[khmer] Suggestion on check_space test

[Ramakrishnan Srinivasan]

Scripts with an option to write to a different directory are:

a. count-median.py
b. count-overlap.py
c. do-partition.py
d. extract-long-sequences.py
e. extract-paired-reads.py
f. extract-partitions.py
g. fastq-to-fasta.py
h. filter-abund.py
i. interleave-reads.py
j. load-into-counting.py
k. normalize-by-median.py
l. sample-reads-randomly.py

The solution is to add an optional parameter that holds output location. We
check for free space in out dir equivalent to the largest input file size.

If it's OK with you, I can take this up.

Also, the script extract-paired-reads.py uses a mix of argparse and
sys.argv[]. Should we maybe modify this to use a single approach?

--
Ram

On Thu, Sep 25, 2014 at 12:08 PM, Ramakrishnan Srinivasan <ramrs at nyu.edu>
wrote:

> I think this is a case of passing the output file path in scripts where
> -in path can be different from -out path (such as in normalize-by-median).
>
> --
> Ram
>
> On Thu, Sep 25, 2014 at 12:06 PM, C. Titus Brown <ctb at msu.edu> wrote:
>
>> On Thu, Sep 25, 2014 at 10:58:46AM -0500, Adina Chuang Howe wrote:
>> > Hi team,
>> >
>> > I was running diginorm today on two different disks (one for the
>> > intermediate normalized files) and one on another disk (containing the
>> raw
>> > sequences) .  I think this will be fairly typical in the future.
>> > Currently, a test (file.py check_space) will error out, given this
>> setup.
>> > I think it'd be nice to be able to bypass this check or at least make it
>> > more robust (to checking the write-out disk only).
>> >
>> > Low priority, but notable, hopefully helpful.
>>
>> Agreed -- see
>>
>> https://github.com/ged-lab/khmer/issues/399
>>
>> --titus
>> --
>> C. Titus Brown, ctb at msu.edu
>>
>> _______________________________________________
>> khmer mailing list
>> khmer at lists.idyll.org
>> http://lists.idyll.org/listinfo/khmer
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.idyll.org/pipermail/khmer/attachments/20140925/2b8aa8ff/attachment.htm>