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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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RDP assign_taxonomy wrapper skips seqs that are too short #297

Closed josenavas closed 11 years ago

josenavas commented 11 years ago

The RDP classifier wrapper in assign_taxonomy.py does not print taxonomic assignments for sequences that are too short for taxonomy assignment with RDP. These raise a ShortSequenceException and are skipped, but instead should have some information written to the taxonomy output file so the sequences will be retained in downstream analysis. For example, some text such as 'Unassignable by RDP: Too short' could be written for these seqs.

gregcaporaso commented 11 years ago

@kylebittinger, do you know if this is still an issue? If so, would you be able to take care of it?

gregcaporaso commented 11 years ago

@kylebittinger, ping.

kylebittinger commented 11 years ago

Should be fixed in line 414 of cogent/app/rdp_classifier.py in PyCogent.

jairideout commented 11 years ago

Looks good to me; closing.