LogsW.LOG_FILE_LASH
self.LOG_FILE_LADISH = LogsW.LOG_FILE_LADISH
# -------------------------------------------------------------
# Init logs
if self.LOG_FILE_JACK is not None:
self.fLogFileJACK = QFile(self.LOG_FILE_JACK)
self.fLogFileJACK.open(QIODevice.ReadOnly)
self.fLogStreamJACK = QTextStream(self.fLogFileJACK)
self.fLogStreamJACK.setCodec("UTF-8")
if self.fLogFileJACK.size() > self.MAX_INITIAL_SIZE:
self.fLogStreamJACK.seek(self.fLogFileJACK.size() - self.MAX_INITIAL_SIZE)
if self.LOG_FILE_A2J is not None:
self.fLogFileA2J = QFile(self.LOG_FILE_A2J)
self.fLogFileA2J.open(QIODevice.ReadOnly)
self.fLogStreamA2J = QTextStream(self.fLogFileA2J)
self.fLogStreamA2J.setCodec("UTF-8")
if self.fLogFileA2J.size() > self.MAX_INITIAL_SIZE:
self.fLogStreamA2J.seek(self.fLogFileA2J.size() - self.MAX_INITIAL_SIZE)
if self.LOG_FILE_LASH is not None:
self.fLogFileLASH = QFile(self.LOG_FILE_LASH)
self.fLogFileLASH.open(QIODevice.ReadOnly)
self.fLogStreamLASH = QTextStream(self.fLogFileLASH)
self.fLogStreamLASH.setCodec("UTF-8")
if self.fLogFileLASH.size() > self.MAX_INITIAL_SIZE:
self.fLogStreamLASH.seek(self.fLogFileLASH.size() - self.MAX_INITIAL_SIZE)
if self.LOG_FILE_LADISH is not None:
self.fLogFileLADISH = QFile(self.LOG_FILE_LADISH)
self.fLogFileLADISH.open(QIODevice.ReadOnly)
self.fLogStreamLADISH = QTextStream(self.fLogFileLADISH)
self.fLogStreamLADISH.setCodec("UTF-8")
if self.fLogFileLADISH.size() > self.MAX_INITIAL_SIZE:
self.fLogStreamLADISH.seek(self.fLogFileLADISH.size() - self.MAX_INITIAL_SIZE)
def closeNow(self):
self.fCloseNow = True
def purgeLogs(self):
self.fPurgeLogs = True
def run(self):
# -------------------------------------------------------------
# Read logs and set text in main thread
while not self.fCloseNow:
if self.fPurgeLogs:
if self.LOG_FILE_JACK:
self.fLogStreamJACK.flush()
self.fLogFileJACK.close()
self.fLogFileJACK.open(QIODevice.WriteOnly)
self.fLogFileJACK.close()
self.fLogFileJACK.open(QIODevice.ReadOnly)
if self.LOG_FILE_A2J:
self.fLogStreamA2J.flush()
self.fLogFileA2J.close()
self.fLogFileA2J.open(QIODevice.WriteOnly)
self.fLogFileA2J.close()
self.fLogFileA2J.open(QIODevice.ReadOnly)
if self.LOG_FILE_LASH:
self.fLogStreamLASH.flush()
self.fLogFileLASH.close()
self.fLogFileLASH.open(QIODevice.WriteOnly)
self.fLogFileLASH.close()
self.fLogFileLASH.open(QIODevice.ReadOnly)
if self.LOG_FILE_LADISH:
self.fLogStreamLADISH.flush()
self.fLogFileLADISH.close()
self.fLogFileLADISH.open(QIODevice.WriteOnly)
self.fLogFileLADISH.close()
self.fLogFileLADISH.open(QIODevice.ReadOnly)
self.fPurgeLogs = False
else:
if self.LOG_FILE_JACK:
textJACK = fixLogText(self.fLogStreamJACK.readAll()).strip()
else:
textJACK = ""
if self.LOG_FILE_A2J:
textA2J = fixLogText(self.fLogStreamA2J.readAll()).strip()
else:
textA2J = ""
if self.LOG_FILE_LASH:
textLASH = fixLogText(self.fLogStreamLASH.readAll()).strip()
else:
textLASH = ""
if self.LOG_FILE_LADISH:
textLADISH = fixLogText(self.fLogStreamLADISH.readAll()).strip()
else:
textLADISH = ""
self.fRealParent.setLogsText(textJACK, textA2J, textLASH, textLADISH)
self.updateLogs.emit()
if not self.fCloseNow:
self.sleep(1)
# -------------------------------------------------------------
# Close logs before closing thread
if self.LOG_FILE_JACK:
self.fLogFileJACK.close()
if self.LOG_FILE_A2J:
self.fLogFileA2J.close()
if self.LOG_FILE_LASH:
self.fLogFileLASH.close()
if self.LOG_FILE_LADISH:
self.fLogFileLADISH.close()
def loadFile(self, fileName):
file = QFile(fileName)
if not file.open(QFile.ReadOnly):
QMessageBox.warning(
self, "Application",
"Cannot read file %s:\n%s." % (fileName, file.errorString()))
return
inf = QTextStream(file)
QApplication.setOverrideCursor(Qt.WaitCursor)
BS.monofont.setPointSize(14)
BS.monofont.setWeight(QFont.Normal)
self.textEdit.setFont(BS.monofont)
self.textEdit.setPlainText(inf.readAll())
inf.seek(0)
Line1 = inf.readLine()
file.close()
if Line1.startswith(">"):
self.read_seq(fileName, "fasta")
elif Line1.upper().startswith("CLUSTAL"):
self.read_seq(fileName, "clustal")
elif Line1.upper().startswith("#NEXUS"):
self.read_seq(fileName, "nexus")
elif Line1.upper().find("STOCKHOLM") > -1:
self.read_seq(fileName, "stockholm")
elif Line1.upper().find("MULTIPLE_ALIGNMENT") > -1 or Line1.upper(
).find("PILEUP") > -1:
self.read_seq(fileName, "msf")
elif len([int(i) for i in Line1.split() if i.isdigit()]) == 2:
self.read_seq(fileName, "phylip-relaxed")
else:
QMessageBox.warning(
self, "Application",
"Cannot extract alignment from file %s" % fileName)
QApplication.restoreOverrideCursor()
return
self.seqs = np.array([list(rec) for rec in self.al],
np.unicode,
order="F")
self.seqnames = [rec.id for rec in self.al]
self.al = [
] # release the memory used by the BioPython construct, not needed now.
# now that I know how big an alignment I have, I redefine the space taken up by the various arrays
self.no_seqs = self.seqs.shape[0]
self.maxseqlen = self.seqs.shape[1]
self.cols = np.full(self.seqs.shape, 0, dtype=np.int32)
self.cons = np.full(self.maxseqlen, ' ', dtype=np.unicode)
self.conschar = np.copy(self.cons)
self.seqlens = np.full(self.no_seqs, self.maxseqlen, dtype=np.int32)
self.startnums = np.full(
self.no_seqs, 1, dtype=np.int64
) # a newly loaded file has all startnums set to 1 by default
#
#set consensus length = length of longest sequence (not counting dots,
#spaces, etc. at the "far" end. May be a problem here for some strange cases
self.consenslen = 0
for i in range(0, self.no_seqs):
while self.seqs[i, self.seqlens[i] - 1] in [' ', '-', '.']:
self.seqlens[i] -= 1
if self.seqlens[i] > self.consenslen:
self.consenslen = self.seqlens[i]
self.setCurrentFile(fileName)
self.statusBar().showMessage("File loaded", 2000)
self.process_seqs()
QApplication.restoreOverrideCursor()
return # from load_file
