Implement index returns filenames instead of read_ids for format_chromap #67
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
…terlab#58) * update seqspec check * add spec parameter back to check function
* support gzipped yaml file for function load_spec * fix bug in function run_check * support gzipped yaml file for function load_spec
We have some read_ids that are just accession and some that are accession.fastq.gz and this causes confusion for generating the tool command lines. I thought I should save some example seqspecs and test that index generates the correct commands in with either type of read id. Also to get this to work I decided to use importlib.resources which required making my test/data directory look like a python module.
Loading a 0.2 yaml will work but some of the attributes will be missing, and this causes all sorts of problems for the seqspec display code
I can then use it to look up additional information such as the filenames. This makes it much easier to resolve pachterlab#64
Also as a convenience I added a get_filenames to the Read object. The original code operated on finding read_ids with the commit that added passing around the parsed seqspec object I could then take the read_ids and look for the fastq filenames. It's untested but in theory if there's multiple File objects you'll get a comma separated list of the filenames for the command line.
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Outdated suggestions cannot be applied.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.
Adds some tests to make test format_kallisto and format_chromap to make sure it returns expected output, and then implements returning the filenames in the format_chromap function instead of read_ids.
This might not be the most elegant solution, but it did work.
fixes #64
Ideally this should be merged after the unit test fix pull request, but it's a separate pull request because it's logically different.