如何使用 Bio.Geo 读取某些 GEO 文件？答案

【问题标题】：How to read certain GEO files with Bio.Geo?如何使用 Bio.Geo 读取某些 GEO 文件？
【发布时间】：2013-11-13 18:29:37
【问题描述】：

我正在尝试按照以下方式使用 Bio.Geo 解析 GEO 文件：

from Bio import Geo
handle = open('GSE40603_combined_L1_L2.txt')
records = Geo.parse(handle)
for record in records:
    print record

但我收到以下错误：

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/lib/python2.7/dist-packages/spyderlib/widgets/externalshell/sitecustomize.py", line 585, in runfile
    execfile(filename, namespace)
  File "/home/ilya/Документы/biology/E coli GCC/GEOanalyzer.py", line 11, in <module>
    for record in records:
  File "/usr/local/lib/python2.7/dist-packages/Bio/Geo/__init__.py", line 60, in parse
    record.table_rows.append(row)
AttributeError: 'NoneType' object has no attribute 'table_rows'

这是那个文件的头：

0   0   63  NC_000913   0   152 NC_000913   0   152 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL  
0   1   81  NC_000913   0   152 NC_000913   153 599 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= thrL  |CDS(+,190,255) gene= thrL  |gene gene= thrA  |CDS(+,337,2799) gene= thrA  note= bifunctional: aspartokinase I (N-terminal); 
0   2   1   NC_000913   0   152 NC_000913   600 698 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= thrA  |CDS[fcd=-312](+,337,2799) gene= thrA  note= bifunctional: aspartokinase I (N-terminal); 
0   3   1   NC_000913   0   152 NC_000913   699 755 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= thrA  |CDS[fcd=-390](+,337,2799) gene= thrA  note= bifunctional: aspartokinase I (N-terminal); 
0   4   1   NC_000913   0   152 NC_000913   756 757 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= thrA  |CDS[fcd=-419](+,337,2799) gene= thrA  note= bifunctional: aspartokinase I (N-terminal); 
0   2620    1   NC_000913   0   152 NC_000913   352429  352483  |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= prpE  |CDS[fcd=-526](+,351930,353816) gene= prpE  note= putative propionyl-CoA synthetase  
0   18818   1   NC_000913   0   152 NC_000913   2560323 2560384 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |misc_feature note= cryptic prophage Eut/CPZ-55  |gene gene= yffO  |CDS[fcd=-220](+,2560133,2560549) gene= yffO  
0   2617    1   NC_000913   0   152 NC_000913   352326  352375  |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= prpE  |CDS[fcd=-420](+,351930,353816) gene= prpE  note= putative propionyl-CoA synthetase  
0   18817   1   NC_000913   0   152 NC_000913   2560275 2560322 |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |misc_feature note= cryptic prophage Eut/CPZ-55  |gene gene= yffO  |CDS[fcd=-165](+,2560133,2560549) gene= yffO  
0   912 1   NC_000913   0   152 NC_000913   113055  113082  |neigh_up NC_000913-start |neigh_down CDS[fcd=114](+,190,255) gene= thrL    |gene gene= coaE  |CDS[fcd=151](-,112599,113219) gene= coaE  note= putative DNA repair protein

我做错了吗？如何读取此类文件？

【问题讨论】：

标签： python parsing bioinformatics biopython

【解决方案1】：

此文件是来自 GEO 的所谓“补充文件”。它由原始提交者提供，因此读取 GEO 格式的工具将无法使用它。

在这种特殊情况下，最好的办法是使用标准 python 工具简单地解析下载的文件。

【讨论】：

谢谢你，@seandavi！这对我来说是全新的。