GEOparse
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guma44
Python library to access Gene Expression Omnibus Database (GEO)
`get_GEO('GPL1641')` fails with OSError: Download failed due to 'Downloaded size do not match the expected size for http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?targ=self&acc=GPL16417&form=text&view=full'. ID could be incorrect or the data might not be public yet....
Hi, thanks for providing such a great library! I'm wondering if there's a way I can get a summary table of GSM metadata for all GSMs in a GSE? Currently...
By skipping the `read_csv` function, we lose the detection of nan values, so columns that are numeric are coded as objects. ie ``` import GEOparse geo = GEOparse.get_GEO("GSE112676") geo.phenotype_data["characteristics_ch1.3.age_onset"] ```...
I noticed that using `download_SRA` already existing SRA files will not be downloaded again. But fastq files will be converted each time. Is there a way to extend this behavior...
While using GEOparse I got the following error: ``` Traceback (most recent call last): File "/usr/local/lib/python3.6/dist-packages/GEOparse/utils.py", line 80, in download_from_url fn.download(silent=silent, force=force) File "/usr/local/lib/python3.6/dist-packages/GEOparse/downloader.py", line 82, in download _download() File...
I found that some GEO files contain carriage return characters in the meta data, causing exceptions (GEOparse.GEOTypes.DataIncompatibilityException). To reproduce the error you can test functions with "GPL10740" dataset as follows:...
When the `entry_line` parameter in the `GEOparse.__parse_entry()` function contains more than an equal sign, the current function raises an exception(GEOparse.GEOTypes.DataIncompatibilityException) as follows: ``` gpl = GEOparse.get_GEO(geo="GPL6101", silent=True, include_data=True, destdir=".") (,...
i'm not sure if this is user error (probably) or library error, but for a particular GEO accession, I can't get GEOparse to download the main supplementary file. check this...
The following code is generating a warning for me: ``` import GEOparse gpl = GEOparse.get_GEO('GPL17481') ``` The output is: ``` >>> import GEOparse >>> gpl = GEOparse.get_GEO('GPL17481') 17-May-2021 13:32:21 DEBUG...
Sorry for being dumb, but I wondered if you could give me some feedback on my code? https://gist.github.com/CholoTook/2eaed8009e48e65bc1b1b65111320a59 I always worry that I'm not using the tool 'canonically' or that...