正则表达式匹配不适用于Pyteomics解析器的简单字符串 [英] regex match not working on simple string with Pyteomics parser
问题描述
我正在对人类蛋白质组进行计算机分析,这意味着我试图在特定位置切碎每种蛋白质的氨基酸序列.我正在使用内部的Pyteomics解析器功能
此处是蛋白质组学的维护者.
错误消息实际上告诉您问题的根源: PyteomicsError:电池组错误,消息:无效的modX序列:{'sequence':'AKDEVQKN'}"
>
这意味着您传递了字典 {'sequence':'AKDEVQKN'}
而不是字符串'AKDEVQKN'
.这实际上发生在这里:
pep_dic = [{'sequence':i} for i in unique_peptides]对于pep_dic中的肽:pep_dic ['parsed_sequence'] = parser.parse(peptides,show_unmodified_termini = False)...
您应该将序列本身传递给 parse
,而不是字典:
pep_dic ['parsed_sequence'] = parser.parse(peptides ['sequence'],show_unmodified_termini = False)
I am performing an in silico digestion of the human proteome, meaning that I am trying to chopped the amino acid sequence of every protein at a certain position. I am using the Pyteomics parser function Pyteomics Parser within a bigger function that I have created.
I am getting this error: PyteomicsError: Pyteomics error, message: "Not a valid modX sequence: {'sequence': 'AKDEVQKN'}"
However, I am unsure how AKDEVQKN doesn't match the modX_reqquence compilier:
_modX_sequence = re.compile(r'^([^-]+-)?((?:[^A-Z-]*[A-Z])+)(-[^-]+)?$')
From my understanding of this regex, it should find any string that doesn't start with (-) and is followed by a series of alphabetical characters.
This is the function I am trying to use it on.
import re
import pyteomics
from pyteomics import fasta, parser
def ButcherShop(df, target, rule,min_length=7,exception=None,max_legnth=100, pH=2.0):
> raw = df[target]
> unique_peptides = set()
> for peptide in raw:
> new_peptides = parser.cleave(peptide, rule=rule,min_length=min_length,exception=exception)
> unique_peptides.update(new_peptides)
> print(f'Done,{len(unique_peptides)} sequences of >= 7 amino acids!')
> pep_dic = [{'sequence': i} for i in unique_peptides]
> for peptides in pep_dic:
> pep_dic['parsed_sequence'] = parser.parse(peptides,show_unmodified_termini=False)
> pep_dic['xlength'] = len(peptides)
> pep_dic['charge'] = int(round(electrochem.charge(peptides, pH=pH)))
> pep_dic['mass']=int(round(Peptide_mass(peptides)))
> pep_dic = [peptide for peptide in pep_dic if peptide['length'] <= int(max_length)]
> pep_df = pd.DataFrame.from_dict(pep_dic)
> return unique_peptides,pep_dic,pep_df
Thank you for any insight on how to address this.
** Update: If I run on a different set, I am getting the same error which may suggest it is the library itself.
Screenshot of Error:
Pyteomics maintainer here.
The error message actually tells you the source of the problem: PyteomicsError: Pyteomics error, message: "Not a valid modX sequence: {'sequence': 'AKDEVQKN'}"
It means that instead of a string 'AKDEVQKN'
you passed a dictionary {'sequence': 'AKDEVQKN'}
. This actually happens here:
pep_dic = [{'sequence': i} for i in unique_peptides]
for peptides in pep_dic:
pep_dic['parsed_sequence'] = parser.parse(peptides,show_unmodified_termini=False)
...
You should pass the sequence itself to parse
, not the dict:
pep_dic['parsed_sequence'] = parser.parse(peptides['sequence'], show_unmodified_termini=False)
这篇关于正则表达式匹配不适用于Pyteomics解析器的简单字符串的文章就介绍到这了,希望我们推荐的答案对大家有所帮助,也希望大家多多支持IT屋!