将 Biopython 输出写入 csv

Question

我目前正在做一个 class 项目，该项目要求我使用 biopython 从 NCBI 网站提取数据并将其写入 CSV 文件，然后我在 R 中对其进行分析。我得到了我需要的所有数据, 但我不完全确定如何将其写入 CSV 文件，因为我们从未在 class 中介绍过它。到目前为止，这是我的代码：

from Bio import Entrez, Medline

Entrez.email = "email.here"

handle = Entrez.esearch(db="pubmed",  # database to search
                        term="Chan CS[Author] AND 2000:2017[Date - Publication]",  # search term
                        retmax=200 # Maximum number of results to return
                        )
record = Entrez.read(handle)
handle.close()

pmid_list = record["IdList"]
print(pmid_list)

其次是

from Bio import Medline
handle = Entrez.efetch(db="pubmed", id=pmid_list, rettype="medline", retmode="text")
records = Medline.parse(handle)

journal_dict = []
datep_dict = []
place_dict = []
for record in records:

    # retrieve journal titles 
    title = record['JT']
    journal_dict.append(title)

    #retrieve date published
    date = record['DP']
    datep_dict.append(date)

    #retrieve place published
    place = record['PL']
    place_dict.append(place)
# Close the efetch handle    
handle.close()

for title in journal_dict:
    print(title)
for date in datep_dict:
    print(date)
for place in place_dict:
    print(place)

最后，我卡住的部分

import csv

我正在尝试让 csv 文件看起来像下面这样

[ID, Journal Title, Publication Date, Place of Publication]
[123, Title1, Date1, Place1]
[124, Title2, Date2, Place2]

如有任何帮助，我们将不胜感激！

Answer 1

在你的第二个代码块中，你的变量名谈论 dictionaries，但你的它们实际上是 lists:

journal_dict = []
datep_dict = []
place_dict = []

所以，让我们解决这个问题（这在以后写入 CSV 时也会很有用）：

record_list = []
for record in records:
    record_dict = {'ID': record['ID'],
                   'Journal Title': record['JT'],
                   'Publication Date': record['DP']
                   'Place of Publication': record['PL']}
    record_list.append(record_dict)

现在让我们将这个字典列表写入 CSV 文件

import csv

with open('medline.csv', 'w', newline='') as csvfile:
    fieldnames = ['ID', 'Journal Title', 'Publication Date', 'Place of Publication']
    writer = csv.DictWriter(csvfile, fieldnames=fieldnames)

    writer.writeheader()
    for record_dict in record_list:
        writer.writerow(record_dict)

将 Biopython 输出写入 csv

Writing Biopython output into csv

python

csv

bioinformatics

biopython