Question: Removing white space from the beginning of the second field (sequence) in a fasta file
0
gravatar for Angie11
11 months ago by
Angie110
Angie110 wrote:

Hello,

Does anyone know of a command (in the linux command line) such as sed to remove white spaces from a specific field only? In my case, I have 2 tab-seperated fields in the format shown below and I would like to remove the white space from the beginning of the second field (the beginning of the sequence) without removing white spaces from the first field. It is a fasta format but I can convert it into a tab delimited text file if needed.

>10_GL0000024 root|cellular organisms|Bacteria|Firmicutes locus=scaffold18562_3:3421:4365:- [Complete]
 MELTFQTATPAERLYTTGQSMQIEGQMGYIGCLQTGMSEDGKGAFPKWSSGREGLNTEEFQQELAGVMDALIHDEQYGGFLKDSDAMRDFCQTHPESGFNNGFAFGFRADTAQYSYLIRLNPCKGEENLSICCYRRDWLDSHMKHAEKGIRFITPHYKEKFRIADGDKVRIRRFDGQVFDRVCRYIDDCHVEIGSELYHICQFAEIMERNGNSVIPLRSSLPFVCYGKVPEKRAIVMFERGFDGYRSASFATKGRTSQKLVDELNGELGVTKAQAAAMQGGATQGWASPAADPKNYDEQGQPIKPRHRDRGDAR

Thank you! Angie

linux protein sequence fasta • 485 views
ADD COMMENTlink modified 11 months ago by Chris Miller21k • written 11 months ago by Angie110
0
gravatar for bari.ballew
11 months ago by
bari.ballew220
USA/NIH
bari.ballew220 wrote:

Take a look at regex anchors, which tie your pattern to the beginning or end of a line. You can use sed to remove whitespace at the beginning of a line only using "^", which anchors the pattern to the beginning of the line.

sed 's/^[\t ]*//' file.fa > secondFile.fa
ADD COMMENTlink written 11 months ago by bari.ballew220
0
gravatar for Chris Miller
11 months ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

if this is a fasta file, then you'll always want to remove leading whitespace, so something like:

sed 's/^\s//' myfile.fa

oughta work fine

ADD COMMENTlink written 11 months ago by Chris Miller21k
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