Thanks a lot Richard! I really appreciate that!
Best,
Thanos
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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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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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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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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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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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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).
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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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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.Tags: None
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