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  • splitting big genbank file

    I have a big gbk file containing multiple gbks, is there any simple way to split this big gbk into small gbks Thanks.

  • #2
    I haven't tried it out but 'seqretsplit' from the EMBOSS package might do what you want. Otherwise it's a quick script in Bioperl or Biopython, e.g. in BioPython (untested)

    Run like python splitgbk.py < input.gbk

    Will create a file for each entry in the current directory.

    -- splitgbk.py

    Code:
    from Bio import SeqIO
    import sys
    
    for rec in SeqIO.parse(sys.stdin, "genbank"):
       SeqIO.write([rec], open(rec.id + ".gbk", "w"), "genbank")

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    • #3
      If you want one file per record, try EMBOSS seqret and the -ossingle_outseq option.

      EDIT: That probably does the same as EMBOSS seqretsplit suggested by Nick while I was writing this.


      Do you just want to break it up into batches, say 10 records in each file? Or, do you have a particular order in mind (which could involve either sorting or random access).
      Last edited by maubp; 03-19-2012, 11:28 AM. Reason: Nick posted at same time

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      • #4
        Come on Peter, I caught you napping again

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        • #5
          split genbank files using awk

          awk -v n=1 '/^\/\//{close("out"n);n++;next} {print > "out"n}' yourfilename.gbk

          Split yourfilename.gbk into multiple files by splitting at "//" (end of record) line.
          Last edited by Richard Finney; 03-20-2012, 09:51 AM.

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          • #6
            Hi all,

            I have the same problem but I want to split the file every 1000 entries. My file has 500,000 records and I want 500 files of 1000 records each. Any suggestions?

            Thanks in advance.
            Thanos

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            • #7
              Thanos - which scripting languages do you know? GenBank records end with a // line (which is what Richard's awk command exploits) so it is very simple to split up a file into sub-files named however you like using Perl, Python or Ruby.

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              • #8
                Hi Peter and thank you for your immediate reply.

                I currently use Perl (not very experienced though). I guess I can try to alter Richard's awk command and implement it in a Perl script for renaming etc.

                Thank you once again.

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                • #9
                  awk -v n=1 -v p=0 '/^\/\//{p++;if(((p%1000)==0)&&(p!=0)){close("out"n);n++;next}} {print > "out"n}' yourfilename.gbk

                  splits at 1000 records.

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                  • #10
                    Thanks a lot Richard! I really appreciate that!

                    Best,
                    Thanos

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