def exportAlignment(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Alignment')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != Gtk.ResponseType.OK:
return
# write out the sequences
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
for cnt in range(0, self.numseqs):
seqfname = self.cons.getSequenceTrace(cnt).getFileName()
desc = 'sequence ' + str(cnt)
if self.cons.getSequenceTrace(cnt).isReverseComplemented():
desc += ' (reverse complemented)'
sw.addAlignedSequence(self.cons.getAlignedSequence(cnt), seqfname,
desc)
sw.write()
def exportConsensus(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Consensus Sequence')
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
fc.destroy()
if response != Gtk.ResponseType.OK:
return
# write out the sequence
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
desc = 'consensus'
seqfname = self.cons.getSequenceTrace(0).getFileName()
if self.numseqs == 2:
seqfname += ', ' + self.cons.getSequenceTrace(1).getFileName()
sw.addUnalignedSequence(self.cons.getCompactConsensus(), seqfname,
desc)
sw.write()
def exportSelected(self, widget):
# create a file chooser dialog to get a file name and format from the user
fc = seqwriter.SeqWriterFileDialog(self, 'Export Selected Sequences')
fc.setShowOptions(True)
fc.set_current_folder(os.getcwd())
response = fc.run()
fname = fc.get_filename()
fformat = fc.getFileFormat()
include_fnames = fc.getIncludeFileNames()
fc.destroy()
if response != Gtk.ResponseType.OK:
return
# write out the sequences
sw = seqwriter.SequenceWriterFactory.getSequenceWriter(fformat)
try:
sw.open(fname)
except IOError:
self.showMessage(
'The file "' + fname + '" could not be opened for writing. ' +
'Verify that you have permission to write to the specified file and directory.'
)
return
items = self.projview.getSelection()
for item in items:
if item.hasParent():
continue
if item.getUseSequence():
desc = item.getNotes()
if item.isFile():
seqfname = item.getName()
else:
children = item.getChildren()
seqfname = children[0].getName(
) + ', ' + children[1].getName()
if not (include_fnames):
seqfname = ''
sw.addUnalignedSequence(item.getCompactConsSequence(),
seqfname, desc)
try:
sw.write()
except seqwriter.SequenceWriterError as err:
self.showMessage('Error: ' + str(err))