Daniel:Notebook/GenomeMiner/2013-7-16: Difference between revisions

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>Djacobse
(Created page with "Back to Calendar Looked more into bowtie 2 format today. Converted .txt files from Dr. Zhang which gave the raw sequences for the probes into .fa file...")
 
>Djacobse
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MATLAB script:
MATLAB script:


<nowiki>
function [] = txt_to_fasta(input,set,outputname)
function [] = txt_to_fasta(input,set,outputname)
file=fopen(input);
file=fopen(input);
Line 14: Line 15:
  fprintf(outfile,'%s\n',M{1}{i});
  fprintf(outfile,'%s\n',M{1}{i});
end
end
</nowiki>

Revision as of 22:50, 16 July 2013

Back to Calendar

Looked more into bowtie 2 format today. Converted .txt files from Dr. Zhang which gave the raw sequences for the probes into .fa files using a MATLAB script I wrote. Jeff informed me this is also easy on Python or Perl. I plan on learning one of these (probably Perl) in order to do future endeavors, as it will not always necessarily be as easy to copy around files as I did this time.

MATLAB script:

function [] = txt_to_fasta(input,set,outputname) file=fopen(input); M=textscan(file,'%s'); nprobe=length(M{1}); outfile=fopen(outputname,'w'); for i=1:nprobe fprintf(outfile,'>Probe_set%i_%i\n',set,i); fprintf(outfile,'%s\n',M{1}{i}); end