def comp(self):
df = pd.read_csv(self.an_fpi, sep='\t', index_col=0)
all_kmers = {}
for i, row in df.iterrows():
print(i)
seq = row['Sequence']
ss = row['Secondary Structure']
miss = row['Missing']
xss = self.add_x(ss, miss)
seq_kmers = tools_lc.seq_to_kmers(seq, self.k)
ss_kmers = tools_lc.seq_to_kmers(xss, self.k)
for seq_kmer, ss_kmer in zip(seq_kmers, ss_kmers):
if tools_lc.lca_motif(seq_kmer,
self.lca) or tools_lc.lce_motif(
seq_kmer, self.lce):
if set(ss_kmer) <= {'S', 'T', 'P', 'X'}:
if seq_kmer in all_kmers:
all_kmers[seq_kmer] += 1
else:
all_kmers[seq_kmer] = 1
for item in all_kmers:
if all_kmers[item] > 200:
print(item)
print(all_kmers[item])
def seq_lca2(self, seqs):
all_kmers = ''
for seq in seqs:
kmers = tools_lc.seq_to_kmers(seq, self.k)
for kmer in kmers:
if tools_lc.lca_motif(kmer, self.lca):
all_kmers += kmer
return all_kmers
def count_lca_and_lce(self, seqs):
all_counts = []
for seq in seqs:
count = 0
kmers = tools_lc.seq_to_kmers(seq, self.k)
for kmer in kmers:
if tools_lc.lce_motif(kmer, self.lce):
if tools_lc.lca_motif(kmer, self.lca):
count += 1
all_counts.append(count)
return all_counts
def count_lca_charge(self, seqs):
lca_counts = []
for seq in seqs:
lca_motifs = 0
kmers = tools_lc.seq_to_kmers(seq, self.k)
for kmer in kmers:
if tools_lc.lca_motif(kmer, self.lca):
if not tools_lc.lce_motif(kmer, self.lce):
if ('K' in kmer) and ('R' in kmer) and ('E' in kmer):
lca_motifs += 1
lca_counts.append(lca_motifs)
return lca_counts
def seq_lca(self, seqs):
seq_kmers = []
lca_counts = []
for seq in seqs:
lca_motifs = 0
kmer_str = ''
kmers = tools_lc.seq_to_kmers(seq, self.k)
for kmer in kmers:
if tools_lc.lca_motif(kmer, self.lca):
kmer_str += kmer
lca_motifs += 1
lca_counts.append(lca_motifs)
seq_kmers.append(kmer_str)
return lca_counts, seq_kmers
