def out():
filename1 = e1.get()
filename2 = e2.get()
outfile = e3.get()
needle_cline = WaterCommandline()
needle_cline.asequence = filename1
needle_cline.bsequence = filename2
needle_cline.gapopen = int(gapopen)
needle_cline.gapextend = int(gapextend)
needle_cline.outfile = "needle.txt"
print(needle_cline)
print(needle_cline.outfile)
stdout, stderr = needle_cline()
print(stdout + stderr)
align = AlignIO.read("needle.txt", "emboss")
file = open("needle.txt", "r")
# print(file.read())
view = ("\n\n%s" % file.read())
root = Tk()
S = Scrollbar(root)
T = Text(root, height=4, width=500)
S.pack(side=RIGHT, fill=Y)
T.pack(side=LEFT, fill=Y)
S.config(command=T.yview)
T.config(yscrollcommand=S.set)
T.insert(END, view)
with open(outfile, "w") as f:
f.write(view)
def test_water_file(self):
"""water with the asis trick, output to a file."""
#Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"],
gapopen="10",
gapextend="0.5")
#Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
#Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"),
errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0: print >> sys.stderr, "\n%s" % cline
self.assertEqual(result.return_code, 0)
filename = result.get_result("outfile")
self.assertEqual(filename, "Emboss/temp with space.water")
assert os.path.isfile(filename)
#Check we can parse the output...
align = AlignIO.read(open(filename), "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
#Clean up,
os.remove(filename)
def test_water_file(self):
"""water with the asis trick, output to a file."""
#Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"],
gapopen="10", gapextend="0.5")
#Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
#Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
#Run the tool,
result, out, err = generic_run(cline)
#Check it worked,
errors = err.read().strip()
self.assert_(errors.startswith("Smith-Waterman local alignment"), errors)
self.assertEqual(out.read().strip(), "")
if result.return_code != 0 : print >> sys.stderr, "\n%s"%cline
self.assertEqual(result.return_code, 0)
filename = result.get_result("outfile")
self.assertEqual(filename, "Emboss/temp with space.water")
assert os.path.isfile(filename)
#Check we can parse the output...
align = AlignIO.read(open(filename),"emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
#Clean up,
os.remove(filename)
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 waterAlign(seq1, seq2, gapopen, gapextend):
water = WaterCommandline()
water.asequence = seq1
water.bsequence = seq2
water.gapopen = gapopen
water.gapextend = gapextend
water.outfile = "needle.txt"
stdout, stderr = water()
print(stdout)
def doWater(contig, seq):
with open("contig.faa", "w") as stuff1:
stuff1.write(">contig\n")
stuff1.write(contig)
with open("seq.faa", "w") as stuff2:
stuff2.write(">seq\n")
stuff2.write(str(seq))
water_cline = WaterCommandline()
water_cline.asequence="contig.faa"
water_cline.bsequence="seq.faa"
water_cline.gapopen=10
water_cline.gapextend=0.5
water_cline.outfile="water.txt"
stdout, stderr = water_cline()
print(stdout + stderr)
values = getStartEnd()
return values
def emboss_local_pairwise_alignment(query_dir, seq_type):
if seq_type == 'fg':
print '\n ...pairwise comparison of functional gene sequences...\n'
elif seq_type == 'ssu':
print '\n ...pairwise comparison of SSU rRNA sequences...\n'
water_cline = WaterCommandline()
water_cline.gapopen=10
water_cline.gapextend=0.5
query_list = [query for query in sorted(glob.glob(query_dir+"/*.fa"))]
for i, a_seq in enumerate(query_list):
water_cline.asequence=str(a_seq)
for j, b_seq in enumerate(query_list[i:]):
water_cline.bsequence=str(b_seq)
align_out = query_dir+"/pairwise_"+str(i+1)+"_"+str(i+j+1)+".aln"
water_cline.outfile=str(align_out)
water_cline()
print 'Done\n'
return query_dir+"/*.aln"
def test_water_file(self):
"""Run water with the asis trick, output to a file."""
# Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"], gapopen="10", gapextend="0.5")
# Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
# Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output...
align = AlignIO.read(cline.outfile, "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(align[0].seq, "ACCCGGGCGCGGT")
self.assertEqual(align[1].seq, "ACCCGAGCGCGGT")
# Clean up,
os.remove(cline.outfile)
def test_water_file(self):
"""water with the asis trick, output to a file."""
# Setup, try a mixture of keyword arguments and later additions:
cline = WaterCommandline(cmd=exes["water"], gapopen="10", gapextend="0.5")
# Try using both human readable names, and the literal ones:
cline.set_parameter("asequence", "asis:ACCCGGGCGCGGT")
cline.set_parameter("-bsequence", "asis:ACCCGAGCGCGGT")
# Try using a property set here:
cline.outfile = "Emboss/temp with space.water"
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output...
align = AlignIO.read(open(cline.outfile), "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Clean up,
os.remove(cline.outfile)
# http://rosalind.info/problems/swat/
from Bio.Emboss.Applications import WaterCommandline
from Bio import ExPASy, SeqIO
if __name__ == "__main__":
ids = open('rosalind_swat.txt').read().split(' ')
for i in ids:
handle = ExPASy.get_sprot_raw(i)
r = SeqIO.read(handle, "swiss")
handle.close()
with open(i, 'w') as f:
SeqIO.write(r, f, 'fasta')
water_cline = WaterCommandline()
water_cline.asequence = ids[0]
water_cline.bsequence = ids[1]
water_cline.outfile = "rosalind_swat_output.txt"
water_cline.gapopen = 10
water_cline.gapextend = 1
water_cline()
for line in open('rosalind_swat_output.txt').readlines():
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
from Bio import ExPASy
from Bio import SeqIO
if __name__ == "__main__":
with open(os.path.join('data', 'rosalind_swat.txt')) as dataset:
ids = dataset.read().split()
for i in ids:
handle = ExPASy.get_sprot_raw(i)
r = SeqIO.read(handle, "swiss")
handle.close()
with open(i, 'w') as f:
SeqIO.write(r, f, 'fasta')
water_cline = WaterCommandline()
water_cline.asequence = ids[0]
water_cline.bsequence = ids[1]
water_cline.outfile = "water.txt"
water_cline.gapopen = 10
water_cline.gapextend = 1
water_cline()
with open('water.txt') as f:
output = f.readlines()
for line in output:
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
# http://rosalind.info/problems/swat/
from Bio.Emboss.Applications import WaterCommandline
from Bio import ExPASy, SeqIO
if __name__ == "__main__":
ids = open('rosalind_swat.txt').read().split(' ')
for i in ids:
handle = ExPASy.get_sprot_raw(i)
r = SeqIO.read(handle, "swiss")
handle.close()
with open(i, 'w') as f:
SeqIO.write(r, f, 'fasta')
water_cline = WaterCommandline()
water_cline.asequence = ids[0]
water_cline.bsequence = ids[1]
water_cline.outfile = "rosalind_swat_output.txt"
water_cline.gapopen = 10
water_cline.gapextend = 1
water_cline()
for line in open('rosalind_swat_output.txt').readlines():
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
from Bio.Emboss.Applications import WaterCommandline
from Bio import ExPASy
from Bio import SeqIO
if __name__ == "__main__":
with open(os.path.join('data', 'rosalind_swat.txt')) as dataset:
ids = dataset.read().split()
for i in ids:
handle = ExPASy.get_sprot_raw(i)
r = SeqIO.read(handle, "swiss")
handle.close()
with open(i, 'w') as f:
SeqIO.write(r, f, 'fasta')
water_cline = WaterCommandline()
water_cline.asequence = ids[0]
water_cline.bsequence = ids[1]
water_cline.outfile = "water.txt"
water_cline.gapopen = 10
water_cline.gapextend = 1
water_cline()
with open('water.txt') as f:
output = f.readlines()
for line in output:
if 'Score:' in line:
print(int(float(line[:-1].split(':')[-1].strip())))
"""
This is the first example of Python script.
"""
a = 10 # variable a
b = 33 # variable b
c = a / b # variable c holds the ratio
# Let's print the result to screen.
print("a:", a, " b:", b, " a/b=", c)
from Bio.Seq import Seq
a = Seq("ATATATACG")
a.alphabet
a.sequence()
from Bio.Emboss.Applications import WaterCommandline
cline = WaterCommandline(gapopen=10, gapextend=0.5)
cline.asequence = "asis:ACCCGGGCGCGGT"
cline.bsequence = "asis:ACCCGAGCGCGGT"
cline.outfile = "temp_water.txt"
print(cline)
