Implement index returns filenames instead of read_ids for format_chromap #6
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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.
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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 pachterlab#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.