pub_soft/ScanNet
3
0
Fork 0
mirror of https://github.com/jertubiana/ScanNet.git synced 2026-06-04 13:44:22 +08:00
Code Issues Packages Projects Releases Wiki Activity

Update sequence_utils.py

Browse Source
This commit is contained in:
Jérôme Tubiana
2021-11-02 09:46:41 +02:00
parent 3efc04f621
commit 541fcae867
1 changed files with 6 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files

12
preprocessing/sequence_utils.py
View File

@@ -50,9 +50,7 @@ def num2seq(num):
return [''.join([aa[min(x, len(aa) - 1)] for x in num_seq]) for num_seq in num]
def load_FASTA(filename, with_labels=False, remove_insertions=True, drop_duplicates=True):
remove_insertions = True
with_labels = True
def load_FASTA(filename, with_labels=True, numerical=True,remove_insertions=True, drop_duplicates=True):
count = 0
current_seq = ''
all_seqs = []
@@ -74,9 +72,11 @@ def load_FASTA(filename, with_labels=False, remove_insertions=True, drop_duplica
[x for x in current_seq if not (x.islower() | (x == '.'))])
all_seqs.append(current_seq)
all_seqs = np.array(list(
map(lambda x: [aadict[y] for y in x], all_seqs[1:])), dtype=curr_int, order="c")
if numerical:
all_seqs = np.array(list(
map(lambda x: [aadict[y] for y in x], all_seqs[1:])), dtype=curr_int, order="c")
else:
all_seqs = np.array(all_seqs[1:])
if drop_duplicates:
all_seqs = pd.DataFrame(all_seqs).drop_duplicates()
if with_labels: