Fasta_reader isn't working.

Question

[Riku]

Dear all,

When I try to use the script, fasta_seq_length.pl in Trinity, it outputed the following error message.

fasta_seq_length.pl fasta > fasta.seq_lens

Can't locate fasta_reader.pm in @INC (you may need to install the fasta_reader module) (@INC contains: /Users/tomitariku/Bioinformatics/Aphelenchoididae/scripts/../../PerlLib /opt/anaconda3/envs/trinity/lib/perl5/5.32/site_perl /opt/anaconda3/envs/trinity/lib/perl5/site_perl /opt/anaconda3/envs/trinity/lib/perl5/5.32/vendor_perl /opt/anaconda3/envs/trinity/lib/perl5/vendor_perl /opt/anaconda3/envs/trinity/lib/perl5/5.32/core_perl /opt/anaconda3/envs/trinity/lib/perl5/core_perl .) at scripts/fasta_seq_length.pl line 8.

It seemed that there is similar problems before, so I have installed Fasta_reader as same way. But it has outputed the same error.

pip install Fasta_reader

What's a problem? Could you please give me a help.

Thanks.

Answer 1

[Mensur Dlakic]

fasta_reader.pm refers to a perl module, not python. I think it is part of Trinity installation in the PerlLib directory:

https://github.com/genome-vendor/trinity/blob/master/PerlLib/Fasta_reader.pm

There should be an explanation in Trinity documentation how to install the program so this directory is visible to perl scripts.

[Riku]

I found out that pm is perl module. But I didn't know how to install the program, because I wasn't able to find an explanetion as you say. And I'm beginner at bioinformatics, so could you please tell me in details if you are okay?

Many thanks to your help.

[Riku]

I solved this problem. I made a path to my environment in anaconda.

Specifically, I changed the first line of the script to my path in anaconda as following. I used vim command, but any means should be fine.

#!/opt/anaconda3/envs/trinity/bin/perl

I'm not an expert so I'm just speculating, I guess I was able to become using fasta-reader of anaconda by the change. However this environment need to have fasta-reader, so you havo to install it in your environment as following if you haven't.

pip install Fasta_reader

I hope this question helps someone!

[Pilar]

hi! in which script have you made changes? I don't have permissions in Fasta_reader.pm