I have a 47gb file to parse. The sequences are in the following format:
>tscs_00041 gene0ea_12345_rframe2_orf
mlaathyykfairrlfpllkdticasysisikhhenfmalsnmpkiwedvevdgnnmqwtrfqttpvmpvyfiaagvfnlsfitnwntkllyrkdilpymtfaynvakniawflshirktkitnhi
>tscs_00044 gene0ea_12341_rframe2_orf
mticasysisikhhenfmaikhhenfmalsnmpkiwedv
I simply want to format this file like:
>tscs_00041
mlaathyykfairrlfpllkdticasysisikhhenfmalsnmpkiwedvevdgnnmqwtrfqttpvmpvyfiaagvfnlsfitnwntkllyrkdilpymtfaynvakniawflshirktkitnhi
>tscs_00044
mticasysisikhhenfmaikhhenfmalsnmpkiwedv
Can anyone share the script?
Something like this (this is untested):
while {} {
if (substr($_,0,1) eq '>') {
my @this = split / /,$_;
print "$this[0]\n";
} else {
print $_;
}
Assuming that you are on unix/linux and don't have white spaces in the sequences themselves:
cut -d' ' -f1 < in.fasta
This may be much faster than the python and perl solutions.
TIMTOWTDI. As far as I understand you need the first and third fields only. You could do this with awk,
awk '{print $1" "$3}' file.fasta
or even with Perl,
while(){
if((my $v1, my $v2) = /^(\S+)\s+\S+\s+(\S+)/){
print "$v1 $v2\n";
}
perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' mysequences.fa
maybe is late, this script you can change the name of all sequences how you want.
example: fastRename -in infield.fasta -o outfile.fasta -l new_label_
https://gist.github.com/cabraham03/a7d3457919b08ac556d8
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