arzwa
commented
4 years ago Hi, since everything was there to implement this, I quickly did so. If you install the latest version from the master branch, you can set additional options for I-ADHoRe using the --iadhore-options flag. Obviously, this option has not been thoroughly tested, so let me know if you have issues with it. Example usage:
wgd syn ugi.gff wgd_dmd/ugi.mcl -ks wgd_ksd/ugi.tsv -f mRNA -a ID --iadhore_options q_value=0.75,prob_cutoff=0.1,cluster_gap=50 with this update you should see output like this:
2020-06-09 10:17:20: INFO I-ADHoRe 3.0 options: {'q_value': '0.5', 'prob_cutoff': '0.2', 'cluster_gap': '50'}
2020-06-09 10:17:20: INFO This is i-ADHoRe v3.0.
Copyright (c) 2002-2010, Flanders Interuniversity Institute for Biotechnology, VIB.
Algorithm designed by Klaas Vandepoele, Cedric Simillion, Jan Fostier, Dieter De Witte,
Koen Janssens, Sebastian Proost, Yvan Saeys and Yves Van de Peer.
2020-06-09 10:17:20: INFO Made output directory wgd_syn2
2020-06-09 10:17:20: INFO Parsing GFF file
2020-06-09 10:17:21: INFO Writing gene lists
2020-06-09 10:17:21: INFO Writing families file
2020-06-09 10:17:21: INFO Writing configuration file
2020-06-09 10:17:21: INFO Running I-ADHoRe 3.0
Process 1/1 is alive on localhost.
2020-06-09 10:17:20: INFO Made output directory wgd_syn2
2020-06-09 10:17:20: INFO Parsing GFF file
2020-06-09 10:17:21: INFO Writing gene lists
2020-06-09 10:17:21: INFO Writing families file
2020-06-09 10:17:21: INFO Writing configuration file
2020-06-09 10:17:21: INFO Running I-ADHoRe 3.0
...To verify whether the right options were used, you can always check the adhore.conf file in the output directory, which contains the configuration file for i-adhore. Hope this helps!
I want to change some parameter of i-adhore, however , it's no use to modify collinearily.py. How can I do for it? Thank you very much.