Question

我是python的新手，正在从文件构建字典，然后迭代字典。我一直在eclipse工作，并没有得到任何输出，甚至没有任何警告。

输入看起来像这样（实际输入明显更大）

[Term]
id: GO:0000010
name: trans-hexaprenyltranstransferase activity
namespace: molecular_function
def: "Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate." [KEGG:R05612, RHEA:20839]
subset: gosubset_prok
xref: KEGG:R05612
xref: RHEA:20839
is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

[Term]
id: GO:0000011
name: vacuole inheritance
namespace: biological_process
def: "The distribution of vacuoles into daughter cells after mitosis or meiosis, mediated by interactions between vacuoles and the cytoskeleton." [GOC:mcc, PMID:10873824, PMID:14616069]
is_a: GO:0007033 ! vacuole organization
is_a: GO:0048308 ! organelle inheritance

[Term]
id: GO:0000012
name: single strand break repair
namespace: biological_process
def: "The repair of single strand breaks in DNA. Repair of such breaks is mediated by the same enzyme systems as are used in base excision repair." [http://www.ultranet.com/~jkimball/BiologyPages/D/DNArepair.html]
subset: gosubset_prok
is_a: GO:0006281 ! DNA repair

[Term]
id: GO:0000014
name: single-stranded DNA endodeoxyribonuclease activity
namespace: molecular_function
def: "Catalysis of the hydrolysis of ester linkages within a single-stranded deoxyribonucleic acid molecule by creating internal breaks." [GOC:mah]
synonym: "single-stranded DNA specific endodeoxyribonuclease activity" RELATED []
synonym: "ssDNA-specific endodeoxyribonuclease activity" RELATED [GOC:mah]
is_a: GO:0004520 ! endodeoxyribonuclease activity

我想要产生的输出是

GO:0000010     molecular_function
trans-hexaprenyltranstransferase activity
GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups

GO:0000011    biological_process
vacuole inheritance
is_a: GO:0007033 ! vacuole organization
is_a: GO:0048308 ! organelle inheritance

GO:0000012    biological_process
single strand break repair
is_a: GO:0006281 ! DNA repair

GO:0000014    molecular_function
single-stranded DNA endodeoxyribonuclease activity
is_a: GO:0004520 ! endodeoxyribonuclease activity

我的代码是：

import re

id_to_info = {} #declare dictionary

def parse_record(term):
    go_id = re.findall(r"id:\s(.*?)\n", term, re.DOTALL)
    name = re.findall(r"name:\s(.*?)\n", term, re.DOTALL)
    namespace = re.findall(r"namespace:\s(.*?)\n", term, re.DOTALL)
    is_a = re.findall(r"is_a:\s(.*?)\n", term, re.DOTALL)
    info = namespace + "\n" + name + "\n" + is_a
    id_to_info[go_id] = info
    for go_id, info in id_to_info.interitems():
        print(go_id + "\t" + info)

def split_record(record):
    sp_file = open(record)
    sp_records = sp_file.read()
    sp_split_records = re.findall(r"(\[.*?)\n\n", sp_records, re.DOTALL)
    for sp_record in sp_split_records:
        parse_record(term=sp_record)
    sp_file.close()

split_record(record="go.rtf")

我真的不知道我哪里出错，但我认为主要问题是我的字典电话？

Answer 1

import re

id_to_info = {} #declare dictionary

def parse_record(term):
    go_id = re.findall(r"id:\s(.*?)\n", term, re.DOTALL)[0]
    name = re.findall(r"name:\s(.*?)\n", term, re.DOTALL)[0]
    namespace = re.findall(r"namespace:\s(.*?)\n", term, re.DOTALL)[0]
    is_a = re.findall(r'is_a:(.*)', term, re.DOTALL)[0]
    info = namespace + "\n" + name + "\n" + is_a
    id_to_info[go_id] = info
    for go_id, info in id_to_info.iteritems():
        print(go_id + "\t" + info)

def split_record(record):
    sp_file = open(record)
    sp_records = sp_file.read()
    sp_split_records = re.findall(r"(\[.*?)\n\n", sp_records, re.DOTALL)
    for sp_record in sp_split_records:
        parse_record(term=sp_record)
    sp_file.close()

split_record(record="go.rtf")

我建议 NOT 使用IDE，而不是使用终端或至少要调试解释器：

Python 2.7.10 (default, Jul 30 2016, 18:31:42) 
[GCC 4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> s = """[Term]
... id: GO:0000010
... name: trans-hexaprenyltranstransferase activity
... namespace: molecular_function
... def: "Catalysis of the reaction: all-trans-hexaprenyl diphosphate + isopentenyl diphosphate = all-trans-heptaprenyl diphosphate + diphosphate." [KEGG:R05612, RHEA:20839]
... subset: gosubset_prok
... xref: KEGG:R05612
... xref: RHEA:20839
... is_a: GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups"""
>>> import re
>>> re.findall(r'is_a:(.*)', s)
[' GO:0016765 ! transferase activity, transferring alkyl or aryl (other than methyl) groups']

同样需要大量打印，Python是动态的，这意味着它没有编译和运行..它会一直运行直到遇到错误。

你的问题：

1）RegEx - 谷歌周围 2）错字 - iteritems！你们都可以阅读 Python文档。他们真的很好..或者选择任何一本书......你会学到的在编写代码和试验解释器时很多。

--- Python爱人！

Answer 2

re.findall 会返回找到的内容列表;你的代码假设字符串。由于每行只有一次点击，只需在可行的情况下添加 [0] 。 is_a 可以回空，所以需要更加温柔的处理。

此外，（键，值）方法是 iteritems （迭代项），而不是 i n teritems 。

以下是更新：

import re

id_to_info = {} #declare dictionary

def parse_record(term):
    go_id = re.findall(r"id:\s(.*?)\n", term, re.DOTALL)[0]
    name = re.findall(r"name:\s(.*?)\n", term, re.DOTALL)[0]
    namespace = re.findall(r"namespace:\s(.*?)\n", term, re.DOTALL)[0]
    is_a = re.findall(r"is_a:\s(.*?)\n", term, re.DOTALL)
    is_a = is_a[0] if is_a else ""
    # print namespace, name, is_a
    info = namespace + "\n" + name + "\n" + is_a
    id_to_info[go_id] = info
    for go_id, info in id_to_info.iteritems():
        print(go_id + "\t" + info)

def split_record(record):
    sp_file = open(record)
    sp_records = sp_file.read()
    sp_split_records = re.findall(r"(\[.*?)\n\n", sp_records, re.DOTALL)
    for sp_record in sp_split_records:
        parse_record(term=sp_record)
    sp_file.close()

split_record(record="go.rtf")

输出：

GO:0000010  molecular_function
trans-hexaprenyltranstransferase activity
GO:0016765 ! transferase activity, transferring alkyl or aryl (other
GO:0000011  biological_process
vacuole inheritance
GO:0007033 ! vacuole organization
GO:0000010  molecular_function
trans-hexaprenyltranstransferase activity
GO:0016765 ! transferase activity, transferring alkyl or aryl (other
GO:0000011  biological_process
vacuole inheritance
GO:0007033 ! vacuole organization
GO:0000010  molecular_function
trans-hexaprenyltranstransferase activity
GO:0016765 ! transferase activity, transferring alkyl or aryl (other
GO:0000012  biological_process
single strand break repair

我会把剩下的格式留给你。： - ）

编译和迭代字典

2 个答案: