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epruesse / SINA

SINA - Reference based multiple sequence alignment
https://sina.readthedocs.io
GNU General Public License v3.0
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Sina does not actually output LCA classification anymore? #91

Closed jvollme closed 3 years ago

jvollme commented 4 years ago

When using the old sina version downloadable from the SILVA website (1.2.11), it is possible to do LCA classification of the sequences with the --search argument. The classification is simply listed in the stderr-output of the run and has to be parsed from it, but it is there.

When using the new version with equivalent arguments, i do not get any classification results. only alignments. Currently i am often more interested in the LCA classification than the alignments.

Where/How do I find the LCA classification results?

hmontenegro commented 4 years ago

If you use the arguments --meta-fmt csv --lca-fields tax_slv, the LCA classification will be one of the columns from the csv file.

edit: I am not involved in the development of SINA in any way.

epruesse commented 4 years ago

The newest version can also just do -o result.csv, with -f specifying which fields.

epruesse commented 3 years ago

Please try the 1.7.0 - binaries should be ready within the hour and bioconda packages within the day.