BCBio的GFF解析器不正确的解析

Question

我正在试验BCBio的GFF解析器，希望我可以将它用于我的工具。我从NCBI的RefSeq数据库中获取了一个测试.gbk文件，并用它来解析.gff文件。

代码我使用（从http://biopython.org/wiki/GFF_Parsing）：

#!/usr/bin/python 
from BCBio import GFF 
from Bio import SeqIO 

def convert_to_GFF3(): 
    in_file = "/var/www/localhost/NC_009925.gbk" 
    out_file = "/var/www/localhost/output/your_file.gff" 
    in_handle = open(in_file) 
    out_handle = open(out_file, "w") 

    GFF.write(SeqIO.parse(in_handle, "genbank"), out_handle) 

    in_handle.close() 
    out_handle.close() 

convert_to_GFF3() 

这里是结果的一部分：

##gff-version 3 
##sequence-region NC_009925.1 1 6503724 
NC_009925.1 annotation remark 1 6503724 . . . accessions=NC_009925;comment=PROVISIONAL REFSEQ: This record has not yet been subject to final%0ANCBI review. The reference sequence was derived from CP000828.%0ASource bacteria from Marine Biotechnology Institute Culture%0ACollection%2C Marine Biotechnology Institute%2C 3-75-1 Heita%2C Kamaishi%2C%0AIwate 026-0001%2C Japan.%0ACOMPLETENESS: full length.;data_file_division=CON;date=10-JUN-2013;gi=158333233;keywords=;organism=Acaryochloris marina MBIC11017;references=location: %5B0:6503724%5D%0Aauthors: Swingley%2CW.D.%2C Chen%2CM.%2C Cheung%2CP.C.%2C Conrad%2CA.L.%2C Dejesa%2CL.C.%2C Hao%2CJ.%2C Honchak%2CB.M.%2C Karbach%2CL.E.%2C Kurdoglu%2CA.%2C Lahiri%2CS.%2C Mastrian%2CS.D.%2C Miyashita%2CH.%2C Page%2CL.%2C Ramakrishna%2CP.%2C Satoh%2CS.%2C Sattley%2CW.M.%2C Shimada%2CY.%2C Taylor%2CH.L.%2C Tomo%2CT.%2C Tsuchiya%2CT.%2C Wang%2CZ.T.%2C Raymond%2CJ.%2C Mimuro%2CM.%2C Blankenship%2CR.E. and Touchman%2CJ.W.%0Atitle: Niche adaptation and genome expansion in the chlorophyll d-producing cyanobacterium Acaryochloris marina%0Ajournal: Proc. Natl. Acad. Sci. U.S.A. 105 %286%29%2C 2005-2010 %282008%29%0Amedline id: %0Apubmed id: 18252824%0Acomment:,location: %5B0:6503724%5D%0Aauthors: %0Aconsrtm: NCBI Genome Project%0Atitle: Direct Submission%0Ajournal: Submitted %2817-OCT-2007%29 National Center for Biotechnology Information%2C NIH%2C Bethesda%2C MD 20894%2C USA%0Amedline id: %0Apubmed id: %0Acomment:,location: %5B0:6503724%5D%0Aauthors: Touchman%2CJ.W.%0Atitle: Direct Submission%0Ajournal: Submitted %2827-AUG-2007%29 Pharmaceutical Genomics Division%2C Translational Genomics Research Institute%2C 13208 E Shea Blvd%2C Scottsdale%2C AZ 85004%2C USA%0Amedline id: %0Apubmed id: %0Acomment:;sequence_version=1;source=Acaryochloris marina MBIC11017;taxonomy=Bacteria,Cyanobacteria,Oscillatoriophycideae,Chroococcales,Acaryochloris 
NC_009925.1 feature source 1 6503724 . + . db_xref=taxon:329726;mol_type=genomic DNA;note=type strain of Acaryochloris marina;organism=Acaryochloris marina MBIC11017;strain=MBIC11017 
NC_009925.1 feature gene 931 1581 . - . db_xref=GeneID:5685235;locus_tag=AM1_0001;note=conserved hypothetical protein;pseudo= 
NC_009925.1 feature gene 1627 2319 . - . db_xref=GeneID:5678840;locus_tag=AM1_0003 

问题就出在第三和第四行：它需要完整的包头信息从.gbk中放入并作为一行，而应该跳过它。最后两行是正确的（输出文件的其余部分也是如此）。我试过使用几个不同的.gbk文件，都产生相同的结果。

仅供参考，这里的.gbk文件的开头：

LOCUS  NC_009925   6503724 bp DNA  circular CON 10-JUN-2013 
DEFINITION Acaryochloris marina MBIC11017 chromosome, complete genome. 
ACCESSION NC_009925 
VERSION  NC_009925.1 GI:158333233 
DBLINK  Project: 58167 
      BioProject: PRJNA58167 
KEYWORDS . 
SOURCE  Acaryochloris marina MBIC11017 
    ORGANISM Acaryochloris marina MBIC11017 
      Bacteria; Cyanobacteria; Oscillatoriophycideae; Chroococcales; 
      Acaryochloris. 
REFERENCE 1 (bases 1 to 6503724) 
    AUTHORS Swingley,W.D., Chen,M., Cheung,P.C., Conrad,A.L., Dejesa,L.C., 
      Hao,J., Honchak,B.M., Karbach,L.E., Kurdoglu,A., Lahiri,S., 
      Mastrian,S.D., Miyashita,H., Page,L., Ramakrishna,P., Satoh,S., 
      Sattley,W.M., Shimada,Y., Taylor,H.L., Tomo,T., Tsuchiya,T., 
      Wang,Z.T., Raymond,J., Mimuro,M., Blankenship,R.E. and 
      Touchman,J.W. 
    TITLE  Niche adaptation and genome expansion in the chlorophyll 
      d-producing cyanobacterium Acaryochloris marina 
    JOURNAL Proc. Natl. Acad. Sci. U.S.A. 105 (6), 2005-2010 (2008) 
    PUBMED 18252824 
REFERENCE 2 (bases 1 to 6503724) 
    CONSRTM NCBI Genome Project 
    TITLE  Direct Submission 
    JOURNAL Submitted (17-OCT-2007) National Center for Biotechnology 
      Information, NIH, Bethesda, MD 20894, USA 
REFERENCE 3 (bases 1 to 6503724) 
    AUTHORS Touchman,J.W. 
    TITLE  Direct Submission 
    JOURNAL Submitted (27-AUG-2007) Pharmaceutical Genomics Division, 
      Translational Genomics Research Institute, 13208 E Shea Blvd, 
      Scottsdale, AZ 85004, USA 
COMMENT  PROVISIONAL REFSEQ: This record has not yet been subject to final 
      NCBI review. The reference sequence was derived from CP000828. 
      Source bacteria from Marine Biotechnology Institute Culture 
      Collection, Marine Biotechnology Institute, 3-75-1 Heita, Kamaishi, 
      Iwate 026-0001, Japan. 
      COMPLETENESS: full length. 
FEATURES    Location/Qualifiers 
    source   1..6503724 
        /organism="Acaryochloris marina MBIC11017" 
        /mol_type="genomic DNA" 
        /strain="MBIC11017" 
        /db_xref="taxon:329726" 
        /note="type strain of Acaryochloris marina" 
    gene   complement(931..1581) 
        /locus_tag="AM1_0001" 
        /note="conserved hypothetical protein" 
        /pseudo 
        /db_xref="GeneID:5685235" 
    gene   complement(1627..2319) 
        /locus_tag="AM1_0003" 
        /db_xref="GeneID:5678840" 
    CDS    complement(1627..2319) 
        /locus_tag="AM1_0003" 
        /codon_start=1 
        /transl_table=11 
        /product="NUDIX hydrolase" 
         /protein_id="YP_001514406.1" 
        /db_xref="GI:158333234" 
        /db_xref="GeneID:5678840" 
        /translation="MPYTYDYPRPGLTVDCVVFGLDEQIDLKVLLIQRQIPPFQHQWA 
       LPGGFVQMDESLEDAARRELREETGVQGIFLEQLYTFGDLGRDPRDRIISVAYYALIN 
       LIEYPLQASTDAEDAAWYSIENLPSLAFDHAQILKQAIRRLQGKVRYEPIGFELLPQK 
       FTLTQIQQLYETVLGHPLDKRNFRKKLLKMDLLIPLDEQQTGVAHRAARLYQFDQSKY 
       ELLKQQGFNFEV" 

有谁知道我怎么能解决这个问题？

我用下面的行过滤掉前两错行：

if "\tannotation\t" in line or "feature\tsource" in line: 

这似乎在几个测试.gbk的工作。但我仍然好奇为什么它首先解析那些人？

Answer 1

答案在您链接的wiki页面（http://biopython.org/wiki/GFF_Parsing#Writing_GFF3）。 “GFF3Writer接收SeqRecord对象的迭代器，并将每个SeqFeature写入GFF3行”。从.gbk文件解析的SeqRecord对象包含此注释，因此它由作者编写。在实施（https://github.com/chapmanb/bcbb/blob/master/gff/BCBio/GFF/GFFOutput.py），你可以看到它完成：

self._write_annotations(rec.annotations, rec.id, len(rec.seq), out_handle) 

在那里，你也可以看到为什么source功能传递。这只是其他功能（基因，CDS）而没有单独处理。

我不知道为什么没有选项或参数（至少我没有找到任何）告诉作者跳过注释。我不知道有任何参数可以在SeqRecords和SeqIO.parse()之间跳过注释。

为了解决您的问题，我单独访问解析的SeqRecords，删除注释和源功能。这种方法的一个缺点是需要额外的内存（以及性能损失），因为我从初始生成器创建了一个List。最后，我只是将列表解析为GFF。我不知道这种方法比你的好多了。

#!/usr/bin/env python 
from BCBio import GFF 
from Bio import SeqIO 

def convert_to_GFF3(): 
    in_file = "input.gbk" 
    out_file = "output.gff" 
    in_handle = open(in_file) 
    out_handle = open(out_file, "w") 

    records = [] 
    for record in SeqIO.parse(in_handle, "genbank"): 
     # delete annotations 
     record.annotations = {} 
     # loop through features to find the source 
     for i in range(0,len(record.features)): 
      # if found, delete it and stop (only expect one source) 
      if(record.features[i].type == "source"): 
       record.features.pop(i) 
       break 
     records.append(record) 

    GFF.write(records, out_handle) 

    in_handle.close() 
    out_handle.close() 

convert_to_GFF3()