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ノート/Pythonその３https://pepper.is.sci.toho-u.ac.jp:443/pepper/index.php?%A5%CE%A1%BC%A5%C8%2FPython%A4%BD%A4%CE%A3%B3 |
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ノート
前のページ
訪問者数 3804 最終更新 2007-11-23 (金) 17:10:50
そのためには、前頁のアクセス時のモードretmodeを、テキストtextではなくXML(xml)にする。
XMLモードで得られるデータの例
<?xml version="1.0"?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2007//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_070101.dtd">
<PubmedArticleSet>
<PubmedArticle>
<MedlineCitation Owner="NLM" Status="Publisher">
<PMID>1803 0674</PMID>
<DateCreated>
<Year>2007</Year>
<Month>11</Month>
<Day>21</Day>
</DateCreated>
<Article PubModel="Print-Electronic">
<Journal>
<ISSN IssnType="Electronic">1098-1004</ISSN>
<JournalIssue CitedMedium="Internet">
<PubDate>
<Year>2007</Year>
<Month>Nov</Month>
<Day>20</Day>
</PubDate>
</JournalIssue>
</Journal>
<ArticleTitle>RNA-based mutation analysis identifies an unusual MSH6 splicing defect and circumvents PMS2 pseudogene interference.</ArticleTitle>
<Pagination>
<MedlinePgn/>
</Pagination>
<Abstract>
<AbstractText>Heterozygous germline mutations in one of the mismatch repair (以下略) </AbstractText>
</Abstract>
<Affiliation>Department of Medical Genetics, Medical University Vienna, Vienna, Austria.</Affiliation>
<AuthorList>
<Author>
<LastName>Etzler</LastName>
<FirstName>J</FirstName>
<Initials>J</Initials>
</Author>
<Author>
<LastName>Peyrl</LastName>
<FirstName>A</FirstName>
<Initials>A</Initials>
</Author>
<Author>
<LastName>Zatkova</LastName>
<FirstName>A</FirstName>
<Initials>A</Initials>
</Author>
<Author>
<LastName>Schildhaus</LastName>
<FirstName>H-U</FirstName>
<Initials>HU</Initials>
</Author>
<Author>
<LastName>Ficek</LastName>
<FirstName>A</FirstName>
<Initials>A</Initials>
</Author>
<Author>
<LastName>Merkelbach-Bruse</LastName>
<FirstName>S</FirstName>
<Initials>S</Initials>
</Author>
<Author>
<LastName>Kratz</LastName>
<FirstName>C P</FirstName>
<Initials>CP</Initials>
</Author>
<Author>
<LastName>Attarbaschi</LastName>
<FirstName>A</FirstName>
<Initials>A</Initials>
</Author>
<Author>
<LastName>Hainfellner</LastName>
<FirstName>J A</FirstName>
<Initials>JA</Initials>
</Author>
<Author>
<LastName>Yao</LastName>
<FirstName>S</FirstName>
<Initials>S</Initials>
</Author>
<Author>
<LastName>Messiaen</LastName>
<FirstName>L</FirstName>
<Initials>L</Initials>
</Author>
<Author>
<LastName>Slavc</LastName>
<FirstName>I</FirstName>
<Initials>I</Initials>
</Author>
<Author>
<LastName>Wimmer</LastName>
<FirstName>K</FirstName>
<Initials>K</Initials>
</Author>
</AuthorList>
<Language>ENG</Language>
<PublicationTypeList>
<PublicationType>JOURNAL ARTICLE</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic">
<Year>2007</Year>
<Month>11</Month>
<Day>20</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo>
<MedlineTA>Hum Mutat</MedlineTA>
<NlmUniqueID>9215429</NlmUniqueID>
</MedlineJournalInfo>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="pubmed">
<Year>2007</Year>
<Month>11</Month>
<Day>22</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2007</Year>
<Month>11</Month>
<Day>22</Day>
<Hour>9</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>aheadofprint</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="doi">10.1002/humu.20657</ArticleId>
<ArticleId IdType="pubmed">18030674</ArticleId>
</ArticleIdList>
</PubmedData>
</PubmedArticle>
</PubmedArticleSet>
これを抽出するためには、パターンマッチングを今ひとつ作り直す必要がある。
まずは�．侫�ールド中に空白やマイナス、ピリオドなどを含むのでそれをも取り出すこと。テストプログラムとしては
testabstract.py
mref = re.compile('.*<PubDate>(.+)</PubDate>.*<ArticleTitle>(.+)</ArticleTitle>.*<AbstractText>(.+)</AbstractText>.*<AuthorList>(.+)</AuthorList>', re.S)
a = mref.search(efetch_result)
print a
pubdate = []
articletitle = []
abstracttext = []
authorlist = []
if a:
pubdate.append(a.group(1))
articletitle.append(a.group(2))
abstracttext.append(a.group(3))
authorlist.append(a.group(4))
else:
pubdate.append("")
articletitle.append("")
abstracttext.append("")
authorlist.append("")
print "[PubDate]" ; print pubdate[0]
print "[Title]" ; print articletitle[0]
print "[Abstract]"; print abstracttext[0]
print "[Authorlist]"; print authorlist[0]
得られた結果は
<_sre.SRE_Match object at 0x00ADE860>
[PubDate]
<Year>2007</Year>
<Month>Nov</Month>
<Day>20</Day>
[Title]
RNA-based mutation analysis （中略） PMS2 pseudogene interference.
[Abstract]
Heterozygous germline mutations （中略）Wiley-Liss, Inc.
[Authorlist]
<Author>
<LastName>Etzler</LastName>
<FirstName>J</FirstName>
<Initials>J</Initials>
</Author>
<Author>
<LastName>Peyrl</LastName>
<FirstName>A</FirstName>
<Initials>A</Initials>
</Author>
（以下略）
この仕組を、前ページのプログラムに加えると、このようなことになる。全体は
getlist_access_abstract.py
if count>3:
count = 3 # For experiments, I limit "count" up to 3 papers.
## Next, get the abstract of each article
articles = []
for i in range(int(count)):
efetch = utils + "/efetch.fcgi?rettype=" + report + "&retmode=xml&retstart=" + str(i) + \
"&retmax=" + "1" + "&db=" + db + "&query_key=" + querykey + "&WebEnv=" + webenv
f = urllib.urlopen(efetch)
efetch_result = f.read()
## print efetch_result
onearticle = []
aref = re.compile('.*<PubDate>(.+)</PubDate>.*<ArticleTitle>(.+)</ArticleTitle>' + \
'.*<AbstractText>(.+)</AbstractText>.*<AuthorList>(.+)</AuthorList>', re.S)
a = aref.search(efetch_result)
if a:
onearticle.append(a.group(1))
onearticle.append(a.group(2))
onearticle.append(a.group(3))
onearticle.append(a.group(4))
else:
onearticle.append("")
onearticle.append("")
onearticle.append("")
onearticle.append("")
articles.append(onearticle)
for i in range(int(count)):
print "--[" + str(i) + "]---------"
print articles[i][0]
print articles[i][1]
print articles[i][2]
print articles[i][3]
これの出力は、abstractout.txtのようになる。
