[Bioperl-l] fasta format

Amir Karger akarger at CGR.Harvard.edu
Wed Dec 9 10:01:45 EST 2009

> Is there any way to use these fasta files with diffrent length of
> lines with this fasta.pm module or will i have to change the format
> of my fasta-files(big databases...) ?


It's not Bioperl, but for a quick fix you can use the Scriptome. Use the change_fasta_to_tab script (http://sysbio.harvard.edu/csb/resources/computational/scriptome/Windows/Tools/Change.html#change_a_fasta_file_into_tabular_format__change_fasta_to_tab_) to change your FASTA into a tab-delimited file. Then use the next tool (change_tab_to_fasta) to change your files back.

To use a tool: change the input and output file names on the website, then cut and paste the Perl script from the green box into a CMD window. The script works one sequence at a time, so it doesn't need a lot of memory. (As long as you have enough disk space to store the tab-delimited copy).

The recreated FASTAs will be 60 characters per line (although you can hand-edit the line after you paste it to be whatever number of characters you'd like).

Let me know if you have a problem.

-Amir Karger
Life Sciences Research Computing, FAS IT
Harvard University

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