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problem in code

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  • rohitgole2003
    this is the sample of file: like that i have lots of file with in the single file LOCUS NM_015698 1669 bp mRNA linear PRI
    Message 1 of 5 , Jul 3, 2005
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      this is the sample of file:

      like that i have lots of file with in the single file


      LOCUS NM_015698 1669 bp mRNA linear PRI
      23-APR-2005
      DEFINITION Homo sapiens G patch domain and KOW motifs (GPKOW), mRNA.
      ACCESSION NM_015698
      VERSION NM_015698.3 GI:39725663
      KEYWORDS .
      SOURCE Homo sapiens (human)
      ORGANISM Homo sapiens
      Eukaryota; Metazoa; Chordata; Craniata; Vertebrata;
      Euteleostomi;
      Mammalia; Eutheria; Euarchontoglires; Primates; Catarrhini;
      Hominidae; Homo.
      REFERENCE 1 (bases 1 to 1669)
      AUTHORS Schindelhauer,D., Hellebrand,H., Grimm,L., Bader,I.,
      Meitinger,T.,
      Wehnert,M., Ross,M. and Meindl,A.
      TITLE Long-range map of a 3.5-Mb region in Xp11.23-22 with a
      sequence-ready map from a 1.1-Mb gene-rich interval
      JOURNAL Genome Res. 6 (11), 1056-1069 (1996)
      PUBMED 8938429
      COMMENT PROVISIONAL REFSEQ: This record has not yet been subject
      to final
      NCBI review. The reference sequence was derived from
      BC000397.2.
      On Dec 11, 2003 this sequence version replaced gi:15811781.
      FEATURES Location/Qualifiers
      source 1..1669
      /organism="Homo sapiens"
      /mol_type="mRNA"
      /db_xref="taxon:9606"
      /chromosome="X"
      /map="Xp11.23"
      gene 1..1669
      /gene="GPKOW"
      /note="synonym: T54"
      /db_xref="GeneID:27238"
      /db_xref="HPRD:HPRD_06737"
      CDS 8..1438
      /gene="GPKOW"
      /note="T54 protein;
      go_component: intracellular [goid 0005622]
      [evidence IEA];
      go_function: nucleic acid binding [goid 0003676]
      [evidence
      IEA];
      go_process: biological_process unknown [goid 0000004]
      [evidence ND]"
      /codon_start=1
      /product="G patch domain and KOW motifs"
      /protein_id="NP_056513.2"
      /db_xref="GI:15811782"
      /db_xref="GeneID:27238"
      /db_xref="HPRD:HPRD_06737"

      /translation="MADSKEGVLPLTAASTAPISFGFTRTSARRRLADSGDGAGPSPE

      EKDFLKTVEGRELQSVKPQEAPKELVIPLIQNGHRRQPPARPPGPSTDTGALADGVVS

      QAVKELIAESKKSLEERENAGVDPTLAIPMIQKGCTPSGEGADSEPRAETVPEEANYE

      AVPVEAYGLAMLRGMGWKPGEGIGRTFNQVVKPRVNSLRPKGLGLGANLTEAQALTPT

      GPSRMPRPDEEQEKDKEDQPQGLVPGGAVVVLSGPHRGLYGKVEGLDPDNVRAMVRLA

      VGSRVVTVSEYYLRPVSQQEFDKNTLDLRQQNGTASSRKTLWNQELYIQQDNSERKRK

      HLPDRQDGPAAKSEKAAPRSQHWLHRDLRVRFVDNMYKGGQYYNTKMIIEDVLSPDTC

      VCRTDEGRVLEGLREDMLETLVPKAEGDRVMVVLGPQTGRVGHLLSRDRARSRALVQL
      PRENQVVELHYDAICQYMGPSDTDDD"
      misc_feature 491..631
      /gene="GPKOW"
      /note="G_patch; Region: glycine rich nucleic binding
      domain"
      /db_xref="CDD:7365"
      variation complement(1302..1303)
      /gene="GPKOW"
      /replace="c"
      /replace="t"
      /db_xref="dbSNP:12012419"
      ORIGIN
      1 gagcaagatg gctgactcca aagagggtgt tttgccgctg acggctgctt
      ccactgcccc
      61 aatttcattc ggcttcactc gcacgtccgc acggaggcgg ctggccgact
      cgggagacgg
      121 cgcggggcca tctccggagg agaaggattt cttgaaaacc gtggaaggga
      gggagctgca
      181 gagtgtgaag ccccaggagg cccccaagga actcgtcatc cctttgatcc
      agaatggcca
      241 tcgcaggcag ccaccagccc ggccccctgg gccatccaca gatactgggg
      ccttggcgga
      301 tggggtggtg tcccaggctg tgaaggagct cattgcggaa tccaagaagt
      ctctggaaga
      361 gagagagaat gcgggtgtcg accccacgct cgctatcccc atgatccaga
      aaggatgcac
      421 ccccagcggg gaaggggcag acagcgaacc ccgggcagag acagtgccag
      aggaggctaa
      481 ttatgaggcg gtccccgtgg aggcctatgg gctggccatg ctgcggggca
      tgggctggaa
      541 acctggcgag ggcatcggcc gcaccttcaa tcaagtagtg aagccccgtg
      tcaactcact
      601 gaggcccaag gggttagggc tgggtgccaa cctgaccgag gcccaggcct
      tgacccccac
      661 tggcccctcc cgcatgccaa gaccagatga ggagcaagag aaagataagg
      aagatcagcc
      721 tcaagggctg gtgcctggag gagctgtggt ggttctttct ggccctcacc
      gaggcctcta
      781 tgggaaggtg gaaggccttg atcctgacaa tgttcgggcc atggttcgtc
      tggctgtggg
      841 gagccgggtg gtgactgtta gtgagtacta cctgcggcct gtctcccagc
      aggagtttga
      901 caagaacacc ttggatctca ggcaacagaa cggaactgcc tcatcacgga
      agaccctctg
      961 gaatcaagaa ctctacatcc agcaggacaa ctcagagagg aagcggaaac
      accttccaga
      1021 ccgacaggat gggcctgcag ccaagagtga gaaagcagcc cccagaagtc
      agcactggtt
      1081 gcacagggac ctgcgtgtgc ggtttgtgga caacatgtac aaaggaggcc
      aatattacaa
      1141 caccaagatg ataattgaag atgtcctaag cccagatacc tgtgtatgtc
      ggacagatga
      1201 aggccgagtc ctggaaggcc tgagggaaga catgctggag accctggttc
      ccaaggcaga
      1261 gggtgaccgt gtgatggtgg tgctgggccc acagactgga agggtgggac
      atttgctgag
      1321 ccgggacaga gcacggagcc gggctttggt gcaactgcca agagaaaatc
      aggtggtgga
      1381 gcttcactac gatgccatct gccagtacat gggccctagt gacacagatg
      atgactgacc
      1441 catgggactc ctcccatccc ccaggctggt accagttctg taccatatga
      gaaagttgcc
      1501 ttcagaaggt gggaagatca ttgttccatc ctctacttct ggtgcagtcc
      tgggacaagg
      1561 acaagggaaa gggatgggtg aaccagtagg gaagctagaa acaaacccaa
      tatttaccaa
      1621 aatttagggt ataataaaaa ccatttcaag taaaaaaaaa aaaaaaaaa
      //
    • Charles K. Clarkson
      ... Alrighty, that answers part of my question. Assuming some lines have wrapped, we now know what the file might look like. Now take a line that matches what
      Message 2 of 5 , Jul 4, 2005
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        rohitgole2003 <> wrote:
        : this is the sample of file:
        :
        : like that i have lots of file with in the single file

        Alrighty, that answers part of my question. Assuming some lines
        have wrapped, we now know what the file might look like. Now take a
        line that matches what you are looking for and tells us what you
        expect to get when done.

        I think this is the only one you are trying to match. What do
        you want to get out of this line (or any other line you are trying
        to match)?

        : CDS 8..1438



        HTH,

        Charles K. Clarkson
        --
        Mobile Homes Specialist
        254 968-8328


        P.S. The subject to your reply post should be
        "RE: [PBML] problem in code" or
        "RE: problem in code". It should not restart the thread.
      • rohit gole
        i have solved my problem actually there is problem with the genebank file actually after finish one genbank file ,the file ends with the sign // And so
        Message 3 of 5 , Jul 4, 2005
        • 0 Attachment
          i have solved my problem
          actually there is problem with the genebank file

          actually after finish one genbank file ,the file ends with the sign "//"
          And so somewhere it is missing and that is why my program was not able to read that and that is why i got the wrong total cds start position

          thanx

          rohit singh
          Biological science and Bio-engineering
          IIT Kanpur



          "Charles K. Clarkson" <cclarkson@...> wrote:
          rohitgole2003 <> wrote:
          : this is the sample of file:
          :
          : like that i have lots of file with in the single file

          Alrighty, that answers part of my question. Assuming some lines
          have wrapped, we now know what the file might look like. Now take a
          line that matches what you are looking for and tells us what you
          expect to get when done.

          I think this is the only one you are trying to match. What do
          you want to get out of this line (or any other line you are trying
          to match)?

          : CDS 8..1438



          HTH,

          Charles K. Clarkson
          --
          Mobile Homes Specialist
          254 968-8328


          P.S. The subject to your reply post should be
          "RE: [PBML] problem in code" or
          "RE: problem in code". It should not restart the thread.




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