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Editorial Team
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Asked: 2026-06-18T15:02:03+00:00

I’m really sorry, I’m having problems with the same old thing – awk and

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I’m really sorry, I’m having problems with the same old thing – awk and sed

I want to convert large text files containing:

>hg19_ct_UserTrack_3545_12513 range=chr1:52035541-52035716 5'pad=0 3'pad=0 strand=+ repeatMasking=none
CACACATACTTTTATTCAAGCCTCAGAGCAACCCTGCAAAATGAGTATTA
TCTCCACTTTACAATCAGGAGGCTGAGTCATAAGGAGGTGAGTCACCTGC
CTAGGGCCACATAGCTAGCAAGGAGCCAAGCTGGAATTTTAAGCCACGTT
TGTCTGATTCTTTCTGCATACCATGC
>hg19_ct_UserTrack_3545_13212 range=chr1:186122154-186122314 5'pad=0 3'pad=0 strand=+ repeatMasking=none
ATCTTCAGGGACAAGTTTTTACAAACTCTCTTAATGGTTTTACCACCCTC
CCTATCAGGACCAAGATCAAATACTTGATGTAAGGCATTTGTTTAATTTT
CTTTAGACAAAGAGGATAGTAATTCTTGCATAAACGTTTTTGTGTATCAT
CCATAAAATAT

etc, etc

To:

>range=chr1:52035541-52035716 5'pad=0 3'pad=0 strand=+ repeatMasking=none
CACACATACTTTTATTCAAGCCTCAGAGCAACCCTGCAAAATGAGTATTA
TCTCCACTTTACAATCAGGAGGCTGAGTCATAAGGAGGTGAGTCACCTGC
CTAGGGCCACATAGCTAGCAAGGAGCCAAGCTGGAATTTTAAGCCACGTT
TGTCTGATTCTTTCTGCATACCATGC
>range=chr1:186122154-186122314 5'pad=0 3'pad=0 strand=+ repeatMasking=none
ATCTTCAGGGACAAGTTTTTACAAACTCTCTTAATGGTTTTACCACCCTC
CCTATCAGGACCAAGATCAAATACTTGATGTAAGGCATTTGTTTAATTTT
CTTTAGACAAAGAGGATAGTAATTCTTGCATAAACGTTTTTGTGTATCAT
CCATAAAATAT

I’ve tried awk 'NR==1{sub(/^[^ ]* /,"")} 1' and sed -i '1s/\w\+ //' but nothing is working.

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1 Answer

  1. Editorial Team

    I assume you want to remove the first word in the lines that begin with a greater-than sign. In that case you can use awk like this:

    awk '{sub(/^>[^ ]* /,">")} 1'

    Remove the restriction, NR==1 means that the following block will only be executed on the first line. Also include > in the pattern and replacement.

    Output:

    >range=chr1:52035541-52035716 5'pad=0 3'pad=0 strand=+ repeatMasking=none
CACACATACTTTTATTCAAGCCTCAGAGCAACCCTGCAAAATGAGTATTA
TCTCCACTTTACAATCAGGAGGCTGAGTCATAAGGAGGTGAGTCACCTGC
CTAGGGCCACATAGCTAGCAAGGAGCCAAGCTGGAATTTTAAGCCACGTT
TGTCTGATTCTTTCTGCATACCATGC
>range=chr1:186122154-186122314 5'pad=0 3'pad=0 strand=+ repeatMasking=none
ATCTTCAGGGACAAGTTTTTACAAACTCTCTTAATGGTTTTACCACCCTC
CCTATCAGGACCAAGATCAAATACTTGATGTAAGGCATTTGTTTAATTTT
CTTTAGACAAAGAGGATAGTAATTCTTGCATAAACGTTTTTGTGTATCAT
CCATAAAATAT
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