merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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CONCOCT's debug outputs should be optional #135

Closed meren closed 9 years ago

meren commented 9 years ago

When one runs mini_test, they can see concoct is generating debug_outr0.csv and debug_outr1.csv files in the mini_test directory. Debug outputs should be optional (in fact there is the parameter in the C code, but it is not used or checked).

Debug should be False by default and the user should be able to change it from the default binary (anvi-cluster-with-concoct) so the python interface class (CONCOCT_INTERFACE) and finally the C code knows about it :)

Tentatively assigning to @farukuzun :)

farukuzun commented 9 years ago

Hey @meren Thanks for assigning :)

Tests

Head: d58d568373da714aa3612bcf35047ddb55fbab35

 Linux machina 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt4-3 (2015-02-03) x86_64 GNU/Linux

Like an average person:

$ anvi-cluster-with-concoct -p test-output/204-MERGED/PROFILE.db -a test-output/ANNOTATION.db -o test-output/anvio_concoct_clusters.txt --source-identifier 'cmdline_concoct'

[*** OUTPUT ***]

$ ls -la debug*
ls: cannot access debug*: No such file or directory

With --debug:

$ anvi-cluster-with-concoct -p test-output/204-MERGED/PROFILE.db -a test-output/ANNOTATION.db -o test-output/anvio_concoct_clusters.txt --source-identifier 'cmdline_concoct' --debug

[*** OUTPUT ***]

$ ls -la debug*
-rw-r--r-- 1 deusex deusex 3720 May 14 04:35 debug_outr0.csv
-rw-r--r-- 1 deusex deusex 3720 May 14 04:35 debug_outr1.csv