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Suggestion count data file filtering #273
Description
Hi,
I was finally able to create proper and accepted input files to run CAFE5.
cafe5 -i Test.CAFE5.tsv -t tree13_ultra.nwk
I was reading through the tutorial and I found a recommendation to filter the gene count input file,
I downloaded the python script, I run Linux Ubuntu 24.04, and I got an error:
python clade_and_size_filter.py -i Test.CAFE5.tsv -o filtered_Test.CAFE5.tsv -s
Traceback (most recent call last):
File "/home/jpac1984/Fam-Evol/clade_and_size_filter.py", line 129, in <module>
lines_to_keep_set = clade_filter(args.input_file, args.clade_str)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jpac1984/Fam-Evol/clade_and_size_filter.py", line 49, in clade_filter
clade_count = sum(1 for sp_count in spp_info if int(sp_count) >= 1)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/jpac1984/Fam-Evol/clade_and_size_filter.py", line 49, in <genexpr>
clade_count = sum(1 for sp_count in spp_info if int(sp_count) >= 1)
^^^^^^^^^^^^^
ValueError: invalid literal for int() with base 10: 'Arcgaz'
I was suprised that the filtering failed but the analysis ran fine:
cat Base_results.txt
Model Base Final Likelihood (-lnL): 205518
Lambda: 0.0021671572091251
Maximum possible lambda for this topology: 0.0233981
56 values were attempted (0% rejected)
I used Orthofinder to find the Orthogroups and then modified the *.GeneCount.tsv in Rstudio to create input file for CAFE5. Perhaps is there any criterion that I can/should use to remove "outliers" or "weird" Orthogroups in R?
Thanks
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