inbalpaz / clans Goto Github PK

Hello,

I started using your clans_cmd.py script to generate CLANS files for the clans.jar executable to process as it is much simpler than loading my FASTA on the CLANS web server (thank you for preparing that, it is really helpful for having a fully Python pipeline for what I need to do).

I have encountered an issue while loading my FASTA file though. When saving the CLANS files through your Python script, I observe there are duplicated edges with different P-values in the HSP field of the XML. An example would be:

0 197:2.99e-121
0 197:1.77e-48
0 24:3.46e-57
0 24:4.08e-29

So the node 0 is connected twice to, e.g., node 197 with two different weights. When compared with the web output, we have just:

0 197:3.0e-121

so it seems that the output of clans_cmd.py is duplicating the nodes.
Some observations:

• Note that this does not happen for all nodes, it only happens for some of them.
• I ran with the default settings, assuming that they would match those of the web interface. I then had to reduce the BLAST Evalue (default is 1.0 in your cfg?). That removed some of the duplicates and would ensure the same number of edges in the two graphs excluding the duplicates (to be checked).
• It seems that for the duplicated entries, the one that matches the web output is always the smallest of the two. By which we could filter the wrong edges, but it would be better if they were not there in the first place.

Note that I am just running the pipeline with:
python clans_cmd.py -infile ../clans_report/fasta_src.fa -saveto ../clans_report/py_yours_output.clans -dorounds 0
which should suffice to reproduce the issue. I am attaching the required files for debugging. Could you indicate why this issue could happen and how I could support you with debugging it?

clans_report.zip

Hi, I encountered difficulties when running the program, and the error "An error has occurred while running the BLAST search" was reported in the terminal. How can I solve this problem? Thank you for your help.