bees.world has asked for the wisdom of the Perl Monks concerning the following question:

Hi monks, I need a simple command for linux shell to extract only annotations (non-sequence data) form genbank file. I dont need sequences at all..lets say :

 ORIGIN
       1 tcagaataaa cagacaaccc acagaatgtg agaaaatatt gcaaattat gcatctg
+aca
       61 aaggtctaat acccagcaat ctataaggaa ctcaaacaaa ttagcaagaa aaaaa
+atccc
      121 atgaaaaggt agacaaatga catgaataga cacttctcaa aataagatat ataaa
+tagcc

//

[download]

I want to delete evrything in between ORIGIN and // Just need annotations. HELP Plzz..

Replies are listed 'Best First'.
Re: seperate/extract only annotations from genbank (gbk) file.
by Neighbour (Friar) on Jun 29, 2011 at 12:44 UTC
    Which bit of your question pertains to Perl?
    Also, if you delete everything between ORIGIN and //, you will end up with nothing, so you could just skip with the whole dataprocessing and use cat /dev/null instead.
[reply]
[d/l]

      oh god..no. I jus wrote the part I want to delete. theres whole lot of data in a genbank file,,ok let me write a sample: 

      LOCUS       NW_927708              12387 bp    DNA     linear   CON 25
+-OCT-2010
DEFINITION  Homo sapiens chromosome 2 genomic contig, alternate assemb
+ly
            Hs_Celera 211000035800763, whole genome shotgun sequence.
ACCESSION   NW_927708
VERSION     NW_927708.1  GI:88954435
DBLINK      Project: 16116
KEYWORDS    WGS.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Eutele
+ostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhin
+i;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 12387)
  AUTHORS   Istrail,S., Sutton,G.G., Florea,L., Halpern,A.L., Mobarry,
+C.M.,
            Lippert,R., Walenz,B., Shatkay,H., Dew,I., Miller,J.R.
  TITLE     Whole-genome shotgun assembly and comparison of human geno
+me
            assemblies
  JOURNAL   Proc. Natl. Acad. Sci. U.S.A. 101 (7), 1916-1921 (2004)
   PUBMED   14769938
REFERENCE   2  (bases 1 to 12387)
  AUTHORS   Venter,J.C., Adams,M.D., Myers,E.W., Li,P.W., Mural,R.J.,
            Sutton,G.G., Smith,H.O., Yandell,M., Evans,C.A., Holt,R.A.
  TITLE     The sequence of the human genome
  JOURNAL   Science 291 (5507), 1304-1351 (2001)
   PUBMED   11181995
COMMENT     REFSEQ INFORMATION: Features on this sequence have been pr
+oduced
            for build 37 version 2 of the NCBI's genome annotation [se
+e
            documentation]. The reference sequence is identical to CH4
+71348.1.
            Assembly Name: Hs_Celera
            The DNA sequence was produced by Celera Genomics. It is in
+cluded in
            the NCBI RefSeq collection as an alternative assembly to t
+he one
            produced by the Genome Reference Consortium. The original 
+whole
            genome shotgun project has the project accession AADB00000
+000.2.
FEATURES             Location/Qualifiers
     source          1..12387
                     /organism="Homo sapiens"
                     /mol_type="genomic DNA"
                     /db_xref="taxon:9606"
                     /chromosome="2"
     gap             7139..7188
                     /estimated_length=50
ORIGIN      
        1 tcagaataaa cagacaaccc acagaatgtg agaaaatatt tgcaaattat gcatc
+tgaca
       61 aaggtctaat acccagcaat ctataaggaa ctcaaacaaa ttagcaagaa aaaaa
+atccc
      121 atgaaaaggt agacaaatga catgaataga cacttctcaa aataagatat ataaa
+tagcc
      181 acaaacatat gaaaaaataa tcaacatcac taatcatcag gtaaatgcaa attaa
+aacca
      241 taatgagata ccaccttatc ccagccagaa tggccattat tagaaagtcc aaaaa
+caata
      301 gatgttggca tggatgtggt gaaaagggaa gagtttacac tgcgggcagg aatgt
+aaatt
//

      [download]

      REGARDING PERL: okk I just need the substitution pattern to remove these sequences info. leaving rest other things at its place..

[reply]
[d/l]
[reply]
Re: seperate/extract only annotations from genbank (gbk) file.
by Anonymous Monk on Jun 29, 2011 at 12:56 UTC
[reply]
      Yeah thanks..I thought I would get something quick here..quite urgent.Anyways am searching..thanks for the links.
[reply]
Re: seperate/extract only annotations from genbank (gbk) file.
by duelafn (Parson) on Jul 01, 2011 at 17:54 UTC
[reply]
[d/l]
      Hi Dean, The regex you gave is not working :( I have tried replacing ".." with other dots combination, but its not working..can you suggest something?
[reply]

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