Comments (12)
This is probably still an issue for a number of things in scripts/.
from khmer.
Related to issue #39.
from khmer.
Has this issue been addressed for filter-abund.py? Thanks
from khmer.
Yes. See recent posts on Khmer list.
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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Reply to this email directly or view it on GitHub.
from khmer.
The only remaining scripts that switch from FASTQ to FASTA are the partitioning scripts -- in particular, the function annotate-partitions.
from khmer.
@ctb What about annotate-partitions?
from khmer.
Ah, this autoclose was from me pushing the slimmer repo to github.
from khmer.
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]
from khmer.
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
from khmer.
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
from khmer.
See #769
from khmer.
All scripts/code now handles this properly; in particular, annotate_partitions is tested in test_scripts.py:test_extract_partitions_fq()
. Closing.
from khmer.
Related Issues (20)
- Is a nodegraph a bloom filter? HOT 3
- Filtering out reads with low-abundance k-mers (contaminant reads) HOT 4
- Normalize-by-median.py script as a module HOT 1
- Screed DeprecationWarning (Python 3.9) HOT 3
- Khmer (specifically `reverse_complement`) only intended for upper-case sequences? HOT 2
- Is the normalize-by-median.py script deterministic? HOT 2
- Malformed citation file
- script for digital normalization of shotgun mategenomic data HOT 8
- Error in khmer installation
- load-graph.py runtime HOT 1
- Error when Interleaving data HOT 1
- LICENSE bug report HOT 2
- normalize-by-median.py the total of the reads indicated in the report does not match the input
- Result differences from input bias HOT 3
- cppcheck is not reporting the many of the warnings which falls under style option/category HOT 1
- New count-min estimator
- https//canadatechmanufacturing
- Plaid Id
- Plaid Id
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from khmer.