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@ykguitar1002000(Y K)

Biopythonのefetchを利用した際に出力される情報のまとめ

Last updated at Posted at 2022-11-17

Biopythonの持つ機能、efetchを利用することでpython経由で配列情報などを取得することができる。
詳しくは提供元のページをみるとよい。

https://biopython.org/docs/1.75/api/Bio.Entrez.html
今回はGoogle colaboratoryで実施し下さいの出力データについてまとめる。

Biopythonのインストール

以下の方法でbiopythonをインストールする。

!pip install biopython

基本操作

biopythonインストール後以下の操作で配列を取得できる。

#moduleのimport
from Bio import Entrez

#idなどは実際のidなどを記入する必要がある。
Entrez.email = xxxx@xxxxx.com
handle = Entrez.efetch(db="protein", id="GenBank_id", rettype="gb", retmode="text")

実際に大腸菌のflavin reductaseを用いて以下のコードを実行してみる。
典型的なgenebankフォーマットがダウンロードされていることがわかります。

Entrez.email = xxxx@xxxxx.com
handle = Entrez.efetch(db="protein", id="PWL87550.1", rettype="gb", retmode="text")
print(handle.read())

この操作で以下のデータが出力される。

LOCUS       PWL87550                 202 aa            linear   ENV 23-MAY-2018
DEFINITION  MAG: flavin reductase [Escherichia coli].
ACCESSION   PWL87550
VERSION     PWL87550.1
DBLINK      BioProject: PRJNA397219
            BioSample: SAMN08295014
DBSOURCE    accession QAMB01000025.1
#以下略

保存したい場合は以下のコードを追記するとよい

with open('PWL87550.1.gb','w') as f:
    f.write(handle.read())

rettypeやretmodeを変更することによって異なる情報やファイルが得られます。
詳しくはこちらのtableを参照します。

proteinデータベースにアクセスする場合

retmode="text", rettypeなし

もっとも単純な場合は以下の操作です。

Entrez.email = e_mail
handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="text")
print(handle.read())

出力結果、ASN.1形式が出力されます。
https://www.ncbi.nlm.nih.gov/Structure/asn1.html

Seq-entry ::= set {
  id id 1,
  class nuc-prot,
  descr {
    source {
      org {
        taxname "Escherichia coli",
        db {
          {
            db "taxon",
            tag id 562
          }
        },
        orgname {
          name binomial {
            genus "Escherichia",
            species "coli"
          },
          attrib "specified",
          mod {
            {
              subtype isolate,
              subname "CIM:MAG 560"
#以下略

retmode="text", rettype="gb"

以下のコードを入力した場合

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="text", rettype="gb")
print(handle.read())

gb形式で出力されます。

LOCUS       PWL87550                 202 aa            linear   ENV 23-MAY-2018
DEFINITION  MAG: flavin reductase [Escherichia coli].
ACCESSION   PWL87550
VERSION     PWL87550.1
DBLINK      BioProject: PRJNA397219
            BioSample: SAMN08295014
DBSOURCE    accession QAMB01000025.1
KEYWORDS    ENV; Metagenome Assembled Genome; MAG.
SOURCE      Escherichia coli (human gut metagenome)
#以下略

retmode="text", rettype="gp"

入力例

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="text", rettype="gp")
print(handle.read())

上と同様にgbフォーマットでダウンロードされます。出力は省略します。

retmode="xml", rettype="gp"

入力例

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="xml", rettype="gp")
print(handle.read())

出力例、以下のようにxml形式のファイルが出力されます。情報の抽出にはこちらの方が使いやすいかもしれません。

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE GBSet PUBLIC "-//NCBI//NCBI GBSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd">\n
<GBSet>\n
  <GBSeq>\n
\n
    <GBSeq_locus>PWL87550</GBSeq_locus>\n
    <GBSeq_length>202</GBSeq_length>\n
    <GBSeq_moltype>AA</GBSeq_moltype>\n
    <GBSeq_topology>linear</GBSeq_topology>\n
    <GBSeq_division>ENV</GBSeq_division>\n
    <GBSeq_update-date>23-MAY-2018</GBSeq_update-date>\n
    <GBSeq_create-date>23-MAY-2018</GBSeq_create-date>\n
    <GBSeq_definition>MAG: flavin reductase [Escherichia coli]</GBSeq_definition>\n

#以下略

retmode="xml", rettype="gpc"

入力例

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="xml", rettype="gpc")
print(handle.read())

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd">\n
<INSDSet>\n
  <INSDSeq>\n
\n
    <INSDSeq_locus>PWL87550</INSDSeq_locus>\n
    <INSDSeq_length>202</INSDSeq_length>\n
    <INSDSeq_moltype>AA</INSDSeq_moltype>\n
    <INSDSeq_topology>linear</INSDSeq_topology>\n
    <INSDSeq_division>ENV</INSDSeq_division>\n
    <INSDSeq_update-date>23-MAY-2018</INSDSeq_update-date>\n
    <INSDSeq_create-date>23-MAY-2018</INSDSeq_create-date>\n
    <INSDSeq_definition>MAG: flavin reductase [Escherichia coli]</INSDSeq_definition>\n
    <INSDSeq_primary-accession>PWL87550</INSDSeq_primary-accession>\n
    <INSDSeq_accession-version>PWL87550.1</INSDSeq_accession-version>\n

retmode="xml", rettype="ipg"

入力例

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="xml", rettype="ipg")
print(handle.read())

出力例。由来となるゲノムのidを獲得可能です。

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<IPGReportSet xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="https://www.ncbi.nlm.nih.gov/data_specs/schema/other/seq_report/IPGReportSet.xsd">\n\n
<IPGReport  ipg="188447752" product_acc="PWL87550.1">\n
<Product  accver="PWL87550.1" name="flavin reductase" taxid="562" slen="202" org="Escherichia coli" kingdom_taxid="2" kingdom="Bacteria"/>\n
<ProteinList>\n
<Protein  accver="PWL87550.1" source="INSDC" name="flavin reductase" taxid="562" org="Escherichia coli" kingdom_taxid="2" kingdom="Bacteria" priority="0">\n
<CDSList>\n
<CDS  accver="QAMB01000025.1" start="220007" stop="220615" strand="+" taxid="562" org="Escherichia coli" kingdom_taxid="2" kingdom="Bacteria" assembly="GCA_003149995.1"/></CDSList></Protein></ProteinList>\n
<Statistics  prot_count="1" nuc_count="1" assmb_count="1"/></IPGReport></IPGReportSet>\n'

retmode="text", rettype="ft"

入力例

handle = Entrez.efetch(db="protein", id='PWL87550.1', retmode="text", rettype="ft")
print(handle.read())

feature tableが出力される。

>Feature gb|PWL87550.1|
1	202	Protein
			product	flavin reductase
8	159	Region
			region	Flavin_Reduct
			note	Flavin reductase like domain
			db_xref	CDD:426345
169	202	Region
			region	rubredoxin_SM
			note	Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ...
			db_xref	CDD:238371
171	171	Site
174	174
189	189
192	192
			site_type	other
			note	iron binding site [ion binding]
			db_xref	CDD:238371
1	202	CDS
			product	flavin reductase
			transl_table	11
			protein_id	gb|PWL87550.1||gnl|WGS:QAMB|DBY14_05325
			inference	COORDINATES: similar to AA sequence:RefSeq:WP_009288844.1

retmode="text", rettype="acc"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="text", rettype="acc")
print(handle.read())

出力、IDのみ出力されます。

PWL87550.1

retmode="text", rettype="fasta"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="text", rettype="fasta")
print(handle.read())

出力例、fasta形式で出力されます。

>PWL87550.1 MAG: flavin reductase [Escherichia coli]
MSYDKNVLFNISYGLYILSANSSNADNACVINTLSQITSSPDTVSVTVNKKNFTNEMIKKTKKLNVSILS
TDADFELIKRFGFQSGRDIDKFVGFKDMYRSQNGIYFINKGANSFISVDIDEIIDFDTHNMFVGHITDTA
VLSDKESLTYSYYQNNIKPKQNENKKTGYVCTVCGYIHESDTLPDDFVCPVCKHGASAFVKL

retmode="xml"、rettype = "acc"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="xml", rettype="fasta")
print(handle.read())

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">\n<TSeqSet>\n<TSeq>\n  <TSeq_seqtype value="protein"/>\n  
<TSeq_accver>PWL87550.1</TSeq_accver>\n  
<TSeq_sid>gnl|WGS:QAMB|DBY14_05325</TSeq_sid>\n  
<TSeq_taxid>562</TSeq_taxid>\n  
<TSeq_orgname>Escherichia coli</TSeq_orgname>\n  
<TSeq_defline>MAG: flavin reductase [Escherichia coli]</TSeq_defline>\n
<TSeq_length>202</TSeq_length>\n
<TSeq_sequence>MSYDKNVLFNISYGLYILSANSSNADNACVINTLSQITSSPDTVSVTVNKKNFTNEMIKKTKKLNVSILSTDADFELIKRFGFQSGRDIDKFVGFKDMYRSQNGIYFINKGANSFISVDIDEIIDFDTHNMFVGHITDTAVLSDKESLTYSYYQNNIKPKQNENKKTGYVCTVCGYIHESDTLPDDFVCPVCKHGASAFVKL</TSeq_sequence>\n
</TSeq>\n\n
</TSeqSet>\n'

retmode="text"、rettype = "seqid"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="text", rettype="seqid")
print(handle.read())

出力例

Seq-id ::= genbank {
  accession "PWL87550" ,
  version 1 }
Seq-id ::= general {
  db "WGS:QAMB" ,
  tag
    str "DBY14_05325" }
Seq-id ::= gi 1391407525

retmode="xml", rettype="docsum"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="xml", rettype="docsum")
print(handle.read())

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">\n
<eSummaryResult>\n\n
<DocSum>\n
\t<Id>1391407525</Id>\n
\t<Item Name="Caption" Type="String">PWL87550</Item>\n
\t<Item Name="Title" Type="String">flavin reductase [Escherichia coli]</Item>\n
\t<Item Name="Extra" Type="String">gi|1391407525|gb|PWL87550.1||gnl|WGS:QAMB|DBY14_05325[1391407525]</Item>\n
\t<Item Name="Gi" Type="Integer">1391407525</Item>\n
\t<Item Name="CreateDate" Type="String">2018/05/23</Item>\n
\t<Item Name="UpdateDate" Type="String">2018/05/23</Item>\n
\t<Item Name="Flags" Type="Integer">0</Item>\n
\t<Item Name="TaxId" Type="Integer">562</Item>\n
\t<Item Name="Length" Type="Integer">202</Item>\n
\t<Item Name="Status" Type="String">live</Item>\n
\t<Item Name="ReplacedBy" Type="String"></Item>\n
\t<Item Name="Comment" Type="String"><![CDATA[  ]]></Item>\n
\t<Item Name="AccessionVersion" Type="String">PWL87550.1</Item>\n
</DocSum>\n</eSummaryResult>\n'

retmode="txt", rettype="uilist"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="txt", rettype="uilist")
print(handle.read())

出力例

1391407525

retmode="xml", rettype="uilist"

入力例

handle = Entrez.efetch(db="protein", id="PWL87550.1", retmode="xml", rettype="uilist")
print(handle.read())

出力例

b'<?xml version="1.0" ?>\n
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20020605//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20020605/uilist.dtd">\n
<IdList>\n
    <Id>1391407525</Id>\n</IdList>\n'

nucleotideデータベースにアクセスする場合

db="nuccore"とします。
入力例, rettypeを指定しない場合です。

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt")
print(handle.read())

ASN.1形式で出力されます。出力例は省略します。

retmode="txt", rettype="acc"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="acc")
print(handle.read())

出力例

NR_024570.1

retmode="txt", rettype="fasta"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="fasta")
print(handle.read())

出力例

>NR_024570.1 Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence
AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAG
CAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGA
TAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGCACAAAGAGGGGGACCTTAGGGCCTCTT
GCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAG
#以下略

retmode="xml", rettype="fasta"

入力例 ``` handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="xml", rettype="fasta") print(handle.read()) ```

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE TSeqSet PUBLIC "-//NCBI//NCBI TSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_TSeq.dtd">\n<TSeqSet>\n<TSeq>\n  
<TSeq_seqtype value="nucleotide"/>\n  
<TSeq_accver>NR_024570.1</TSeq_accver>\n  
<TSeq_taxid>562</TSeq_taxid>\n  
<TSeq_orgname>Escherichia coli</TSeq_orgname>\n  
<TSeq_defline>Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence</TSeq_defline>\n  
<TSeq_length>1450</TSeq_length>\n  
<TSeq_sequence>AGTTTGATCATGGCTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAACAGGAAGCAGCTTGCTGCTTTGCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGCACAAAGAGGGGGACCTTAGGGCCTCTTGCCATCGGATGTGCCCAGATGGGAT
#以下略

retmode="txt", rettype="seqid"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="seqid")
print(handle.read())

出力例

Seq-id ::= other {
  accession "NR_024570" ,
  version 1 }
Seq-id ::= gi 219722938

retmode="txt", rettype="gb"

入力例 ``` handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="gb") print(handle.read()) ```

出力例

LOCUS       NR_024570               1450 bp    rRNA    linear   BCT 11-MAR-2019
DEFINITION  Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence.
ACCESSION   NR_024570
VERSION     NR_024570.1
DBLINK      Project: 33175
            BioProject: PRJNA33175
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
REFERENCE   1
  AUTHORS   Cilia,V., Lafay,B. and Christen,R.
  TITLE     Sequence heterogeneities among 16S ribosomal RNA sequences, and
            their effect on phylogenetic analyses at the species level
  JOURNAL   Mol. Biol. Evol. 13 (3), 451-461 (1996)
#以下略

retmode="xml", rettype="gb"

入力例 ``` handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="xml", rettype="gb") print(handle.read()) ```

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n<!DOCTYPE GBSet PUBLIC "-//NCBI//NCBI GBSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/NCBI_GBSeq.dtd">\n<GBSet>\n  <GBSeq>\n\n    <GBSeq_locus>NR_024570</GBSeq_locus>\n    <GBSeq_length>1450</GBSeq_length>\n    <GBSeq_strandedness>single</GBSeq_strandedness>\n    <GBSeq_moltype>rRNA</GBSeq_moltype>\n    <GBSeq_topology>linear</GBSeq_topology>\n    <GBSeq_division>BCT</GBSeq_division>\n    <GBSeq_update-date>11-MAR-2019</GBSeq_update-date>\n    <GBSeq_create-date>07-JAN-2009</GBSeq_create-date>\n    <GBSeq_definition>Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence</GBSeq_definition>\n    <GBSeq_primary-accession>NR_024570</GBSeq_primary-accession>\n    <GBSeq_accession-version>NR_024570.1</GBSeq_accession-version>\n    <GBSeq_other-seqids>\n      <GBSeqid>ref|NR_024570.1|</GBSeqid>\n      <GBSeqid>gi|219722938</GBSeqid>\n    </GBSeq_other-seqids>\n    <GBSeq_project>PRJNA33175</GBSeq_project>\n    <GBSeq_keywords>\n      <GBKeyword>RefSeq</GBKeyword>\n    </GBSeq_keywords>\n    <GBSeq_source>Escherichia coli</GBSeq_source>\n    <GBSeq_organism>Escherichia coli</GBSeq_organism>\n    <GBSeq_taxonomy>Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia</GBSeq_taxonomy>\n    <GBSeq_references>\n  
#以下略

retmode="xml", rettype="gbc"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="xml", rettype="gbc")
print(handle.read())

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n<!DOCTYPE INSDSet PUBLIC "-//NCBI//INSD INSDSeq/EN" "https://www.ncbi.nlm.nih.gov/dtd/INSD_INSDSeq.dtd">\n<INSDSet>\n  <INSDSeq>\n\n    <INSDSeq_locus>NR_024570</INSDSeq_locus>\n    <INSDSeq_length>1450</INSDSeq_length>\n    <INSDSeq_strandedness>single</INSDSeq_strandedness>\n    <INSDSeq_moltype>rRNA</INSDSeq_moltype>\n    <INSDSeq_topology>linear</INSDSeq_topology>\n    <INSDSeq_division>BCT</INSDSeq_division>\n    <INSDSeq_update-date>11-MAR-2019</INSDSeq_update-date>\n    <INSDSeq_create-date>07-JAN-2009</INSDSeq_create-date>\n    <INSDSeq_definition>Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence</INSDSeq_definition>\n    <INSDSeq_primary-accession>NR_024570</INSDSeq_primary-accession>\n    <INSDSeq_accession-version>NR_024570.1</INSDSeq_accession-version>\n    <INSDSeq_other-seqids>\n      <INSDSeqid>ref|NR_024570.1|</INSDSeqid>\n      <INSDSeqid>gi|219722938</INSDSeqid>\n    </INSDSeq_other-seqids>\n    <INSDSeq_project>PRJNA33175</INSDSeq_project>\n    <INSDSeq_keywords>\n      <INSDKeyword>RefSeq</INSDKeyword>\n    </INSDSeq_keywords>\n    <INSDSeq_source>Escherichia coli</INSDSeq_source>\n    <INSDSeq_organism>Escherichia coli</INSDSeq_organism>\n  
#以下略

retmode="txt", rettype="gbwithparts"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="gbwithparts")
print(handle.read())

出力例

LOCUS       NR_024570               1450 bp    rRNA    linear   BCT 11-MAR-2019
DEFINITION  Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence.
ACCESSION   NR_024570
VERSION     NR_024570.1
DBLINK      Project: 33175
            BioProject: PRJNA33175
KEYWORDS    RefSeq.
SOURCE      Escherichia coli
  ORGANISM  Escherichia coli
            Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Escherichia.
#以下略

retmode="txt", rettype="fasta_cds_na"

入力例

handle = Entrez.efetch(db="nuccore", id='HQ828986.1', retmode="txt", rettype="fasta_cds_na")
print(handle.read())

出力例

>lcl|HQ828986.1_cds_AEM44333.1_1 [protein=putative NDP-hexose 2, 3-dehydratase] [protein_id=AEM44333.1] [location=complement(<1..1400)] [gbkey=CDS]
ATGTCACCCAAGCTCGCGGCGGCGACCGTACTGCGGCCACGGCAGGACGCGGGCCCCGCCGGCAGGATCG
CCCGCTCCGCGGCCACGGCCGAGGGCGCGCACCTGGCTCCGGGCGAGTTCCACGCGTGGTTCGCCCAGCG
GCGCGCGGCTCATTCCTTCCGCGTCGACCGCATCCCCTTCGCGGAGCTGGAGGGCTGGTCCACCCAGCGG
GACACCGGCAACCTGGTGCACCGCAGCGGGCGGTTCTTCAGCGTCGAGGGCCTGGCGGTGAGCGTGGACG
GCGGCCCGGACGGCTGGCACCAGCCCGTCATCCGCCAGCCGGAGACCGGCATTCTGGGCATCCTCGTCAA
GGAGTTCGACGGCGTCCTGCACTGCCTGATGCAGGCCAAGATG
#以下略、CDSのDNA配列のfastaが出力される。

retmode="txt", rettype="fasta_cds_aa"

入力例

handle = Entrez.efetch(db="nuccore", id='HQ828986.1', retmode="txt", rettype="fasta_cds_aa")
print(handle.read())

出力例

>lcl|HQ828986.1_prot_AEM44333.1_1 [protein=putative NDP-hexose 2, 3-dehydratase] [protein_id=AEM44333.1] [location=complement(<1..1400)] [gbkey=CDS]
MSPKLAAATVLRPRQDAGPAGRIARSAATAEGAHLAPGEFHAWFAQRRAAHSFRVDRIPFAELEGWSTQR
DTGNLVHRSGRFFSVEGLAVSVDGGPDGWHQPVIRQPETGILGILVKEFDGVLHCLMQAKMEPGNPNLLQ
LSPTVQATRSNYTKVHRGADVKYIEYFTRPERGAVLADVLQSEHGSWFLHKHNRNMIVETTGDVPPDDDF
RWLTLGQIAELLRLDNVVNMDARTVLSCVPRTAAQCEPAALHSDAELRAWLTEARARHDVHAERVPLAGL
PGWARDDSSIHHLEGRYFEVVAASVQAGSREVTSWTQPLIRPRGRGVVAFLTRRINGVPHLLAHARTEGG
#以下略、CDSのアミノ酸配列のfastaが出力される

retmode="xml", rettype="docsum"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="xml", rettype="docsum")
print(handle.read())

出力例

b'<?xml version="1.0" encoding="UTF-8"  ?>\n
<!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD esummary v1 20041029//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20041029/esummary-v1.dtd">\n
<eSummaryResult>\n
\n
<DocSum>\n
\t<Id>219722938</Id>\n
\t<Item Name="Caption" Type="String">NR_024570</Item>\n
\t<Item Name="Title" Type="String">Escherichia coli strain U 5/41 16S ribosomal RNA, partial sequence</Item>\n
\t<Item Name="Extra" Type="String">gi|219722938|ref|NR_024570.1|[219722938]</Item>\n
\t<Item Name="Gi" Type="Integer">219722938</Item>\n
\t<Item Name="CreateDate" Type="String">1996/03/29</Item>\n
\t<Item Name="UpdateDate" Type="String">2019/03/11</Item>\n
\t<Item Name="Flags" Type="Integer">512</Item>\n
\t<Item Name="TaxId" Type="Integer">562</Item>\n
\t<Item Name="Length" Type="Integer">1450</Item>\n
\t<Item Name="Status" Type="String">live</Item>\n
\t<Item Name="ReplacedBy" Type="String"></Item>\n
\t<Item Name="Comment" Type="String"><![CDATA[  ]]></Item>\n
\t<Item Name="AccessionVersion" Type="String">NR_024570.1</Item>\n
</DocSum>\n</eSummaryResult>\n'

retmode="txt", rettype="uilist"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="txt", rettype="uilist")
print(handle.read())

出力例

219722938

retmode="xml", rettype="uilist"

入力例

handle = Entrez.efetch(db="nuccore", id='NR_024570', retmode="xml", rettype="uilist")
print(handle.read())

出力例

b'<?xml version="1.0" ?>\n
<!DOCTYPE eEfetchResult PUBLIC "-//NLM//DTD efetch 20020605//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20020605/uilist.dtd">\n
<IdList>\n
    <Id>219722938</Id>\n
</IdList>\n'
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