Re^2: How to get non-redundant DNA sequences from a FASTA file?


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Re^2: How to get non-redundant DNA sequences from a FASTA file?

by Anonymous Monk

on Sep 06, 2015 at 12:14 UTC ( [id://1141192]=note: print w/replies, xml )

Need Help??

in reply to Re: How to get non-redundant DNA sequences from a FASTA file?
in thread How to get non-redundant DNA sequences from a FASTA file?

Hi biohisham,

I am trying to use your solution for redundant fasta file but Ive got this message:Global symbol "%hash" requires explicit package name at redundant.fasta line 14.

Global symbol "%hash" requires explicit package name at redundant.fast
+a line 18.
Global symbol "%hash" requires explicit package name at redundant.fast
+a line 19.
Global symbol "%hash" requires explicit package name at redundant.fast
+a line 20.
Global symbol "%hash" requires explicit package name at redundant.fast
+a line 21.
[download]

I installed BioPerl: cpan>install CJFIELDS/BioPerl-1.6.924.tar.gz Data-Dumper: cpan>SMUELLER/Data-Dumper-2.154.tar.gz and also EDWARDSON/Data-Dumper-Hash-0.001.tar.gz

I really appreciate your answer about how to solve it. Btw, I am newbie. Thanks Eric

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Re^3: How to get non-redundant DNA sequences from a FASTA file? by Not_a_Number (Prior) on Sep 06, 2015 at 12:32 UTC
You (and biohisham) need to declare `%hash` before using it. Simply put this line: `my %hash;` before the first `while` loop.	[reply] [d/l] [select]
Re^4: How to get non-redundant DNA sequences from a FASTA file? by Anonymous Monk on Sep 07, 2015 at 11:08 UTC
Hi Not_a_Number, Many thanks for your suggestion. Now the script is working nicely. Regards.	[reply]

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