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 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
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(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Clean up,
os.remove(cline.outfile)
def test_water_piped(self):
"""Run water with asis trick, output piped to stdout."""
cline = WaterCommandline(
cmd=exes["water"],
asequence="asis:ACCCGGGCGCGGT",
bsequence="asis:ACCCGAGCGCGGT",
gapopen=10,
gapextend=0.5,
auto=True,
filter=True,
)
self.assertEqual(
str(cline),
exes["water"]
+ " -auto -filter"
+ " -asequence=asis:ACCCGGGCGCGGT"
+ " -bsequence=asis:ACCCGAGCGCGGT"
+ " -gapopen=10 -gapextend=0.5",
)
# Run the tool,
child = subprocess.Popen(
str(cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"),
)
child.stdin.close()
# Check we could read it's output
align = AlignIO.read(child.stdout, "emboss")
self.assertEqual(len(align), 2)
self.assertEqual(str(align[0].seq), "ACCCGGGCGCGGT")
self.assertEqual(str(align[1].seq), "ACCCGAGCGCGGT")
# Check no error output:
self.assertEqual(child.stderr.read(), "")
self.assertEqual(0, child.wait())
child.stdout.close()
child.stderr.close()
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 getCellBarcodeAlignment(read, fil):
"""
use stdin and stdout to simplify water
asequence: one SMRT read
bsequence: {index}_CBC-list.fasta
return: best matched CBC for this SMRT read and the corresponding score
"""
water_cline = WaterCommandline(asequence='stdin',
filter=True,
bsequence=fil,
gapopen=10.0,
gapextend=.5,
stdout=True)
child = subprocess.Popen(str(water_cline),
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
universal_newlines=True,
shell=(sys.platform != "win32"))
rec = SeqRecord(Seq(read), id="temp")
SeqIO.write(rec, child.stdin, "fasta")
child.stdin.close()
seqs, scores = [], []
line = child.stdout.readline()
eof = False
while True:
if not line:
eof = True
if eof:
break
if '2:' in line[:8]:
seqs.append(line.strip().split(':')[1])
elif 'Score' in line:
scores.append(float(line.split(':')[1]))
line = child.stdout.readline()
assert len(seqs) == len(
scores), "ERROR: incorrect alignment file line counting."
return seqs[scores.index(max(scores))], max(scores)
def main():
comm = MPI.COMM_WORLD
rank = comm.Get_rank()
loc = '01-fix_orientation'
chunk = 'chunk-' + '{:03}'.format(rank + 1)
if not os.path.exists(loc):
os.mkdir(loc)
for fragment in ('inside', 'inside_rc', 'outside', 'outside_rc'):
subloc = loc + '/' + fragment
if not os.path.exists(subloc):
os.mkdir(subloc)
infile = os.path.join('00-external', fragment + '.txt')
data = os.path.join('00-data', chunk + '.fasta')
if not os.path.isfile(data):
continue
outfile = os.path.join(subloc, chunk + '.txt')
water_cline = WaterCommandline(asequence=infile,
bsequence=data,
gapopen=10.0,
gapextend=.5,
outfile=outfile)
stdout, stderr = water_cline()
def water(*id, gop=10, gex=0.5, out='emb.aln'):
"""Alignement global par la methode de Needleman"""
lso = list(SeqIO.parse(workfile, "fasta"))
mkfasx('seqa.fas', id[0])
mkfasx('seqb.fas', *id[1:])
water_cline = WaterCommandline(asequence='seqa.fas',
bsequence='seqb.fas',
gapopen=gop,
gapextend=gex,
outfile=out)
stdout, stderr = water_cline()
os.remove('seqa.fas')
os.remove('seqb.fas')
if len(id) < 3:
align = AlignIO.read(out, "emboss")
return align
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 emboss_water(seq_a_file: str, seq_b_file: str, out_file: str):
""" Do a global pairwise alignment using EMBOSS
Args:
seq_a_file: First sequence
seq_b_file: second sequence
out_file: Output file
Returns:
r [subprocess object]: Execute the commandline command for EMBOSS
"""
water_cline = WaterCommandline(asequence=seq_a_file,
bsequence=seq_b_file,
outfile=out_file,
verbose=True,
gapextend=1,
gapopen=10)
cmd = str(water_cline)
cmd = cmd.split(" ")
cmd.append("-aformat=msf")
return subprocess.run(cmd, check=True)
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)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
#Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
#TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
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)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "genbank"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
#Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
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)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "fasta"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
# 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())))
# Get telomere ref sequence
ref_length = int(math.ceil(float(size / float(6))))
if strand == "+":
telo_ref = "TTAGGC" * ref_length
elif strand == "-":
telo_ref = "GCCTAA" * ref_length
else:
print("ERROR: strand must be + or -")
sys.exit(1)
# Perform alignment with water
with open("its_seq.temp", "w") as fi:
fi.write(str(seq))
with open("telo.temp", "w") as ft:
ft.write(telo_ref)
water_cmd = WaterCommandline(gapopen=10,
gapextend=0.5,
asequence="its_seq.temp",
bsequence="telo.temp",
stdout=True,
auto=True)
stdout, stderr = water_cmd()
identity = re.findall("# Identity:.*\((.+)\%\)", stdout)[0]
outfile.write(line.strip() + "\t" + str(identity) + "\n")
outfile.close()
os.remove("its_seq.temp")
os.remove("telo.temp")
def water_aligner(TR_frame, seqrec_array, m, go, ge, args):
""" Performs TR alignment using the provided EMBOSS-water aligner executable.
TR_frame: A data frame containing TR instances
seqrec_array: An array containing indexed seqrecord instances from the query feature array
m: match score
go: gap open penalty
ge: gap extension penalty
min_match: The minimum percentage similarity to accept the alignment, otherwise realign with reverse complement or remove
"""
tr_count = len(TR_frame)
missing_features = 0 ## counter for instances of missing features in the query lib
water_log = open("./TR_aln.log",
"w") ## file to dump water subprocess output
vprint(subprocessID, "Starting alignments...", "prYellow")
print(
f"\n\t\t\tEMBOSS-water Smith-Waterman Aligner.\n\t\t\tmatch={m}\n\t\t\tgap_open={go}\n\t\t\tgap_extend={ge}\n",
flush=True)
for i, tr in enumerate(TR_frame):
time = strftime("%H:%M:%S", localtime())
print("\r{time} {subprocess} :: Aligning TR {i}/{tr_count}".format(
time=time,
subprocess=prYellow(subprocessID),
i=i + 1,
tr_count=tr_count),
end="... ",
file=sys.stdout,
flush=True)
## generate a homolog dict from the TR and track the number of missing features from the query library
rfa_out, qfa_out, missing = tr.get_homologs_fasta(seqrec_array, args.m)
missing_features += missing
aln_out = path.join(args.o, f"{tr.id}.water")
flank1_out = path.join(args.o, f"{tr.id}_F1.water")
flank2_out = path.join(args.o, f"{tr.id}_F2.water")
def run_alignment(water_cline, a_prefix):
""" Runs water alignment using a Biopython water commandline object and a prefix to identify which sequence is being aligned
"""
p = Popen(str(water_cline),
stdin=PIPE,
stdout=PIPE,
stderr=PIPE,
shell=True)
output, err = p.communicate()
rc = p.returncode
if rc == 0:
print(f"\nAlignment of {a_prefix}:{tr.id} exited with 0",
file=water_log)
else:
print(
f"\nAlignment of {a_prefix}:{tr.id} exited with {rc} and warning:\n{str(err)}",
file=water_log)
## align full TR region
water_cline = WaterCommandline(args.w,
asequence=rfa_out,
bsequence=qfa_out,
gapopen=go,
gapextend=ge,
outfile=aln_out)
run_alignment(water_cline, "FULL")
## align flank 1
water_cline = WaterCommandline(args.w,
asequence=f"asis:{tr.flank1}",
bsequence=qfa_out,
gapopen=go,
gapextend=ge,
outfile=flank1_out)
run_alignment(water_cline, "flank1")
## align flank 2
water_cline = WaterCommandline(args.w,
asequence=f"asis:{tr.flank2}",
bsequence=qfa_out,
gapopen=go,
gapextend=ge,
outfile=flank2_out)
run_alignment(water_cline, "flank2")
if i > 10:
break
print(f"Done with {missing_features} missing seqeuences.\n", flush=True)
water_log.close()
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "fasta"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
#Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
#EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
#TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
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)
#Should be able to access this via any alias:
self.assertEqual(result.get_result("-outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"swiss"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
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 test_water_file3(self):
"""Run water with the asis trick and GenBank file, output to a file."""
# Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
# TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "genbank"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
# Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
# EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
# TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "swiss"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
def GetExec(inF, outF):
# Create User Modifiable search check boxes.
plugin_exe = r"C:/mEMBOSS/water.exe"
cline = WaterCommandline(plugin_exe, infile=inF, outfile=outF)
p = subprocess.Popen(str(self.cline))
p.wait()
# 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())))
import Bio.Seq
import os
from Bio.Emboss.Applications import WaterCommandline
from Bio.Align.Applications import ClustalwCommandline
fasta = open('/home/nastia/fasta_end.txt', 'r')
string = fasta.readline()
outfileput = open('/home/nastia/Desktop/output.txt', 'w')
while len(string) > 0:
m = string.find('\t')
n = string.rfind('\t')
my_seq_1 = Bio.Seq.Seq(string[m + 1:n])
my_seg_2 = Bio.Seq.Seq(string[n + 1:-1])
cline = WaterCommandline(gapopen=10,
gapextend=0.5,
asequence=my_seq_1,
bsequence=my_seg_2,
outfile='/home/nastia/Desktop/Water.txt')
#os.system('clustalw'+cline)
#print(type(cline))
#print(cline)
#outfileput.write(cline)
string = fasta.readline()
outfileput.close()
def test_water_file4(self):
"""water with the asis trick and SwissProt file, output to a file."""
#Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/sp004"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
#EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
#TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
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)
#Should be able to access this via any alias:
self.assertEqual(result.get_result("-outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file), "swiss"),
AlignIO.parse(open(out_file), "emboss"),
local=True)
#Clean up,
os.remove(out_file)
"""
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)
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 test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
# Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
# TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(in_file, "genbank"),
AlignIO.parse(out_file, "emboss"),
local=True)
# Clean up,
os.remove(out_file)
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())))
def test_water_file2(self):
"""Run water with the asis trick and nucleotide FASTA file, output to a file."""
# Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "fasta"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file2(self):
"""water with the asis trick and nucleotide FASTA file, output to a file."""
#Setup,
query = "ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACGCAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG"
out_file = "Emboss/temp_test2.water"
in_file = "Fasta/f002"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
cline.set_parameter("-gapopen", "10")
cline.set_parameter("-gapextend", "0.5")
cline.set_parameter("-outfile", out_file)
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)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"fasta"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
def test_water_file4(self):
"""Run water with the asis trick and SwissProt file, output to a file."""
# Setup,
query = "DVCTGKALCDPVTQNIKTYPVKIENLRVMI"
out_file = "Emboss/temp_test4.water"
in_file = "SwissProt/P0A186.txt"
self.assertTrue(os.path.isfile(in_file))
if os.path.isfile(out_file):
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("-asequence", "asis:%s" % query)
cline.set_parameter("-bsequence", in_file)
# EMBOSS should work this out, but let's be explicit:
cline.set_parameter("-sprotein", True)
# TODO - Tell water this is a SwissProt file!
cline.set_parameter("-gapopen", "20")
cline.set_parameter("-gapextend", "5")
cline.set_parameter("-outfile", out_file)
self.assertEqual(str(eval(repr(cline))), str(cline))
# Run the tool,
self.run_water(cline)
# Check we can parse the output and it is sensible...
self.pairwise_alignment_check(
query,
SeqIO.parse(in_file, "swiss"),
AlignIO.parse(out_file, "emboss"),
local=True,
)
# Clean up,
os.remove(out_file)
def test_water_file3(self):
"""water with the asis trick and GenBank file, output to a file."""
#Setup,
query = "TGTTGTAATGTTTTAATGTTTCTTCTCCCTTTAGATGTACTACGTTTGGA"
out_file = "Emboss/temp_test3.water"
in_file = "GenBank/cor6_6.gb"
self.assert_(os.path.isfile(in_file))
if os.path.isfile(out_file) :
os.remove(out_file)
cline = WaterCommandline(cmd=exes["water"])
cline.set_parameter("asequence", "asis:%s" % query)
cline.set_parameter("bsequence", in_file)
#TODO - Tell water this is a GenBank file!
cline.set_parameter("gapopen", "1")
cline.set_parameter("gapextend", "0.5")
cline.set_parameter("outfile", out_file)
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)
self.assertEqual(result.get_result("outfile"), out_file)
assert os.path.isfile(out_file)
#Check we can parse the output and it is sensible...
self.pairwise_alignment_check(query,
SeqIO.parse(open(in_file),"genbank"),
AlignIO.parse(open(out_file),"emboss"),
local=True)
#Clean up,
os.remove(out_file)
