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RE: [PBML] problem in code

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  • Charles K. Clarkson
    ... First we need to see is examples of what a line of data might look like. Then we would need to know what you are trying to pull out of those sample lines.
    Message 1 of 5 , Jul 3, 2005
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      rohitgole2003 <> wrote:

      : please
      : if anybody can figure out the problem in the code,i will be very
      : thankful:
      :
      : problem is: actually i want to print the "CDS" starting number
      : of a 'genbank' file and then printing the corresponding
      : accession number, (the single file contains more then 20
      : thousand of genbank file means lots of genbank file is copied to
      : a single file)
      :
      : but on running the program i am not getting the corresponding
      : CDS number with the accession number
      :
      : but when i run the program to find out the size of array
      : containing the CDS number i got less than the lenth (sic) of
      : array containing accession number

      First we need to see is examples of what a line of data might
      look like. Then we would need to know what you are trying to pull
      out of those sample lines. Can you provide those sample lines of
      data?


      HTH,

      Charles K. Clarkson
      --
      Mobile Homes Specialist
      254 968-8328
    • 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 2 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 3 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 4 of 5 , Jul 4, 2005
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            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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