EMBL格式 (`skbio.io.format.embl` ）¶

EMBL格式将序列及其注释存储在一起。注释部分的开头用一行以单词“ID”开头。序列的开始部分用一个以单词“SQ”开头的行来标记。“//”（终止符）行也不包含数据或注释，并指定条目的结尾。有关EMBL文件格式的更多信息，请访问此处 [1].

EMBL文件可能以.EMBL或.txt扩展名结尾。这里可以看到EMBL文件的一个示例 [2].

功能级别产品¶

如上所述 [3] "Feature-level products contain nucleotide sequence and related annotations derived from submitted ENA assembled and annotated sequences. Data are distributed in flatfile format, similar to that of parent ENA records, with each flatfile representing a single feature" . 虽然这些条目中只包含要素的序列，但是要素是从父条目派生的，不能作为区间元数据应用。由于这个原因，区间元数据从特性级产品中被忽略，因为它们将被一个泛型序列对象的子集所忽略。

格式支持¶

有嗅探员：是的

注意：目前没有蛋白质支持

1499期追踪了目前蛋白质支持的发展 [4]

读者	writer	对象类
是的	是的	`skbio.sequence.Sequence`
是的	是的	`skbio.sequence.DNA`
是的	是的	`skbio.sequence.RNA`
不	不	`skbio.sequence.Protein`
是的	是的	发电机 `skbio.sequence.Sequence` 物体

格式规范¶

State: Experimental as of 0.5.1

前面的节 `FH (Feature Header)`¶

之前的所有章节 FH (Feature Header) 将被读入 metadata . 节的头及其内容作为键值对存储在中 metadata . 对于 RN (Reference Number) 节，其值以列表形式存储，因为在一个EMBL记录中通常有多个引用节。

`FT` 部分¶

见 Genbank FEATURES section

`SQ` 部分¶

中的序列 SQ 对于从ENA下载的EMBL文件，节始终是小写的。对于RNA分子， t （胸腺嘧啶），而不是 u （尿嘧啶）用于序列中。所有EMBL编写器在编写EMBL文件时都遵循这些约定。

示例

读取EMBL文件¶

假设我们有以下EMBL文件示例：

>>> embl_str = '''
... ID   X56734; SV 1; linear; mRNA; STD; PLN; 1859 BP.
... XX
... AC   X56734; S46826;
... XX
... DT   12-SEP-1991 (Rel. 29, Created)
... DT   25-NOV-2005 (Rel. 85, Last updated, Version 11)
... XX
... DE   Trifolium repens mRNA for non-cyanogenic beta-glucosidase
... XX
... KW   beta-glucosidase.
... XX
... OS   Trifolium repens (white clover)
... OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
... OC   Spermatophyta; Magnoliophyta; eudicotyledons; Gunneridae;
... OC   Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae;
... OC   Trifolieae; Trifolium.
... XX
... RN   [5]
... RP   1-1859
... RX   DOI; 10.1007/BF00039495.
... RX   PUBMED; 1907511.
... RA   Oxtoby E., Dunn M.A., Pancoro A., Hughes M.A.;
... RT   "Nucleotide and derived amino acid sequence of the cyanogenic
... RT   beta-glucosidase (linamarase) from white clover
... RT   (Trifolium repens L.)";
... RL   Plant Mol. Biol. 17(2):209-219(1991).
... XX
... RN   [6]
... RP   1-1859
... RA   Hughes M.A.;
... RT   ;
... RL   Submitted (19-NOV-1990) to the INSDC.
... RL   Hughes M.A., University of Newcastle Upon Tyne, Medical School,
... RL   Newcastle
... RL   Upon Tyne, NE2 4HH, UK
... XX
... DR   MD5; 1e51ca3a5450c43524b9185c236cc5cc.
... XX
... FH   Key             Location/Qualifiers
... FH
... FT   source          1..1859
... FT                   /organism="Trifolium repens"
... FT                   /mol_type="mRNA"
... FT                   /clone_lib="lambda gt10"
... FT                   /clone="TRE361"
... FT                   /tissue_type="leaves"
... FT                   /db_xref="taxon:3899"
... FT   mRNA            1..1859
... FT                   /experiment="experimental evidence, no additional
... FT                   details recorded"
... FT   CDS             14..1495
... FT                   /product="beta-glucosidase"
... FT                   /EC_number="3.2.1.21"
... FT                   /note="non-cyanogenic"
... FT                   /db_xref="GOA:P26204"
... FT                   /db_xref="InterPro:IPR001360"
... FT                   /db_xref="InterPro:IPR013781"
... FT                   /db_xref="InterPro:IPR017853"
... FT                   /db_xref="InterPro:IPR033132"
... FT                   /db_xref="UniProtKB/Swiss-Prot:P26204"
... FT                   /protein_id="CAA40058.1"
... FT                   /translation="MDFIVAIFALFVISSFTITSTNAVEASTLLDIGNLSRS
... FT                   SFPRGFIFGAGSSAYQFEGAVNEGGRGPSIWDTFTHKYPEKIRDGSNADITV
... FT                   DQYHRYKEDVGIMKDQNMDSYRFSISWPRILPKGKLSGGINHEGIKYYNNLI
... FT                   NELLANGIQPFVTLFHWDLPQVLEDEYGGFLNSGVINDFRDYTDLCFKEFGD
... FT                   RVRYWSTLNEPWVFSNSGYALGTNAPGRCSASNVAKPGDSGTGPYIVTHNQI
... FT                   LAHAEAVHVYKTKYQAYQKGKIGITLVSNWLMPLDDNSIPDIKAAERSLDFQ
... FT                   FGLFMEQLTTGDYSKSMRRIVKNRLPKFSKFESSLVNGSFDFIGINYYSSSY
... FT                   ISNAPSHGNAKPSYSTNPMTNISFEKHGIPLGPRAASIWIYVYPYMFIQEDF
... FT                   EIFCYILKINITILQFSITENGMNEFNDATLPVEEALLNTYRIDYYYRHLYY
... FT                   IRSAIRAGSNVKGFYAWSFLDCNEWFAGFTVRFGLNFVD"
... XX
... SQ   Sequence 1859 BP; 609 A; 314 C; 355 G; 581 T; 0 other;
...      aaacaaacca aatatggatt ttattgtagc catatttgct ctgtttgtta ttagctcatt
...      cacaattact tccacaaatg cagttgaagc ttctactctt cttgacatag gtaacctgag
...      tcggagcagt tttcctcgtg gcttcatctt tggtgctgga tcttcagcat accaatttga
...      aggtgcagta aacgaaggcg gtagaggacc aagtatttgg gataccttca cccataaata
...      tccagaaaaa ataagggatg gaagcaatgc agacatcacg gttgaccaat atcaccgcta
...      caaggaagat gttgggatta tgaaggatca aaatatggat tcgtatagat tctcaatctc
...      ttggccaaga atactcccaa agggaaagtt gagcggaggc ataaatcacg aaggaatcaa
...      atattacaac aaccttatca acgaactatt ggctaacggt atacaaccat ttgtaactct
...      ttttcattgg gatcttcccc aagtcttaga agatgagtat ggtggtttct taaactccgg
...      tgtaataaat gattttcgag actatacgga tctttgcttc aaggaatttg gagatagagt
...      gaggtattgg agtactctaa atgagccatg ggtgtttagc aattctggat atgcactagg
...      aacaaatgca ccaggtcgat gttcggcctc caacgtggcc aagcctggtg attctggaac
...      aggaccttat atagttacac acaatcaaat tcttgctcat gcagaagctg tacatgtgta
...      taagactaaa taccaggcat atcaaaaggg aaagataggc ataacgttgg tatctaactg
...      gttaatgcca cttgatgata atagcatacc agatataaag gctgccgaga gatcacttga
...      cttccaattt ggattgttta tggaacaatt aacaacagga gattattcta agagcatgcg
...      gcgtatagtt aaaaaccgat tacctaagtt ctcaaaattc gaatcaagcc tagtgaatgg
...      ttcatttgat tttattggta taaactatta ctcttctagt tatattagca atgccccttc
...      acatggcaat gccaaaccca gttactcaac aaatcctatg accaatattt catttgaaaa
...      acatgggata cccttaggtc caagggctgc ttcaatttgg atatatgttt atccatatat
...      gtttatccaa gaggacttcg agatcttttg ttacatatta aaaataaata taacaatcct
...      gcaattttca atcactgaaa atggtatgaa tgaattcaac gatgcaacac ttccagtaga
...      agaagctctt ttgaatactt acagaattga ttactattac cgtcacttat actacattcg
...      ttctgcaatc agggctggct caaatgtgaa gggtttttac gcatggtcat ttttggactg
...      taatgaatgg tttgcaggct ttactgttcg ttttggatta aactttgtag attagaaaga
...      tggattaaaa aggtacccta agctttctgc ccaatggtac aagaactttc tcaaaagaaa
...      ctagctagta ttattaaaag aactttgtag tagattacag tacatcgttt gaagttgagt
...      tggtgcacct aattaaataa aagaggttac tcttaacata tttttaggcc attcgttgtg
...      aagttgttag gctgttattt ctattatact atgttgtagt aataagtgca ttgttgtacc
...      agaagctatg atcataacta taggttgatc cttcatgtat cagtttgatg ttgagaatac
...      tttgaattaa aagtcttttt ttattttttt aaaaaaaaaa aaaaaaaaaa aaaaaaaaa
... //
... '''

现在我们可以把它理解为 DNA 对象：

>>> import io
>>> from skbio import DNA, RNA, Sequence
>>> embl = io.StringIO(embl_str)
>>> dna_seq = DNA.read(embl)
>>> dna_seq
DNA
----------------------------------------------------------------------
Metadata:
    'ACCESSION': 'X56734; S46826;'
    'CROSS_REFERENCE': <class 'list'>
    'DATE': <class 'list'>
    'DBSOURCE': 'MD5; 1e51ca3a5450c43524b9185c236cc5cc.'
    'DEFINITION': 'Trifolium repens mRNA for non-cyanogenic beta-
                   glucosidase'
    'KEYWORDS': 'beta-glucosidase.'
    'LOCUS': <class 'dict'>
    'REFERENCE': <class 'list'>
    'SOURCE': <class 'dict'>
    'VERSION': 'X56734.1'
Interval metadata:
    3 interval features
Stats:
    length: 1859
    has gaps: False
    has degenerates: False
    has definites: True
    GC-content: 35.99%
----------------------------------------------------------------------
0    AAACAAACCA AATATGGATT TTATTGTAGC CATATTTGCT CTGTTTGTTA TTAGCTCATT
60   CACAATTACT TCCACAAATG CAGTTGAAGC TTCTACTCTT CTTGACATAG GTAACCTGAG
...
1740 AGAAGCTATG ATCATAACTA TAGGTTGATC CTTCATGTAT CAGTTTGATG TTGAGAATAC
1800 TTTGAATTAA AAGTCTTTTT TTATTTTTTT AAAAAAAAAA AAAAAAAAAA AAAAAAAAA

既然这是一个mRNA分子，我们可能想把它解读为 RNA . 就像EMBL文件通常有 t 而不是 u 在序列中，我们可以把它理解为 RNA 通过转换 t 到 u ：

>>> embl = io.StringIO(embl_str)
>>> rna_seq = RNA.read(embl)
>>> rna_seq
RNA
----------------------------------------------------------------------
Metadata:
    'ACCESSION': 'X56734; S46826;'
    'CROSS_REFERENCE': <class 'list'>
    'DATE': <class 'list'>
    'DBSOURCE': 'MD5; 1e51ca3a5450c43524b9185c236cc5cc.'
    'DEFINITION': 'Trifolium repens mRNA for non-cyanogenic beta-
                   glucosidase'
    'KEYWORDS': 'beta-glucosidase.'
    'LOCUS': <class 'dict'>
    'REFERENCE': <class 'list'>
    'SOURCE': <class 'dict'>
    'VERSION': 'X56734.1'
Interval metadata:
    3 interval features
Stats:
    length: 1859
    has gaps: False
    has degenerates: False
    has definites: True
    GC-content: 35.99%
----------------------------------------------------------------------
0    AAACAAACCA AAUAUGGAUU UUAUUGUAGC CAUAUUUGCU CUGUUUGUUA UUAGCUCAUU
60   CACAAUUACU UCCACAAAUG CAGUUGAAGC UUCUACUCUU CUUGACAUAG GUAACCUGAG
...
1740 AGAAGCUAUG AUCAUAACUA UAGGUUGAUC CUUCAUGUAU CAGUUUGAUG UUGAGAAUAC
1800 UUUGAAUUAA AAGUCUUUUU UUAUUUUUUU AAAAAAAAAA AAAAAAAAAA AAAAAAAAA

我们也可以 trascribe 一个序列，并验证它将是一个 RNA 序列

>>> rna_seq == dna_seq.transcribe()
True

使用生成器读取EMBL文件¶

我们有一个包含多个记录的EMBL文件：我们可以实例化一个生成器对象来处理多个记录

>>> import skbio
>>> embl = io.StringIO(embl_str)
>>> embl_gen = skbio.io.read(embl, format="embl")
>>> dna_seq = next(embl_gen)

有关详细信息，请参阅 skbio.io

引用