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I Want a one line FASTA!

Hi everyone. I want to write a FASTA file but my sequence once it has been written has to be on one unique line in my FASTA file and not splitted up as we find when we take our file from a databank. e.g.
I do not want this situation but I want all my lines aligned .
Thanx a lot!

  2 Comments

Image Analyst
on 20 Jan 2019
I don't even understand that syntax - how it could even run on the command line. What is lcl? What is the structure KQ001645? Why do you have an assignment in brackets [locus_tag=AK88_00001]? And why does it follow the OR test "lcl | KQ0......." with a space? etc.
Post your code where we can actually copy it and run it.
Stephen Cobeldick on 20 Jan 2019
Bio_Ing_Sapienza's "Answer" moved here:
.....That is not a code...Is the original fasta file that taken from NCBI and splitted in several line.Above every thing there is the header of my sequence, and then there is my aminoacid sequence. I want that sequence that you see in the screenshot THAT IS NOT EVIDENTLY A SCRIPT, to be on a single line....I'm trying to use fastawrite and regexp with the regular expression
EXPR='.*';
regexp(sequence{1},EXPR,'match','dotexceptnewline');
%this return me the framgents without problems but in the moment that I use FASTAWRITE it returns me the sequence once
%once more splitted in the same way I started.

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1 Answer

Answer by Arthur Goldsipe on 20 Jan 2019
 Accepted Answer

The fastawrite has a hard-coded limit of 70 characters per line. This follows NCBI recommendations. If you want to incease the maximum line length, I can think of 2 options. Either you modify the file created by fastawrite or you edit variable maxcols in fastawrite to be larger than your longest sequences.

  1 Comment

it works. just modiefied the maxcols. Thanks a lot!

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