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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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Remove Error for sequences < 20000 bp #14

Closed vinisalazar closed 4 years ago

vinisalazar commented 4 years ago

Hi,

I'm trying to run Phigaro in batch from custom scripts, but I am failing because it gives me the following message:

Error! Your fasta file contains at least one sequence length < 20000.  The short sequences are:

Do you want to start Phigaro without these sequences? [Y/n]

This is causing me to have to filter these sequences prior to running Phigaro. Would it be able to implement an argument to the main Phigaro CLI script to simply ignore this error? Any workarounds are appreciated :)

Thank you for any assistance you can provide,

V

PollyTikhonova commented 4 years ago

At version 2.1.9 you can find the parameter -d or --delete-shorts that allows you to exclude short sequences automatically.