resolve the hang problem #226 #254
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
@hunglin59638 can you account for the missing intermediate files i.e |
hunglin59638
commented
Nov 1, 2023
app/BWT.py
Outdated
| @@ -114,6 +114,19 @@ def __init__(self, aligner, include_wildcard, include_baits, read_one, read_two, | |||
|
|
|||
| self.output_tab = os.path.join(self.working_directory, "{}.temp.txt".format(self.output_file)) | |||
| self.output_tab_sequences = os.path.join(self.working_directory, "{}.seqs.temp.txt".format(self.output_file)) | |||
| # Parse tab-delimited file into dictionary for mapped reads | |||
| self.alignments = {} | |||
| with open(self.output_tab_sequences, 'r') as csvfile: | |||
There was a problem hiding this comment.
I moved the code for parsing the tab file to a dictionary to the BWT initialization.
However, at this time, the file ('{}.seqs.temp.txt'.format(self.output_file)) has not been generated yet.
This issue is fixed in the next commit (17dc039), which introduces a function called 'BWT.preload_alignments'.
Once the '.seqs.temp.txt' file is generated, it will be parsed.
There was a problem hiding this comment.
Ok, @hunglin59638 got it. Thanks.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Replacing multiprocessing with concurrent.futures to resolve the hang
Preloading output_tab_sequences into dictionary to improve program efficiency
Testing with SRA fastq: DRR387644
It's illummia 150bp paired-end reads from Klebsiella pneumoniae
File size is 541M.
It took about 4.5 minutes to finish.
The current codes (778b83d) spent more than 1 hr, so I didn't wait it.