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  • calcultate Max, min of contigs length

    Hi Everyone
    I want to calculate max, min length of contig file. but i dont know about perl, and i want to mems share script in perl to calculate max, min.
    Thanks.

  • #2
    HMMER ships with some excellent little sequence analysis/conversion/etc. tools. I think for this task esl-seqstat would be perfect..
    savetherhino.org

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    • #3
      There is an awk script example on http://www.researchgate.net/post/Ful...ng_contig_file that should produce the info you need. You will have to run it on a unix system and on command line.

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      • #4
        Originally posted by GenoMax View Post
        There is an awk script example on http://www.researchgate.net/post/Ful...ng_contig_file that should produce the info you need. You will have to run it on a unix system and on command line.
        Can you more explained for me? or Is there a software for it
        Last edited by Votinhkiem90; 09-28-2013, 06:46 AM.

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        • #5
          Originally posted by Votinhkiem90 View Post
          Can you more explained for me?
          I assume you have access to a computer running linux/unix? If you do not then the following will not work.

          In a terminal window run the following command while you are in the directory where you contig file is (in multi-FASTA format). Command reproduced here from the original link in post #3.

          Code:
          $ awk 'BEGIN{flag=0;print "Contig ID\tContig Length\tA\tT\tG\tC\tN\tOtherCharacters"}{if($0~/^>/){if(flag==1){tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}id=$0;flag=1;aCount=gCount=cCount=tCount=nCount=xCount=0;}else{aCount+=gsub(/[aA]/,"A",$0);tCount+=gsub(/[tT]/,"T",$0);gCount+=gsub(/[gG]/,"G",$0);cCount+=gsub(/[cC]/,"C",$0);nCount+=gsub(/[nN]/,"N",$0);xCount+=gsub(/[^ATGCNatgcn]/,"X",$0);}}END{tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}' INPUT_FILE >OUTPUT_FILE
          Replace the INPUT_FILE with your contig file name. Replace OUTPUT_FILE with a file name you want to use for the result.

          Comment


          • #6
            Originally posted by GenoMax View Post
            I assume you have access to a computer running linux/unix? If you do not then the following will not work.

            In a terminal window run the following command while you are in the directory where you contig file is (in multi-FASTA format). Command reproduced here from the original link in post #3.

            Code:
            $ awk 'BEGIN{flag=0;print "Contig ID\tContig Length\tA\tT\tG\tC\tN\tOtherCharacters"}{if($0~/^>/){if(flag==1){tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}id=$0;flag=1;aCount=gCount=cCount=tCount=nCount=xCount=0;}else{aCount+=gsub(/[aA]/,"A",$0);tCount+=gsub(/[tT]/,"T",$0);gCount+=gsub(/[gG]/,"G",$0);cCount+=gsub(/[cC]/,"C",$0);nCount+=gsub(/[nN]/,"N",$0);xCount+=gsub(/[^ATGCNatgcn]/,"X",$0);}}END{tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}' INPUT_FILE >OUTPUT_FILE
            Replace the INPUT_FILE with your contig file name. Replace OUTPUT_FILE with a file name you want to use for the result.
            Thank all, How to sort to max to min lengthcontigs?

            Comment


            • #7
              Originally posted by Votinhkiem90 View Post
              Thank all, How to sort to max to min lengthcontigs?
              Assume you ran GenoMax's awk code to create the output. In that case the following would sort the contigs based on their length.
              Code:
              sort -t $'\t' -k2 -n -r INPUT_FILE > OUTPUT_FILE

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