def GetExec(self, optList, frame):
# Respond to the "embossn" type command.
self.frame = frame
plugin_exe = r"C:/mEMBOSS/water.exe"
self.outfile = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\water.txt"
self.outtype = "fasta"
cline = WaterCommandline(plugin_exe, asequence=str(self.frame.paramBoxes[1].GetValue()), bsequence=str(self.frame.paramBoxes[3].GetValue()))
cline.outfile = self.outfile
cline.gapopen = self.param[7].GetValue()
cline.gapextend = self.param[9].GetValue()
if self.param[10].GetValue():
cline.similarity = True
else:
cline.similarity = False
if self.frame.abet=="AA":
cline.snucleotide = True
cline.sprotein = False
elif self.frame.abet=="DNA" or self.frame.abet=="RNA":
cline.snucleotide = True
cline.sprotein = False
if self.frame.options:
t = self.boxList[3].GetValue()
if t != '':
cline.datafile = str(t)
return str(cline)
def GetExec(self, optList, frame):
# Respond to the "embossn" type command.
self.frame = frame
plugin_exe = r"C:/mEMBOSS/water.exe"
self.outfile = r"C:\Users\francis\Documents\Monguis\BioGui\plugins\water.txt"
self.outtype = "fasta"
cline = WaterCommandline(
plugin_exe,
asequence=str(self.frame.paramBoxes[1].GetValue()),
bsequence=str(self.frame.paramBoxes[3].GetValue()))
cline.outfile = self.outfile
cline.gapopen = self.param[7].GetValue()
cline.gapextend = self.param[9].GetValue()
if self.param[10].GetValue():
cline.similarity = True
else:
cline.similarity = False
if self.frame.abet == "AA":
cline.snucleotide = True
cline.sprotein = False
elif self.frame.abet == "DNA" or self.frame.abet == "RNA":
cline.snucleotide = True
cline.sprotein = False
if self.frame.options:
t = self.boxList[3].GetValue()
if t != '':
cline.datafile = str(t)
return str(cline)
def generate_water_cmd(macierz, pliki_fasta_rodzina):
"""
Generuje polecenia wywolania programu water EMBOSS dla wszystkich sekwencji podanych jako nazwy plikow je zawierajacych
:param macierz: lokalizacja/nazwa pliku z macierza substytucji PAM/BLOSUM
:param pliki_fasta_fodzina: lista lokalizacji/nazw plikow z sekwencjami bialkowymi fasta nalezacymi do danej rodziny
:return: polecenie wywolania programu water
"""
records = []
for file in pliki_fasta_rodzina:
handle = open(file, "rU")
records.extend(list(SeqIO.parse(handle, "fasta")))
handle.close()
from Bio.Emboss.Applications import WaterCommandline
all_water_cmd = []
for i in range(len(records)):
for j in range(len(records)):
if i < j:
water_cmd = WaterCommandline(gapopen=100, gapextend=10)#maksymalne wartosci aby uzyskac uliniowienia bezspacjowe
water_cmd.asequence = "asis:" + str(records[i].seq)
water_cmd.bsequence = "asis:" + str(records[j].seq)
water_cmd.stdout = True
water_cmd.sprotein=True
water_cmd.datafile=macierz
all_water_cmd.append(str(water_cmd))
return all_water_cmd
