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mazzalab / pyntacle

A high performance python package for network analysis based on non canonical metrics
http://pyntacle.css-mendel.it
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[cmd] error in communities fastgreedy command #50

Closed Bioswinger closed 4 years ago

Bioswinger commented 4 years ago

Case study 2 notebook

command used :pyntacle communities fastgreedy -i APID_CAEEL_Level2_maincomponent.adjm -d ./CAEEL_communities -o CAEEL_Interactome --min-nodes 40 --plot-format png

error received:

usage: pyntacle communities fastgreedy [-h] [-f] [-N] [-d] [-M] [-m] [-C] [-c] [-L] [--input-separator] [--save-binary] [-o] [-u] [--no-output-header] [--output-separator] --input-file [FILE] [--weights FILE] [--weights-format] [--clusters]
pyntacle communities {fastgreedy, infomap, leading-eigenvector, community-walktrap} [arguments] fastgreedy: error: argument : invalid choice: 'png' (choose from 'fastgreedy', 'infomap', 'leading-eigenvect
mazzalab commented 4 years ago

the option --plot-format was removed since version 1.1 and after the introduction of PyntacleInk. The correct command is:

pyntacle communities fastgreedy -i APID_CAEEL_Level2_maincomponent.adjm -d ./CAEEL_communities -o CAEEL_Interactome --min-nodes 40 --plot-format png

please correct, thanks