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Min length of gene families #51
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Hi Tim, There isn't a parameter that can be accessed from the main command currently. If you want a quick hack the you can modify the line below in run_PIRATE.pl to include "-t 75"
e.g.
I am happy to add a branch with this option to the main script and include it in the next release. All the best, |
Hi Sion - thanks for the super quick reply. Will use this hack and also would be interested in having a branch available in the next release. Tim |
When I get a spare minute I will set one up for you :) |
I don't see the nohup warnings you were getting when I created a branch with the same option. Are you still seeing them and are the outputs okay? S |
I found an error message with link_clysters.pl but it looks like it maybe an issue of rerunning PIRATE in the same directory with different settings. When I sent outputs to a fresh directory it didn't occur. I will push to master shortly. Thank you for your help and testing. S |
Hi @SionBayliss! I noticed the PR for this feature was merged then reverted (#55). Are there still plans to implement this in the future? Thanks! |
I have merged this with another commit that I wanted to push together. The revert was due to reading about the nohup errors after merging and then slightly panicking. I have pushed them both to master now. The master branch has all of the changes that I previously reverted. |
I should have waited! Thanks Sion! |
Noticed that the min_length for the members of gene families is 123 bp, although some genes in the input were as small as 75 bp. Is there a parameter that can be altered that allows these small genes to be included in families?
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