/FixFAST5

Fixing Oxford Nanopore FAST5 files which are missing entries

Primary LanguagePython

FixFAST5

Fixing Oxford Nanopore FAST5 files which are missing entries.

The scripts were written by HalfPhoton and provided in a github issue. I am just bringing them together here to make it easier on myself should I come accross this problem again in the future.

The scripts in this repository require pod5 tools to be installed.

Find problems in FAST5 files

python find_fast5_issues.py FOLDER_CONTAINING_FAST5_FILES/

Extract bad reads

grep -o "read_[0-9a-f-]*" issues.txt > bad_reads.txt

Delete broken entries from FAST5 files

python delete_fast5_reads.py FOLDER_CONTAINING_FAST5_FILES/ bad_reads.txt

All in one

python find_fast5_issues.py FOLDER_CONTAINING_FAST5_FILES/ && \
grep -o "read_[0-9a-f-]*" issues.txt > bad_reads.txt && \
python delete_fast5_reads.py FOLDER_CONTAINING_FAST5_FILES/ bad_reads.txt