Open
Conversation
sivkovic
requested changes
Feb 9, 2026
sivkovic
requested changes
Feb 12, 2026
| all_sample_ids.extend(samples) | ||
|
|
||
| # Write all parsed sample names to output file | ||
| with open(output_file, "w") as f: |
Collaborator
There was a problem hiding this comment.
We do not need to write parsed sample names to output file. Only primaryIds
| directories_set = set(all_directories) | ||
|
|
||
| unique_to_samples = samples_set - directories_set | ||
| #print(f"Unique to samples: {unique_to_samples}") |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
parse_cohort_file
Should parse one or more cohort files and writes a combined list of sample IDs to an output file. No longer converts to PrimaryIds
Single file
python3 parse_cohort_files.py parse cohort1.txt parsed_samples.txt
Multiple files
python3 parse_cohort_files.py parse cohort1.txt cohort2.txt parsed_samples.txt
Directory wildcard
python3 parse_cohort_files.py parse /home/cohortfiles/*.txt parsed_samples.txt
list_directories
Lists all subdirectories within a given parent directory and writes them to an output file.
python3 parse_cohort_files.py list_dir /home/BAM/ bam_directories.txt
compare_files
Compares two files and reports difference to an output file
python3 parse_cohort_files.py compare <file1.txt> <file2.txt> <report_file>