BCBio的GFF解析器解析错误

Question

我正在试验BCBio的GFF解析器，希望我能将它用于我的工具。我从NCBI的RefSeq数据库中获取了一个测试.gbk文件，并使用它将其解析为.gff文件。

我使用的代码(来自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()

以下是结果的一部分：

##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

问题出在第三行和第四行:它从.gbk获取完整的标题信息，并将其作为一行放入，而它应该跳过它。最后两行是正确的(输出文件的其余部分也是如此)。我尝试使用了几种不同的.gbk文件，结果都是一样的。

作为参考，这里是.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"

有人知道我怎么解决这个问题吗？

我使用下面这行代码过滤掉了前两行错误的代码：

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

这似乎可以在几个测试.gbk上工作，但我仍然很好奇，为什么它一开始就解析那些？

Answer 1

答案就在你链接的维基页面(http://biopython.org/wiki/GFF_Parsing#Writing_GFF3)。“GFF3Writer接受SeqRecord对象的迭代器，并将每个SeqFeature写成一个GFF3行”。从.gbk文件解析的SeqRecord对象包含这个注释，因此它是由编写器编写的。在实现(https://github.com/chapmanb/bcbb/blob/master/gff/BCBio/GFF/GFFOutput.py)中，您可以看到它是在哪里完成的：

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

在这里，您还可以看到传递source特性的原因。这只是一个特征，与其他特征(基因、CDS)一样，不能单独处理。

我不知道为什么没有选项或参数(至少我还没有找到)来告诉作者跳过注释。在使用SeqIO.parse()读取SeqRecords时，我也不知道有什么参数可以跳过注释。

为了解决您的问题，我将单独访问已解析的SeqRecords，删除注释和源特征。这种方法的一个缺点是需要额外的内存(以及性能损失)，因为我是从初始生成器创建一个列表。最后，我只是将列表解析为GFF。我不知道这种方法是否比你的好很多。

#!/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()