v0.3.0 updates #50
Merged
v0.3.0 updates #50
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
…ed barcode file, add a longer error message and fixing unit tests. (#39) * Guarantee consistent ordering when removing duplicate fastq names The Python set() does not have a guranteed order. * Implement a load_example_spec function Yes it's replacing 2 lines of code with one line, but it does make doing imports easier too * Test map_read_id_to_regions * Give a longer error message seqspec fails to find a region or read. Just crashing when if the lists were empty made debugging seqspecs harder, hopefully seeing the the name that wasn't found and the list of choices will help figure out what's wront with the spec or call * join_onlists now processes a list of file contents * run_onlist_region or _read returns a list of objects now * find_onlist_file was removed * read_list was split into two functions So rename the test functions to better match the new names * Extend to_YAML to also support returning seqspec as a string This makes it behave like the yaml.dump() function. * Re-implement testing for a local copy of single barcode files And add a different testing implementation that's testing the validate_onlist_args function. I did have to return the calculated onlist_path to make it easier to test the function. * join_onlists was being called with the wrong argument It needs the barcode text and not the onlist barcode metadata * Make sure written barcode file is not double spaced I noticed that the barcode file was being written as AAA GGGG GGG TTTT and it looked like both the join_onlist functions and the write_onlist function was adding a newline character.This removes adding the newline from the joined list and lets the write function handle it.
…out relevant info like reads and library elements, added a USING_SEQSPEC.md
…abulary. updated seqspec tool docs to include a description of the various region types that are included in each of the seqspec index tools
…or the File object, utils checks for url redirects with 302 status codes
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
sbooeshaghi
temporarily deployed
to
github-pages
GitHub Actions
Inactive
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.
see docs/CHANGELOG.md for updates.