adding *.fna files and fixing bug in msat scanning

Author: Brant Faircloth

main.py

@@ -31,7 +31,7 @@ def __init__(self, parent = None, config = 'msatcommander.conf'):
     def open(self):
         '''get the input filename - mutiple file input is not supported'''
         self.infile = QtGui.QFileDialog.getOpenFileName(self,\
-            "Select Fasta to Search",os.path.expanduser('~'), "Fasta (*.fsa *.fa *.fasta)")
+            "Select Fasta to Search",os.path.expanduser('~'), "Fasta (*.fsa *.fa *.fasta *.fna)")
         # ==================
         # = DEBUG EASIFIER =
         # ==================
@@ -525,13 +525,14 @@ def readSearchSave(self):
                         #pdb.set_trace()
                         # fixing bug in primer number reporting reported by Jarek Byrk
                         # Max Planck Institute for Evolutionary Biology
-                        locus_specific_primer = record.primers[motif][record.matches[motif].index(match)]
-                        if record.primers:
-                            self.storePrimers(index, msat_index, locus_specific_primer)
-                        if record.primers \
-                            and (self.pigtailPrimersCheckBox.isChecked() \
-                            or self.tagPrimersCheckBox.isChecked()):
-                            self.storeTaggedPrimers(index, msat_index, locus_specific_primer)
+                        if self.designPrimersCheckBox.isChecked():
+                            locus_specific_primer = record.primers[motif][record.matches[motif].index(match)]
+                            if record.primers:
+                                self.storePrimers(index, msat_index, locus_specific_primer)
+                            if record.primers \
+                                and (self.pigtailPrimersCheckBox.isChecked() \
+                                or self.tagPrimersCheckBox.isChecked()):
+                                self.storeTaggedPrimers(index, msat_index, locus_specific_primer)
                         msat_index += 1
 
             if self.combineLociCheckBox.isChecked():
@@ -560,13 +561,14 @@ def readSearchSave(self):
                         # ensure the same bug doesn't hit us as above:
                         #QtCore.pyqtRemoveInputHook()
                         #pdb.set_trace()
-                        locus_specific_primer = record.primers[motif][pos]
-                        if record.primers:
-                            self.storePrimers(index, combine_index, locus_specific_primer)
-                        if record.primers \
-                            and (self.pigtailPrimersCheckBox.isChecked() \
-                            or self.tagPrimersCheckBox.isChecked()):
-                            self.storeTaggedPrimers(index, combine_index, locus_specific_primer)
+                        if self.designPrimersCheckBox.isChecked():
+                            locus_specific_primer = record.primers[motif][pos]
+                            if record.primers:
+                                self.storePrimers(index, combine_index, locus_specific_primer)
+                            if record.primers \
+                                and (self.pigtailPrimersCheckBox.isChecked() \
+                                or self.tagPrimersCheckBox.isChecked()):
+                                self.storeTaggedPrimers(index, combine_index, locus_specific_primer)
                         combine_index += 1
 
             self.conn.commit()

setup.py

@@ -38,7 +38,7 @@
     pass
 print 'Building app...'
 
-VER = '1.0.6-beta'
+VER = '1.0.8-beta'
 NAME = 'msatcommander'
 APPNAME = '%s-%s' % (NAME, VER)
 FULLAPPNAME = '%s.app' % APPNAME

ui_msatcommander.py

@@ -397,7 +397,7 @@ def setupUi(self, msatcommander):
         msatcommander.setTabOrder(self.customTagCheckBox, self.hexanucSpinBox)
 
     def retranslateUi(self, msatcommander):
-        msatcommander.setWindowTitle(QtGui.QApplication.translate("msatcommander", "msatcommander-1.0.6-beta", None, QtGui.QApplication.UnicodeUTF8))
+        msatcommander.setWindowTitle(QtGui.QApplication.translate("msatcommander", "msatcommander-1.0.8-beta", None, QtGui.QApplication.UnicodeUTF8))
         self.groupBox.setTitle(QtGui.QApplication.translate("msatcommander", "Search Parameters", None, QtGui.QApplication.UnicodeUTF8))
         self.dinucCheckBox.setText(QtGui.QApplication.translate("msatcommander", "Dinucleotide", None, QtGui.QApplication.UnicodeUTF8))
         self.pentanucCheckBox.setText(QtGui.QApplication.translate("msatcommander", "Pentanucleotide", None, QtGui.QApplication.UnicodeUTF8))