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
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
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
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
