Is that you have an space or a lack of the end of line code?
If your data are tab separated, and you have an space only at the end of the lane, you can do the following
cat file.fasta | tr -d " " > newfile.fasta
But notice that this will get rid of all spaces, including those at the middle of the lane.
•
written
by
Antonio R. Franco
Note for sed on Mac OS X, you have to use [[:space:]] instead of \s:
sed "s/[[:space:]]*$//g" in.fasta > out.fasta
Not a bioinformatics questions, you should try Stack Overflow for this, but here is a quick answer in perl:
perl -i.bak -pe 's/\h+$//' sequences.fa
Try the following:
perl -i.bak -pe "s/\s+$/\n/;" sequences.fa
Note that this will remove all trailing whitespace characters from each line (including newline), and replace with a single newline.
•
written
by
harold.smith.tarheel
What's your perl version ? The \h character class was introduced in perl 5.10.
Not sure why it didn't work for you. I tested it with 5.12 and 5.20 and it worked fine.
Oh my gawk!
All previous solutions would risk modifying your fasta header as well. This one will not.
gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +/ ) {gsub(/ +/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' myfasta.fa >output.fa
If you only want to remove the spaces at the end of the lines:
gawk 'BEGIN{line=0}{ if ($0 !~/^>/ && $0 ~/ +$/ ) {gsub(/ +$/, //); line++} print}END{print line" lines with white spaces treated" > "/dev/stderr"}' myfasta.fa>output.fa
To be fair, that is at low probability :-)
Yes, they could alter the header but only by removing white space from the end of it (the $ sigil anchors the match at the end of the line). The problem reported was with white spaces at the end of lines, whether the problem was limited to non-header lines wasn't specified.
I was just being paranoid and want to present gawk-based solution :-)
•
written
by
biocyberman
If your data are tab separated, and you have an space only at the end of the lane, you can do the following
cat file.fasta | tr -d " " > newfile.fasta
But notice that this will get rid of all spaces, including those at the middle of the lane.
•
written
by
Antonio R. Franco
Hi,
I think you could make use of the python rstrip() string method. Just call it while reading your fasta file, and it will handle the the white spaces as you want.
for line in open('path_to_fasta_file'):
print line.rstrip()
Copy the code into a file, say my_script.py, and run
python my_script.py
There you go
Wouldn't this also strip the newline characters?
Log in to answer this question.
