I Want a one line FASTA!

4 次查看（过去 30 天）
Bio_Ing_Sapienza
Bio_Ing_Sapienza 2019-1-20
评论： Bio_Ing_Sapienza 2019-1-20
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 个评论
Image Analyst
Image Analyst 2019-1-20
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.
Stephen23
Stephen23 2019-1-20
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.

请先登录，再进行评论。

请先登录，再回答此问题。

采纳的回答

Arthur Goldsipe
Arthur Goldsipe 2019-1-20
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.

更多回答（0 个）

类别

在 Help Center 和 File Exchange 中查找有关 Filename Construction 的更多信息

标签

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by