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Removing white space from the beginning of the second field (sequence) in a fasta file

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

sequence protein fasta linux
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updated by Chris Miller Chris Miller • written by Angie11 • Angie11

2 answers

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
• 0 views • link
written by bari.ballew bari.ballew

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

• 0 views • link
written by Chris Miller Chris Miller

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