broadinstitute / catch / 306

Builds Branch Commit Type Ran Committer Via Coverage
306 master 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 a... push web-flow travis-ci-com pending completion   set done
305 download-seqs Describe 'download:TAXID' input format in README Pull #27 web-flow travis-ci-com pending completion   set done
304 download-seqs Describe 'download:TAXID' input format in README push haydenm travis-ci-com pending completion   set done
301 download-seqs Add unit test for construct_influenza_genome_neighbors() This requires creating a mock function for fetch_influenza_genomes_table(), so that it does not need to be run. push haydenm travis-ci-com pending completion   set done
300 download-seqs Skip test for construct_neighbors_for_influenza() on Travis CI This integration test requires an FTP call, which Travis CI does not seem to permit. push haydenm travis-ci-com pending completion   set done
298 download-seqs Fix unit tests for encoded URLs In different Python versions, the order of the key=value pairs (separated by '&' characters) in the url can differ. This changes the unit tests to permit different orders. push haydenm travis-ci-com pending completion   set done
297 download-seqs Add ncbi_neighbors module This module contains functions for fetching genome neighbors and FASTA files from NCBI. push haydenm travis-ci-com pending completion   set done
296 master Merge pull request #25 from broadinstitute/cluster-genomes Add options to cluster input sequences and design on each cluster This PR addresses #24. Issue #24 gives background and reasons for this feature. In short, [`design.py`](https://git... push web-flow travis-ci-com pending completion   set done
294 cluster-genomes Parallelize creation of distance matrix for clustering Filling in the condensed distance matrix, in the cluster module, is (by far) the bottleneck of clustering input sequences. But this can be easily parallelized. This commit uses a multiprocess... push haydenm travis-ci-com pending completion   set done
295 cluster-genomes Parallelize creation of distance matrix for clustering Filling in the condensed distance matrix, in the cluster module, is (by far) the bottleneck of clustering input sequences. But this can be easily parallelized. This commit uses a multiprocess... Pull #25 web-flow travis-ci-com pending completion   set done
293 cluster-genomes Describe --cluster-and-design-separately argument in README Pull #25 web-flow travis-ci-com pending completion   set done
292 cluster-genomes Describe --cluster-and-design-separately argument in README push haydenm travis-ci-com pending completion   set done
291 cluster-genomes Add --cluster-from-fragments argument to design.py push haydenm travis-ci-com pending completion   set done
290 cluster-genomes Pass along target_genomes as a method argument This commit attempts to make sure that filter objects do not store state dependent on what they are filtering (probes and their target genomes). This is necessary to re-use the same filter object mul... push haydenm travis-ci-com pending completion   set done
289 master Add updated V-All probe sets This adds probe sets that update V-All. There are three included in this commit. They all target the same input data. One has 250,000 probes, one has 350,000 probes, and one has 700,000 probes. Probes are 75 nt long, ... push haydenm travis-ci-com pending completion   set done