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egonozer / in_silico_pcr

Perl script for simulating PCR reactions. Extract sequences from a query based on primer sequences.
GNU General Public License v3.0
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Error: Use of uninitialized value... #3

Closed pneumowidow closed 3 years ago

pneumowidow commented 3 years ago

Hi,

I've been trying to use your script to extract sequences but I keep getting the following errors:

Use of uninitialized value in substr at in_silico_PCR.pl line 357.
Use of uninitialized value in addition (+) at in_silico_PCR.pl line 377.

I thought it had something to do with the multiple scaffolds in the fasta files, so I used artemis to extract the exact amplicon with both primers at the start and the end of the sequence and tries again, but I still got no output and the same errors above. I've looked online to try to figure out what the problem is, but can't seem to find a solution. I am not a perl user, so I'm completely out of my element here. Can you please help me out?

Thank you

egonozer commented 3 years ago

I did some testing and found that you'll get that error if the forward primer sequence is found at the very end of the input sequence. This error doesn't pop up if you use the -c option, but it still shouldn't be there. I dropped a quick fix as version 0.5.1.

pneumowidow commented 3 years ago

It works now with the -c option. Thank you very much. I didn't see that earlier