Skip to content
This repository has been archived by the owner on Nov 9, 2023. It is now read-only.

refactoring of split_libraries.py into separate scripts for quality filter and demultiplexing #12

Open
gregcaporaso opened this issue Oct 14, 2012 · 6 comments

Comments

@gregcaporaso
Copy link
Contributor

No description provided.

@ghost ghost assigned walterst Oct 14, 2012
@gregcaporaso
Copy link
Contributor Author

Imported from trac issue 12. Created by caporaso on 2011-04-25T14:10:36, last modified: 2011-12-07T14:02:43

@gregcaporaso
Copy link
Contributor Author

@walterst, what's the status on this? Will it be ready for 1.6.0?

@walterst
Copy link
Contributor

I'd be worried about the limited time to test it fully as a workflow, but
I'll have the individual scripts in place in a couple of days (could be
used in place of split_libraries.py when applicable, and can get further
tests later to make sure it works as a workflow named "split_libraries.py"
but in the development version, I'd want that to be in place for many
months before committing it to a release version).

On Tue, Nov 27, 2012 at 9:22 PM, Greg Caporaso notifications@github.comwrote:

@walterst https://github.com/walterst, what's the status on this? Will
it be ready for 1.6.0?


Reply to this email directly or view it on GitHubhttps://github.com//issues/12#issuecomment-10790232.

@gregcaporaso
Copy link
Contributor Author

OK, so we'll keep split_libraries.py as is for this release, and refactor for 1.7.0?

@walterst
Copy link
Contributor

Yep but the individual scripts (demultiplex_fasta.py and
quality_filter_fasta.py) will be implemented, just not the workflow that
calls these two and replaces split_libraries.py.

On Wed, Nov 28, 2012 at 7:44 AM, Greg Caporaso notifications@github.comwrote:

OK, so we'll keep split_libraries.py as is for this release, and refactor
for 1.7.0?


Reply to this email directly or view it on GitHubhttps://github.com//issues/12#issuecomment-10804872.

@gregcaporaso
Copy link
Contributor Author

I think we might not want to add these yet because that would create two independent ways that users could demultiplex/quality filter their 454 data, which could turn into a big support issue.

walterst added a commit to walterst/qiime that referenced this issue Nov 22, 2013
….py quality filtering). Addresses issue biocore#12 and biocore#1190 . Also did code optimization for writing quality file faster in demultiplex_fasta.py
adamrp pushed a commit to adamrp/qiime that referenced this issue Jun 11, 2014
Summarize otu by cat and tefl file to otu table to HDF5
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Projects
None yet
Development

No branches or pull requests

2 participants