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  • Shishir
    Member
    • Nov 2012
    • 22

    #1

    Any script to format headers in fasta files?

    I have a 47GB file to parse. The sequences are in 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
    Could anyone share the script.
  • Richard Finney
    Senior Member
    • Feb 2009
    • 701

    #2
    cut -f1 -d" " inputold.fa > outputnew.fa

    Comment

    • Shishir
      Member
      • Nov 2012
      • 22

      #3
      Thanks Richard!

      Comment

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