How to combine all the seqences in a fasta file to one sequence?

[wmseq]

Hi every one,

I have a fasta file like this like this:
>GL132456
ABCDEDERFSE
>GL123456
ABDFDRAGDTGEGAGFDAS
>GL125436
AFGHSRSGFGSHSFG
I want to combine all the sequences to one sequence, like this:
ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

Thanks a lot!

Richard

[rhinoceros]

Maybe:

grep -v ">" your.fasta | sed -e 's/\n//g' -e 's/ //g' > youredited.fasta

Select all lines than don't have ">", remove newlines, remove spaces, direct output to a new file.

[fahmida]

Maybe:

grep -v ">" your.fasta | sed -e 's/\n//g' -e 's/ //g' > youredited.fasta

Select all lines than don't begin with ">", remove newlines, remove spaces, direct output to a new file.

Just a minor update of above would create the required output:

grep -v ">" your.fasta|tr '\n' ' ' | sed -e 's/ //g' > youredited.fasta

Output:

ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

[liweixie]

use cat command

[wmseq]

I have checked all the commands. No one worked for my data.
Thanks!

[rhinoceros]

I have checked all the commands. No one worked for my data.
Thanks!

You're doing it wrong then because they do work:

$ cat file.fasta 
>GL132456
ABCDEDERFSE
>GL123456
ABDFDRAGDTGEGAGFDAS
>GL125436
AFGHSRSGFGSHSFG

$ grep -v ">" file.fasta | tr '\n' ' ' | sed -e 's/ //g' > youredited.fasta

$ cat youredited.fasta 
ABCDEDERFSEABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

[wmseq]

I am sorry for my mistake, because my sequence is as follows.
>GL132456
ABCDEDERFSE
DGA
>GL123456
ABDFDRAGDTGEGAGFDAS
>GL125436
AFGHSRSGFGSHSFG

After I used the commands, I got the following sequence with white space in it.
ABCDEDERFSE
DGA
ABDFDRAGDTGEGAGFDASAFGHSRSGFGSHSFG

thank you for your patience!

[RDW]

perl -pe 'chomp;s/>.+//' input.fasta >out.txt