filter_by_length

[Wyclif3]

Hi,
I have been trying to filter my genes to retain only those genes with more than 75% of the sequences using the "hybpiper filter_by_length dna --seq_lengths_file seq_lengths.tsv --length_filter 90 --percent_filter 0.80" but I get an error (hybpiper: error: argument : invalid choice: 'filter_by_length' (choose from 'assemble', 'stats', 'retrieve_sequences', 'paralog_retriever', 'recovery_heatmap', 'check_dependencies', 'check_targetfile', 'fix_targetfile')
Could I get some help regarding this?
Thank you.
Wyclif

[chrisjackson-pellicle]

Hi @Wyclif3,

Can you tell me which version of HybPiper you're using? You can check with the command hybpiper --version. The hybpiper filter_by_length command was introduced in version 2.1.8 (see https://github.com/mossmatters/HybPiper/blob/master/change_log.md).

Cheers,

Chris

[Wyclif3]

Hi Chris,
I am using hybpiper 2.1.7 I tried to update it but still didnt work. does it mean I have to uninstall the old version then install the new one?

Best,
Wyclif

[chrisjackson-pellicle]

Hi @Wyclif3 - I'm not sure what you mean by "I tried to update it but still didnt work". What didn't work?

You're probably best off removing the old version and installing the latest version.

Cheers,

Chris