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Results for "multiple fasta"

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• • Jit@jit.aber

  

  awk 'BEGIN {RS = ">" ; FS = "\n" ; ORS = ""} {if ($2) print ">"$0}' all_p_ctg.fa > all_p_ctg_CORRECTED.fa #remove #empty #clean #fasta

  2350 days ago

• • Jit@jit.aber

  

  #Remove a #sequence by id from multifasta: cat vaga.fa | awk '{if (substr($0,1) == ">scaffold_1 1087316 bp") censor=1; else if (substr($0,1,1) == ">") censor=0; if (censor==0) print $0}' > fixed.fasta

  2350 days ago

• • Jit@jit.aber

  

  get the fasta genes using gff3 and genome.fa sequence: ~/Tools/bedtools2/bin/bedtools getfasta -fi vaga.fa -bed Adineta_vaga.v2.gff3 -fo Adineta_vaga_genes.fa

  2317 days ago

• • Jit@jit.aber

  

  #GFA to #FASTA file conversion. awk '/^S/{print ">"$2"\n"$3}' in.gfa | fold > out.fa

  2297 days ago

• • Jit@jit.aber

  

  #GFA to #Fasta file conversion. $ grep '^S' example.gfa |awk '{print ">"$2; print $3}' > example.fa

  2290 days ago

• • Rahul Nayak@rahul

  

  #Convert #fasta file to uppercase/lowercase, without altering the annotation line $ awk '{ if ($0 !~ />/) {print toupper($0)} else {print $0} }' name.fasta

  2251 days ago

• • Jit@jit.aber

  

  Glob multiple files in Linux with Perl. my @soundfiles = grep {/\.(wav|mid|mp3|rm|ogg)$/i} glob("*"); #Perl #Linux #Glob

  2244 days ago

• • Jit@jit.aber

  

  Convert lowercase letter to N:$ sed -e '/^>/! s/[[:lower:]]/N/g' in.fasta > out.fasta #Convert #Lowercase #Fasta #N

  2234 days ago

• • Manisha Mishra@manisha

  

  Extract fasta with Ids. $ perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(id1 id2)}print if $c' fasta.file #extract #fasta #sequence #ids

  2225 days ago

• • Manisha Mishra@manisha

  

  Remove the sequence by fasta ids. awk 'BEGIN{while((getline<"ids.txt")>0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa #Remove #Delete #ids #fasta

  2225 days ago

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