Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Convert to uppercase #22

Merged
merged 2 commits into from
Apr 7, 2015
Merged

Convert to uppercase #22

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
c45eddb
Convert sequences to uppercase
Apr 7, 2015
a4b7614
Require uppercase when checking
Apr 7, 2015
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions ariba/refcheck.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ def fix(self, outprefix):
log_out_fh = pyfastaq.utils.open_file_write(log_out)

for seq in file_reader:
seq.seq = seq.seq.upper()
if len(seq) < self.min_length:
print(seq.id, 'Too short. Skipping', sep='\t', file=log_out_fh)
print(seq, file=bad_seqs_out_fh)
Expand Down
2 changes: 1 addition & 1 deletion ariba/tests/data/refcheck_test_fix_in.fa
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
>gene1
TTGTCGTAA
>gene2
TTGTCGTCGTCGTAA
ttgtcgtcgtcgtaa
>gene3
TTGTCGTCGTCGTCGTAA
>gene3
Expand Down