def getSequence():
sequence = None
if request.method == 'POST':
if 'file1' in request.files:
f = request.files['file1']
sequence = 0
state['seq'][1]['status'] = 'next'
elif 'file2' in request.files:
f = request.files['file2']
sequence = 1
fasta = Fasta(fh=f)
fasta.read()
print(fasta.format())
seq = state['seq'][sequence]
seq['fasta'] = fasta
seq['status'] = 'loaded'
# if both sequences have been selected, check whether the sequences are DNA or protein
state['params']['seqtype'] = 'protein'
if state['seq'][0]['status'] is 'loaded' and state['seq'][1][
'status'] is 'loaded':
if state['seq'][0]['fasta'].isACGT(
) and state['seq'][1]['fasta'].isACGT():
state['params']['seqtype'] = 'DNA'
return render_template('dashboard.html', state=state)
scoremax = score[0]
for s in score:
scoremin = min(scoremin, s)
scoremax = max(scoremax, s)
return scoremin, scoremax
# --------------------------------------------------------------------------------------------------
# Testing
# --------------------------------------------------------------------------------------------------
if __name__ == '__main__':
match = Diagonal()
fasta = Fasta(filename=sys.argv[1])
fasta.read()
fasta1 = fasta.copy()
fasta2 = fasta.copy()
fasta2.id = 'seq 2'
fasta2.doc = 'Sequence 2'
fasta1.seq = fasta1.seq[:200]
fasta2.seq = fasta2.seq[:400]
dataframes = [{
'data': 'dots',
'fn': match.windowThreshold,
'var': ['x', 'y', 'score']
}, {
'data': 'scoredist',
# Testing
# --------------------------------------------------------------------------------------------------
if __name__ == '__main__':
import sys
from sequence.fasta import Fasta
from plotter import Plotter
match = Windowmatch()
print('done {}'.format(type(match)))
print(match.alphabet)
# match.readNCBI('table/NUC4.4.matrix')
print(match.format())
fasta1 = Fasta(filename=sys.argv[1])
fasta1.read()
fasta2 = Fasta()
fasta2.id = 'seq2'
fasta2.doc = ' bases 1:50'
fasta2.seq = fasta1.seq[:50]
fasta1.seq = fasta1.seq[:200]
match.s1 = fasta1
match.s2 = fasta2
l1, l2 = match.seqToInt()
print(l1, l2)
match.window = 10
match.threshold = 5