def main(args):
seq = list(Sequence.fromFile(args.sequenceFilename))
score = Score.fromFile(args.substitutionMatrix)
openingPenality = args.openingPenality
extendingPenality = args.extendingPenality
local = args.local
if not args.nseq1:
for i in range(len(seq)):
seq1 = seq[i]
for j in range(i + 1, len(seq)):
seq2 = seq[j]
if local:
localAlignement(seq1, seq2, openingPenality, extendingPenality, score, args.substitutionMatrix)
else:
globalAlignement(seq1, seq2, openingPenality, extendingPenality, score, args.substitutionMatrix)
print("\n" + "#"*80 + "\n")
else:
if not (1 <= args.nseq1 <= len(seq) and 1 <= args.nseq2 <= len(seq)):
parser.error("-1 and -2 option must be in range of the number of sequences.")
seq1 = seq[args.nseq1 - 1]
seq2 = seq[args.nseq2 - 1]
if local:
localAlignement(seq1, seq2, openingPenality, extendingPenality, score, args.substitutionMatrix)
else:
globalAlignement(seq1, seq2, openingPenality, extendingPenality, score, args.substitutionMatrix)
def getOccurences(filename):
occurences = []
nbSeq = 0
for sequence in Sequence.fromFile(filename):
nbSeq += 1
for i, aa in enumerate(sequence):
if i < len(occurences):
if aa != "-":
occurences[i][aa] = occurences[i].get(aa, 0) + 1
else:
if aa != "-":
occurences.append({aa: 1})
else:
occurences.append({})
return occurences, nbSeq
