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Results for "FASTA"

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  • Rahul Nayak

    Add number in fasta header $ awk '/^>/{$0=$0"_"(++i)}1' infile.fa #fasta #header #add #number #count

    Tags: fasta, header, add, number, count

    1956 days ago

  • Neelam Jha

    (smrttools) ➜ allBam for i in *.bam; do bamtools convert -format fasta -in $i -out $i.fasta; done #Convert #fasta

    Tags: Convert, fasta

    1918 days ago

  • Rahul Nayak

    One liner to remove the description information from a fasta file and just keep the identifier $ perl -p -i -e 's/>(.+?) .+/>$1/g' sample1.fa #clean #header #fasta

    Tags: clean, header, fasta

    1904 days ago

  • Neelam Jha

    #Rename the #fasta #header and #keep first $ perl -ne 'if (/^(>\S+)/){print "$1\n";}else{print $_;}' realTestDATA.fa > realTestDATA_headerCorrected.fa #Perl

    Tags: Rename, fasta, header, keep, Perl

    1626 days ago

  • Neelam Jha

    Multifasta 2 singlefasta cat toy.fasta| awk '{ if (substr($0, 1, 1)==">" {filename=(substr($0,2) ".fa")} print $0 > filename }' #Split #fasta #multifasta

    Tags: Split, fasta, multifasta

    1616 days ago

  • LEGE

    Count number of fasta sequence $ awk '/^>/ { f = !a[$0]++ } f' aaaa.fa > bbbb.fa #count #fasta #oneliner

    Tags: count, fasta, oneliner

    970 days ago

  • BioStar

    Delete all the headers from multifasta file $ awk 'BEGIN {print ">"ARGV[1]};!/^>/{print}' test.fa #fasta #delete #header #multifasta

    Tags: fasta, delete, header, multifasta

    98 days ago

  • Jit

    perl -nle 'if (/^>/) { $sl = 0; print; next } next if ($sl >= 200); $_ = substr($_, 0, 200-$sl) if ($sl + length($_) > 200); $sl += length($_); print;' file.fa >new.fa #Perl #Extract #Fasta

    Tags: Perl, Extract, Fasta

    3615 days ago

  • Jit

    Remove N from a fasta file. Go to vi editor, type :%s/N\{25,\}//g and press enter. #Vim #vi #N #Replace #Fasta

    Tags: Vim, vi, N, Replace, Fasta

    3615 days ago

  • Jit

    Remove the blank space from a fasta file. perl -nlwe 'tr/ //d; print if length' fileName #Delete #Space #Fasta #Perl #Oneliner

    Tags: Delete, Space, Fasta, Perl, Oneliner

    3615 days ago

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