All scripts should output the sequence format they take in (FASTA/FASTA, FASTQ/FASTQ) by default about khmer

[ctb]

This is probably still an issue for a number of things in scripts/.

[emcd]

Related to issue #39.

[suryasaha]

Has this issue been addressed for filter-abund.py? Thanks

[ctb]

Yes. See recent posts on Khmer list.

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C. Titus Brown, [email protected]

On Apr 20, 2013, at 12:52, suryasaha [email protected] wrote:

Has this issue been addressed for filter-abund.py? Thanks

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[ctb]

The only remaining scripts that switch from FASTQ to FASTA are the partitioning scripts -- in particular, the function annotate-partitions.

[mr-c]

@ctb What about annotate-partitions?

[mr-c]

Ah, this autoclose was from me pushing the slimmer repo to github.

[ctb]

On Tue, Apr 01, 2014 at 10:29:28AM -0700, Michael R. Crusoe wrote:

@ctb What about annotate-partitions?

I believe it does, but we don't have any tests for FQ. => issue.

--t

C. Titus Brown, [email protected]

[camillescott]

Note: the record object returned by readparser is slightly different than that returned by screed, in that it has the 'accuracy' attribute but keeps it empty for fasta, while screed simply omits the 'accuracy' attribute for fasta record objects. Related: #328

[mr-c]

One approach (to the issue @camillescott raised) would be to override __getattr__ either in a Python wrapper of the CPython implementation of the ReadParser reads or by providing a custom tp_getattr on the CPython side: https://docs.python.org/2.7/extending/newtypes.html#type-specific-attribute-management

[ctb]

See #769

[ctb]

All scripts/code now handles this properly; in particular, annotate_partitions is tested in test_scripts.py:test_extract_partitions_fq(). Closing.