biopythonを使用してgbファイルからデータを抽出します

Question

私はgbファイルを持っています。タンパク質の遺伝子名とサイズをコードする特定の機能を抽出する必要があります。

LOCUS  NC_008137    15318 bp DNA  linear MAM 15-APR-2009 
DEFINITION Phalanger interpositus mitochondrion, complete genome. 
ACCESSION NC_008137 
VERSION  NC_008137.1 GI:108793518 
DBLINK  Project: 17043 
KEYWORDS . 
SOURCE  mitochondrion Phalanger interpositus (Stein's cuscus) 
    ORGANISM Phalanger interpositus 
      Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; 
      Mammalia; Metatheria; Diprotodontia; Phalangeridae; Phalanger. 
REFERENCE 1 (bases 1 to 15318) 
    AUTHORS Munemasa,M., Nikaido,M., Donnellan,S., Austin,C.C., Okada,N. and 
      Hasegawa,M. 
    TITLE  Phylogenetic analysis of diprotodontian marsupials based on 
      complete mitochondrial genomes 
    JOURNAL Genes Genet. Syst. 81 (3), 181-191 (2006) 
    PUBMED 16905872 
REFERENCE 2 (bases 1 to 15318) 
    CONSRTM NCBI Genome Project 
    TITLE  Direct Submission 
    JOURNAL Submitted (12-JUN-2006) National Center for Biotechnology 
      Information, NIH, Bethesda, MD 20894, USA 
REFERENCE 3 (bases 1 to 15318) 
    AUTHORS Munemasa,M., Nikaido,M., Donnellan,S., Austin,C.C., Okada,N. and 
      Hasegawa,M. 
    TITLE  Direct Submission 
    JOURNAL Submitted (08-NOV-2005) Tokyo Institute of Technology, Graduate 
      School of Bioscience and Biotechnology; Nagatsuta-cho 4259-B-21, 
      Midori-ku, Kanagawa 226-8501, Japan 
COMMENT  REVIEWED REFSEQ: This record has been curated by NCBI staff. The 
      reference sequence was derived from AB241057. 
      Genome sequence lacks part of non-coding region. 
      COMPLETENESS: full length. 
FEATURES    Location/Qualifiers 
    source   1..15318 
        /organism="Phalanger interpositus" 
        /organelle="mitochondrion" 
        /mol_type="genomic DNA" 
        /db_xref="taxon:356347" 
        /tissue_type="liver" 
        /common="Stein's cuscus" 
    tRNA   1..69 
        /product="tRNA-Phe" 
    rRNA   72..1018 
        /product="s-rRNA" 
        /note="12S ribosomal RNA" 
    tRNA   1020..1088 
        /product="tRNA-Val" 
    rRNA   1089..2653 
        /product="l-rRNA" 
        /note="16S ribosomal RNA" 
    tRNA   2654..2727 
        /product="tRNA-Leu" 
        /codon_recognized="UUR" 
    gene   2729..3685 
        /gene="ND1" 
        /db_xref="GeneID:4117948" 
    CDS    2729..3685 
        /gene="ND1" 
        /codon_start=1 
        /transl_table=2 
        /product="NADH dehydrogenase subunit 1" 
        /protein_id="YP_637062.1" 
        /db_xref="GI:108793519" 
        /db_xref="GeneID:4117948" 
        /translation="MFIINLLMYIIPILLAIAFLTLVERKALGYMQFRKGPNVVGPYG 
        LLQPIADGMKLFSKEPLQPVTSSTTMFIIAPTLALTLSLTMWTPLPMPHSLIDLNLGL 
        LFILALSGLSVYSILWSGWASNSKYALMGALRAVAQTISYEVTLAIILLSIMLINGSF 
        TLKNLITTQENMWLIITTWPLVMMWYVSTLAETNRAPLDLTEGESELVSGFNVEYAAG 
        PFAMFFLAEYANIMLMNAMTTILFLGSSINHNFTHLNTLSFMTKTIALTFLFLWVRAS 
        YPRFRYDQLMHLLWKNFLPMTLAMCLWFISIPIALSCIPPQI" 
    misc_feature 2729..3682 
        /gene="ND1" 
        /note="NADH dehydrogenase; Region: NADHdh; cl00469" 
        /db_xref="CDD:186018" 
    tRNA   3686..3751 
        /product="tRNA-Ile" 
    tRNA   complement(3750..3821) 
        /product="tRNA-Gln" 
    tRNA   3821..3878 
        /product="tRNA-Met" 
    gene   3889..4932 
        /gene="ND2" 
        /db_xref="GeneID:4117949" 
    CDS    3889..4932 
        /gene="ND2" 
        /codon_start=1 
        /transl_table=2 
        /product="NADH dehydrogenase subunit 2" 
        /protein_id="YP_637063.1" 
        /db_xref="GI:108793520" 
        /db_xref="GeneID:4117949" 
        /translation="MSPYILLIMLTSLLLGTSLTLFSNHWLTAWMGLEINTLAIIPMM 
        TYPNHPRATESAIKYFLTQSTASMMLMFAIINNAWMTNQWTLLQTSDQTSSTIMTLAL 
        AMKLGLAPFHFWVPEVTQGIPLTSGMILLTWQKIAPTSLMYQISPSLNMKILVMLALL 
        STILGGWGGLNQTHMRKILAYSSIAHMGWMTIIILINPTLTLLNLAIYITTTLTLFLA 
        LNHSSITKIKSLANLWNKSSSMTIVIALTLLSLGGLPPLTGFMPKWLILQELITYNNI 
        ATATMMAMSALLNLFFYMRIIYTTTLTMPPSINNSKLQWPHPQTKTTNIIPLLTIISS 
        FLLPLTPLSITLS" 

seqFeatureとサブ機能を使用しましたが、機能しませんでした。私が取得する必要があり、このファイルから

私はbiopythonする新たなんだとどのようにして助けをしたいと思い

（ND1と2729..3685、ND2と3889..4932を、もっと...があった場合）これを行う。

Answer 1

投稿したgenbankファイルが完全ではない、セクションが欠落しており、//終了行がありません。パーサーはそれを読み込もうとしている。

私はPhalanger interpositusミトコンドリアの正しいファイルをhereから得ました。
その後（py3kコード）：

>>> 
>>> from Bio import SeqIO 
>>> arch = "C:/code/NC_008137.gbk" 
>>> record = SeqIO.parse(arch, "genbank") 
>>> rec = next(record)      # there is only one record 
>>> for f in rec.features: 
    if f.type == 'gene': 
     print(f.qualifiers['gene'], f.location) 


['ND1'] [2728:3685] 
['ND2'] [3888:4932] 
['COX1'] [5365:6919] 
['COX2'] [7052:7737] 
['ATP8'] [7798:8005] 
['ATP6'] [7959:8640] 
['COX3'] [8639:9423] 
['ND3'] [9488:9837] 
['ND4L'] [9906:10203] 
['ND4'] [10196:11574] 
['ND5'] [11773:13582] 
['ND6'] [13578:14082] 
['CYTB'] [14155:15301] 
>>>