broadinstitute / catch / 306

94%

push

travis-ci-com

Merge pull request #27 from broadinstitute/download-seqs

Add ability to automatically download sequences for a taxonomy

This PR adds an option to specify input in the form of an NCBI taxonomy ID. When specified this way, CATCH will fetch all accessions (genome neighbors) for the taxonomy, download sequences of those accessions, and use them as input.

This adds the `ncbi_neighbors` module to make calls to NCBI's Entrez system. To use this feature, the format for input datasets to design.py is `download:TAXID`. TAXID is an NCBI taxonomy ID. This PR also updates the README to describe this feature and changes the main example to use it.

1560 of 1777 branches covered (87.79%)

249 of 249 new or added lines in 2 files covered. (100.0%)

5400 of 5708 relevant lines covered (94.6%)

2.84 hits per line