def __init__(self, fastas, min_repeats, standard_level):
super(SSRWorker, self).__init__()
self.fastas = fastas
self.min_repeats = min_repeats
self.motifs = motif.StandardMotif(standard_level)
self.fasta_counts = len(self.fastas)
self.progress = 0
def __init__(self, fastas, seed_repeat, seed_length, max_eidts,
mis_penalty, gap_penalty, score, standard_level):
super(ISSRWorker, self).__init__()
self.fastas = fastas
self.motifs = motif.StandardMotif(standard_level)
self.fasta_counts = len(self.fastas)
self.seed_repeat = seed_repeat
self.seed_length = seed_length
self.max_eidts = max_eidts
self.mis_penalty = mis_penalty
self.gap_penalty = gap_penalty
self.score = score
def __init__(self, fastas, min_repeats, standard_level):
super(SSRWorker, self).__init__()
self.fastas = fastas
self.min_repeats = min_repeats
self.motifs = motif.StandardMotif(standard_level)
self.fasta_counts = len(self.fastas)
self.progress = 0
parameters = Data(mono=min_repeats[0],
di=min_repeats[1],
tri=min_repeats[2],
tetra=min_repeats[3],
penta=min_repeats[4],
hexa=min_repeats[5],
level=standard_level)
self.db.set_option("ssr_parameters", json.dumps(parameters))
def __init__(self, fastas, seed_repeat, seed_length, max_edits,
mis_penalty, gap_penalty, score, standard_level):
super(ISSRWorker, self).__init__()
self.fastas = fastas
self.motifs = motif.StandardMotif(standard_level)
self.fasta_counts = len(self.fastas)
self.seed_repeat = seed_repeat
self.seed_length = seed_length
self.max_edits = max_edits
self.mis_penalty = mis_penalty
self.gap_penalty = gap_penalty
self.score = score
parameters = Data(seed_repeat=seed_repeat,
seed_length=seed_length,
max_edits=max_edits,
mis_penalty=mis_penalty,
gap_penalty=gap_penalty,
min_score=score,
level=standard_level)
self.db.set_option('issr_parameters', json.dumps(parameters))
def search_ssr(name, seq, repeats, level):
motifs = motif.StandardMotif(level)
ssrs = tandem.search_ssr(seq, repeats)
return [[name, motifs.standard(ssr[0])] + list(ssr) for ssr in ssrs]
def search_issr(name, seq, level, min_srep, min_slen, max_edits, mis_penalty,
gap_penalty, min_score):
motifs = motif.StandardMotif(level)
issrs = tandem.search_issr(seq, min_srep, min_slen, max_edits, mis_penalty,
gap_penalty, min_score, 500)
return [[name, motifs.standard(ssr[0])] + list(ssr) for ssr in issrs]
