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move sweep-reads3.py and assemstats3.py into scripts/ #187

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ctb opened this issue Oct 21, 2013 · 6 comments
Open

move sweep-reads3.py and assemstats3.py into scripts/ #187

ctb opened this issue Oct 21, 2013 · 6 comments
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Python
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1.4

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@ctb
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ctb commented Oct 21, 2013

next up on the hit list... ;)
@ghost ghost assigned ctb Oct 21, 2013
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ctb commented Oct 22, 2013

Also filter-below-abund, fastq-to-fasta.

@mr-c mr-c modified the milestones: 1.0.2+ Release, unscheduled May 8, 2014
@ctb ctb mentioned this issue Jun 12, 2014
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mr-c commented Jul 11, 2014

Steps to promote filter-below-abund.py to scripts:
(use filter-abund.py as a reference)

  • test coverage 95%+
  • argparse
  • configure # of threads via CLI (default 1)
  • configure the cutoff via CLI (default 50)
  • help text in argparse

@mr-c mr-c mentioned this issue Aug 11, 2014
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mr-c commented Aug 11, 2014

I'm going to upgrade filter-below-abund.py as it is used in Kalamazoo and the upgrade is needed to wrap it for Galaxy. That tool upgrade is now being tracked in #576

@SensibleSalmon
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I could take this on, unless there are other suggestions.

Also, kalamazoo?

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ctb commented Sep 30, 2014

I think this is a legacy issue that needs to be updated; let's
chat later.

On Tue, Sep 30, 2014 at 07:57:47AM -0700, bocajnotnef wrote:

I could take this on, unless there are other suggestions.

Also, kalamazoo?

Reply to this email directly or view it on GitHub:

#187 (comment)

C. Titus Brown, ctb@msu.edu

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mr-c commented Sep 30, 2014

Kalamazoo is https://khmer-protocols.readthedocs.org/en/latest/metagenomics/index.html

@ctb ctb removed their assignment Jun 12, 2015
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