Exemple #1
0
 def sequenceSripts(self):
     seq = sequence(self.file1, self.file2, self.id1, self.id2, self.chain1,
                    self.chain2, self.parameterfile, self.dirname)
     if self.id1 != self.id2:
         if self.chain1 == "" and self.chain2 == "":
             seq.validFASTA(self.file1, self.id1)
             seq.queryFASTA(self.file1, self.id1)
             seq.validFASTA(self.file2, self.id2)
             seq.queryFASTA(self.file2, self.id2)
         else:
             seq.validPDB(self.file1, self.id1, self.chain1)
             seq.sequencePDB(self.file1, self.id1, self.chain1)
             seq.surfacePDB(self.file1, self.id1, self.chain1)
             seq.validPDB(self.file2, self.id2, self.chain2)
             seq.sequencePDB(self.file2, self.id2, self.chain2)
             seq.surfacePDB(self.file2, self.id2, self.chain2)
     else:
         if self.chain1 == "" and self.chain2 == "":
             seq.validFASTA(self.file1, self.id1)
             seq.queryFASTA(self.file1, self.id1)
         else:
             if self.chain1 != self.chain2:
                 seq.validPDB(self.file1, self.id1, self.chain1)
                 seq.sequencePDB(self.file1, self.id1 + "_1", self.chain1)
                 seq.surfacePDB(self.file1, self.id1 + "_1", self.chain1)
                 seq.validPDB(self.file1, self.id1, self.chain2)
                 seq.sequencePDB(self.file1, self.id1 + "_2", self.chain2)
                 seq.surfacePDB(self.file1, self.id1 + "_2", self.chain2)
             else:
                 seq.validPDB(self.file1, self.id1, self.chain1)
                 seq.sequencePDB(self.file1, self.id1, self.chain1)
                 seq.surfacePDB(self.file1, self.id1, self.chain1)
     return
Exemple #2
0
 def sequenceSripts(self):
     seq = sequence(
         self.file1, self.file2, self.id1, self.id2, self.chain1, self.chain2, self.parameterfile, self.dirname
     )
     if self.id1 != self.id2:
         if self.chain1 == "" and self.chain2 == "":
             seq.validFASTA(self.file1, self.id1)
             seq.queryFASTA(self.file1, self.id1)
             seq.validFASTA(self.file2, self.id2)
             seq.queryFASTA(self.file2, self.id2)
         else:
             seq.validPDB(self.file1, self.id1, self.chain1)
             seq.sequencePDB(self.file1, self.id1, self.chain1)
             seq.surfacePDB(self.file1, self.id1, self.chain1)
             seq.validPDB(self.file2, self.id2, self.chain2)
             seq.sequencePDB(self.file2, self.id2, self.chain2)
             seq.surfacePDB(self.file2, self.id2, self.chain2)
     else:
         if self.chain1 == "" and self.chain2 == "":
             seq.validFASTA(self.file1, self.id1)
             seq.queryFASTA(self.file1, self.id1)
         else:
             if self.chain1 != self.chain2:
                 seq.validPDB(self.file1, self.id1, self.chain1)
                 seq.sequencePDB(self.file1, self.id1 + "_1", self.chain1)
                 seq.surfacePDB(self.file1, self.id1 + "_1", self.chain1)
                 seq.validPDB(self.file1, self.id1, self.chain2)
                 seq.sequencePDB(self.file1, self.id1 + "_2", self.chain2)
                 seq.surfacePDB(self.file1, self.id1 + "_2", self.chain2)
             else:
                 seq.validPDB(self.file1, self.id1, self.chain1)
                 seq.sequencePDB(self.file1, self.id1, self.chain1)
                 seq.surfacePDB(self.file1, self.id1, self.chain1)
     return
Exemple #3
0
 def psiblastSripts(self):
     seq = sequence(self.file1, self.file2, self.id1, self.id2, self.chain1,
                    self.chain2, self.parameterfile, self.dirname)
     blast = psiblast(self.id1, self.id2, self.psiblast, self.parameterfile,
                      self.dirname)
     if self.id1 != self.id2:
         blast.searchPSIBLAST(self.id1, self.psiblast)
         blast.searchPSIBLAST(self.id2, self.psiblast)
         blast.validXML(self.id1)
         blast.validXML(self.id2)
         blast.sequencesXML(self.id1, self.psiblast)
         blast.sequencesXML(self.id2, self.psiblast)
     else:
         if self.chain1 == "" and self.chain2 == "":
             seq.copySequence(self.id1)
             blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
             blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
             blast.validXML(self.id1 + "_1")
             blast.validXML(self.id1 + "_2")
             blast.sequencesXML(self.id1 + "_1", self.psiblast)
             blast.sequencesXML(self.id1 + "_2", self.psiblast)
         else:
             if self.chain1 != self.chain2:
                 blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
                 blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
                 blast.validXML(self.id1 + "_1")
                 blast.validXML(self.id1 + "_2")
                 blast.sequencesXML(self.id1 + "_1", self.psiblast)
                 blast.sequencesXML(self.id1 + "_2", self.psiblast)
             else:
                 seq.copySequence(self.id1)
                 blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
                 blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
                 blast.validXML(self.id1 + "_1")
                 blast.validXML(self.id1 + "_2")
                 blast.sequencesXML(self.id1 + "_1", self.psiblast)
                 blast.sequencesXML(self.id1 + "_2", self.psiblast)
     return
Exemple #4
0
 def psiblastSripts(self):
     seq = sequence(
         self.file1, self.file2, self.id1, self.id2, self.chain1, self.chain2, self.parameterfile, self.dirname
     )
     blast = psiblast(self.id1, self.id2, self.psiblast, self.parameterfile, self.dirname)
     if self.id1 != self.id2:
         blast.searchPSIBLAST(self.id1, self.psiblast)
         blast.searchPSIBLAST(self.id2, self.psiblast)
         blast.validXML(self.id1)
         blast.validXML(self.id2)
         blast.sequencesXML(self.id1, self.psiblast)
         blast.sequencesXML(self.id2, self.psiblast)
     else:
         if self.chain1 == "" and self.chain2 == "":
             seq.copySequence(self.id1)
             blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
             blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
             blast.validXML(self.id1 + "_1")
             blast.validXML(self.id1 + "_2")
             blast.sequencesXML(self.id1 + "_1", self.psiblast)
             blast.sequencesXML(self.id1 + "_2", self.psiblast)
         else:
             if self.chain1 != self.chain2:
                 blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
                 blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
                 blast.validXML(self.id1 + "_1")
                 blast.validXML(self.id1 + "_2")
                 blast.sequencesXML(self.id1 + "_1", self.psiblast)
                 blast.sequencesXML(self.id1 + "_2", self.psiblast)
             else:
                 seq.copySequence(self.id1)
                 blast.searchPSIBLAST(self.id1 + "_1", self.psiblast)
                 blast.searchPSIBLAST(self.id1 + "_2", self.psiblast)
                 blast.validXML(self.id1 + "_1")
                 blast.validXML(self.id1 + "_2")
                 blast.sequencesXML(self.id1 + "_1", self.psiblast)
                 blast.sequencesXML(self.id1 + "_2", self.psiblast)
     return