gbff 文件解析 更新VirusDB数据库

数据来源：https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/

codebook：Dealing with GenBank files in Biopython

gbff 文件解析

gbff是genbank格式的一种变体
使用Biopython中的Bio.SeqIO模块进行解析

from Bio import SeqIO
from tqdm import tqdm
# 读取genbank文件
gb_file = "viral.all.genomic.gbff"

gb_ls = []
for gb_record in tqdm(SeqIO.parse(open(gb_file,'r'),'genbank')):
    gb_ls.append(gb_record)
import pandas as pd
df_genbank = pd.DataFrame(columns=['seq_num',
                                   'access',
                                   'genpart',
                                   'organ',
                                   'source',
                                   'tax',
                                   'topo',
                                   'order','family','subfamily','genus',
                                   'Baltimore class',
                                   'Definition',
                                   'Sequence_Length'])

for i,gb_record in tqdm(enumerate(gb_ls)):
    _accessions =   gb_record.annotations['accessions']
    _genpart    =   gb_record.annotations['molecule_type']
    _organism   =   gb_record.annotations['organism']
    _source     =   gb_record.annotations['source']
    _taxonomy   =   gb_record.annotations['taxonomy']
    _topology   =   gb_record.annotations['topology']
    _order      =   []
    _family     =   []
    _subfamily  =   []
    _genus      =   []
    _Baltimore  =   []
    _definition =   gb_record.description
    _seqlen     =   len(gb_record.seq)

# 加tax分类学信息
    for j in _taxonomy:
        if 'virales' in j:
            _order = j
        if 'viridae' in j:
            _family = j
        if 'virinae' in j:
            _subfamily = j
        if 'virus' in j:
            _genus = j

# Baltimore 分类，似乎缺少信息，
    baltimore_mapping = {
        'DNA'   :   'I',
        'ss-DNA':   'II',
        'ds-RNA':   'III',
        '':   'IV',
        '':   'V',
        '':   'VI',
        '':   'VII'
    }


    _ = [i+1,
         _accessions,
         _genpart,
         _organism,
         _source,
         _taxonomy,
         _topology,
         _order,_family,_subfamily,_genus,
         _Baltimore,
         _definition,
         _seqlen]
    df_genbank.loc[i] = _

df_genbank

example in viral.all.genomic.gbff

LOCUS       NC_001798             154675 bp    DNA     linear   VRL 16-MAY-2016
DEFINITION  Human herpesvirus 2 strain HG52, complete genome.
ACCESSION   NC_001798
VERSION     NC_001798.2
DBLINK      BioProject: PRJNA15218
KEYWORDS    RefSeq.
SOURCE      Human alphaherpesvirus 2 (Herpes simplex virus 2)
  ORGANISM  Human alphaherpesvirus 2
            Viruses; Duplodnaviria; Heunggongvirae; Peploviricota;
            Herviviricetes; Herpesvirales; Herpesviridae; Alphaherpesvirinae;
            Simplexvirus.
REFERENCE   1  (bases 1 to 154675)
  AUTHORS   Davison,A.J.
  TITLE     Evolution of sexually-transmitted and -transmissible human
            herpesviruses
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 154675)
  CONSRTM   NCBI Genome Project
  TITLE     Direct Submission
  JOURNAL   Submitted (12-MAY-2015) National Center for Biotechnology
            Information, NIH, Bethesda, MD 20894, USA
REFERENCE   3  (bases 1 to 154675)
  AUTHORS   Holton,M. and Davison,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (01-NOV-2013) MRC - University of Glasgow Centre for
            Virus Research, 8 Church Street, Glasgow G11 5JR, UK
  REMARK    Sequence update by submitter
REFERENCE   4  (bases 1 to 154675)
  AUTHORS   Davison,A.J.
  TITLE     Direct Submission
  JOURNAL   Submitted (05-AUG-2011) MRC - University of Glasgow Centre for
            Virus Research, 8 Church Street, Glasgow G11 5JR, UK
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence is identical to JN561323.
            On May 12, 2015 this sequence version replaced NC_001798.1.
            The original gene nomenclature has been retained. Genes presumably
            inherited from the common ancestor of alpha-, beta- and
            gammaherpesviruses (core genes) and non-core genes presumably
            inherited from the ancestor of alphaherpesviruses (alpha genes) are
            indicated. Initiation codons are assigned with as much confidence
            as is possible for each protein-coding region. A standard protein
            nomenclature has been applied so that orthologs have the same name
            in all herpesviruses.
            
            ##Assembly-Data-START##
            Assembly Method       :: Maq v. 0.7.1, BWA v. 0.6.2-r126
            Sequencing Technology :: Illumina
            ##Assembly-Data-END##
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..154675
                     /organism="Human alphaherpesvirus 2"
                     /mol_type="genomic DNA"
                     /strain="HG52"
                     /isolation_source="herpetic ulcer near a woman's anus"
                     /host="Homo sapiens"
                     /db_xref="taxon:10310"
                     /country="United Kingdom"
                     /collected_by="J.F. Peutherer or C.A.C. Ross"
                     /acronym="HHV-2"
                     /acronym="HSV-2"
                     /note="collected prior to 1971; originally called strain
                     HSG 52; genes UL41 and US8 are frameshifted in majority
                     and minority populations, respectively; original sequence
                     (INSD accession Z86099) determined by Sanger sequencing of
                     plasmids amended by Illumina sequencing of both viral DNA
                     and polyA RNA harvested at 10 h after infection"
     repeat_region   1..9300
                     /note="TRL; inverted repeat flanking UL"
                     /rpt_type=inverted
     gene            complement(<1..7814)
                     /gene="LAT"
                     /locus_tag="HHV2s01"
                     /db_xref="GeneID:24271495"
     ncRNA           complement(join(<1..4838,7065..7767))
                     /ncRNA_class="other"
                     /gene="LAT"
                     /locus_tag="HHV2s01"
                     /product="LAT"
                     /db_xref="GeneID:24271495"
     repeat_region   1..254
                     /note="'a' sequence"
                     /rpt_type=direct
                     /rpt_type=inverted
                     /rpt_type=terminal
     variation       11
                     /gene="LAT"
                     /locus_tag="HHV2s01"
                     /replace="c"
     gene            440..1743
                     /gene="RL1"
                     /locus_tag="HHV2p77"
                     /db_xref="GeneID:1487286"
     CDS             join(440..934,1089..1379)
                     /gene="RL1"
                     /locus_tag="HHV2p77"
                     /note="virion protein; inhibits stress-induced
                     translational arrest; related to eIF2 phosphatase
                     regulatory subunit GADD34; binds protein phosphatase 1 to
                     form a holoenzyme capable of dephosphorylating eIF2-alpha;
                     involved in translational regulation"
                     /codon_start=1
                     /product="neurovirulence protein ICP34.5"
                     /protein_id="YP_009137150.1"
                     /db_xref="GeneID:1487286"
                     /translation="MSRRRGPRRRGPRRRPRPGAPAVPRPGAPAVPRPGALPTADSQM
                     VPAYDSGTAVESAPAASSLLRRWLLVPQADDSDDADYAGNDDAEWANSPPSEGGGKAP
                     EAPHAAPAAACPPPPPRKERGPQRPLPPHLALRLRTTTEYLARLSLRRRRPPASPPAD
                     APRGKVCFSPRVQVRHLVAWETAARLARRGSWARERADRDRFRRRVAAAEAVIGPCLE
                     PEARARARARARAHEDGGPAEEEEAAAAARGSSAAAGPGRRAV"

Baltimore病毒分类 wiki