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  • Program edit an ace file to simultaneously extract read information from all contig?

    Hi guys

    I need to extract the read names composition of all contigs from an ace file of an assembly. I know tablet and other tools do this but only browsing the file contig by contig by my ace has 65000 contigs (UGG). Doe anyone knows
    a tool capable to let to edit the ace and extract this particular info from all
    contigs simultanously?? perhaps converting the ace to bam??

    Thanks in advance

    Carlos

  • #2
    forget it i already have the solution which quite easy
    thankl you anyway

    Comment


    • #3
      And what was your solution?

      I would try parsing the ACE file with Biopython to get the read names - but you could probably do it with a regular expression at the Unix command line too.

      Comment


      • #4
        Yes, i will make a small perl or php script to parse the file.
        I wrote the question so fastly i guess because i wrongly though that .ace cannot be edit as a plane file. So there is no problem to parse it with any script.

        Comment

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