def importFastaSeq(self):
if not self.project:
showWarning('Failure','Please create a new CCPN project.', parent=self)
return
fileTypes = [ FileType('Fasta', ['*.fsa']),
FileType('All', ['*']) ]
fileSelectPopup = FileSelectPopup(self, file_types=fileTypes,
title='Import Fasta sequence file', dismiss_text='Cancel',
selected_file_must_exist=True, multiSelect=False,)
fileName = fileSelectPopup.getFile()
if not os.path.exists(fileName):
showWarning('Failure','No such file.', parent=self)
return
if fileName:
name = os.path.split(fileName)[1]
if '.' in name:
name = name.split('.')[0]
fastaObj = FastaFormat(self.project, self, verbose=True)
fastaObj.readSequence(fileName, minimalPrompts=True)
self.eciFrame.updateAll()
return fastaObj
nmrEntry.addApplicationData(appData)
# Print it.
entryAppData = nmrEntry.findFirstApplicationData()
print 'Application data: [%s]' % entryAppData
# Find it based on the application and keyword values.
keywds2 = {'application': 'Fasta format', 'keyword': 'sequence file'}
seqFileFromAppData = nmrEntry.findFirstApplicationData(**keywds2).value
# Read in a sequence to create a molSystem object - can also set the
# Tkinter object to None for using all text-based format converter sub
# routines.
fastaObj = FastaFormat(project, None)
fastaObj.readSequence(seqFileFromAppData, minimalPrompts=1)
# Connect the molSystem to the BMRB Entry.
nmrEntry.setMolSystem(project.sortedMolSystems()[0])
# Also create a new study object.
keywordList = ['NMR', 'Structure determination']
study = entryStore.newStudy(name=project.name, keywords=keywordList)
# And connect to the Entry object.
nmrEntry.setStudy(study)
affStore = project.newAffiliationStore(name=project.name)
#
# Give the location of the sequence file
#
sequenceFile = os.path.join(dataDir, sequenceFileName)
#
# Create a FastaFormat instance
#
# Again, if this was PDB format, this would read:
#
# formatObject = PdbFormat(ccpnProject,guiRoot)
#
formatObject = FastaFormat(ccpnProject, guiRoot)
#
# Call the readSequence method from the fastaFormat instance
# and pass in the name of the file to read
#
# This line would be the same for a PDB format - the read/write methods
# are the same for all formats (except for some format-specific keywords
# in some cases)
#
formatObject.readSequence(sequenceFile, minimalPrompts=1)
#
# Testing to see if all is there...
#
import memops.api.Implementation as Implementation
# Get FastaFormat class for format conversion.
from ccpnmr.format.converters.FastaFormat import FastaFormat
if __name__ == '__main__':
# CCPN project.
project = Implementation.MemopsRoot(name = 'readFasta')
# Create a Tkinter object.
guiRoot = Tkinter.Tk()
# Create a FastaFormat object and associate it with the CCPN project and
# Tkinter object.
fastaObj = FastaFormat(project, guiRoot)
# Give the location of the sequence file.
seqDir = '../data/seq'
seqFile = os.path.join(seqDir, 'fasta.seq')
# Call the readSequence method from the fastaFormat instance
# and pass in the name of the file to read.
fastaObj.readSequence(seqFile, minimalPrompts = 1)
# Check to see if molSystem and molecule objects are in the CCPN project.
print '\nProject object: [%s]' % project
print "'list' of MolSystem objects: [%s]" % project.sortedMolSystems()
print "'list' of Molecule objects: [%s]" % project.sortedMolecules()
# Select first available molecule.
# # Give the location of the sequence file # sequenceFile = os.path.join(dataDir,sequenceFileName) # # Create a FastaFormat instance # # Again, if this was PDB format, this would read: # # formatObject = PdbFormat(ccpnProject,guiRoot) # formatObject = FastaFormat(ccpnProject,guiRoot) # # Call the readSequence method from the fastaFormat instance # and pass in the name of the file to read # # This line would be the same for a PDB format - the read/write methods # are the same for all formats (except for some format-specific keywords # in some cases) # formatObject.readSequence(sequenceFile,minimalPrompts = 1) # # Testing to see if all is there... #