stdout/stderr management

gem-pasteur / Integron_Finder

Bioinformatics tool to find integrons in bacterial genomes

GNU General Public License v3.0

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stdout/stderr management #47

Closed asetGem closed 6 years ago

asetGem commented 7 years ago

[x] silence prodigal stderr
[x] Change stdout of integron_finder: at the end of the processing of a replicon, print a line with: <range>/<#replicons> <replicon_ID> <#integrons> <#in0> <#CALIN>

bneron commented 6 years ago

Change stdout of integron_finder: at the end of the processing of a replicon, print a line with: /<#replicons> <#integrons> <#in0> <#CALIN>

can you explicit what is <#replicons> on so on. if you can give an example of the desired output, it will be great

jeanrjc commented 6 years ago

Well, I don't remember or what @asetGem meant, but I guess it could be an incremental number in case of multifasta. Like how many replicons have been processed so far.

A desired output would look like:

#    replicon_id   N_integrons    N_In0    N_CALIN 
1    replicon_01                   1           0                 1
2    replicon_02                   2           1                 5

There should be an option to switch it off too, in case there are tons of sequences.

bneron commented 6 years ago

done in summary file