[Biopython] How to read certain GEO files with Bio.Geo?
Ilya Flyamer
flyamer at gmail.com
Thu Nov 14 20:27:34 UTC 2013
Hello everyone!
I have just recently posted a question on Stackoverflow here (
http://stackoverflow.com/questions/19961582/how-to-read-certain-geo-files-with-bio-geo),
but I am not getting any answers there.
I have a problem parsing a particular GEO file (accession number GSE40603).
I do it according to the tutorial in this way:
from Bio import Geo
handle = open('GSE40603_combined_L1_L2.txt')
records = Geo.parse(handle)for record in records:
print record
But I get an error:
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'
Here is the head of that file:
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
Am I doing something wrong? How do I read such files?
Thank you in advance!
Best,
Ilya Flyamer
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