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 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 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"
# 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())))
# 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())))
"""
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)
