Every now and then, when I am given "GSE" accession number and I wish to convert it to "SRP", I receive with empty output, this for example happened to me Today for GSE209835:
The problematic nature of this issue is that If only one GSE is being converted at a time, one can immediately see that it was not converted. However, when say dozens of GSE numbers are simultaneously converted, then the one that is "missing" is simply missing, and its sometimes hard to spot it (one would have to check if the number of accession numbers in query and output is matching and if not, then which one is missing. E.g. this command shows this behavior:
At the same time, its not that those metadata are not at all in the database, because if I for example find SRP number, which for the example GSE209835 is SRP388275, then I can find other types of metadata, e.g.:
Moreover, if I instead run this type of command pysradb search --query 'SRP388275' --detailed | grep "GSE209835" I can see that the GSE209835 is "hidden" in the metadata (at least the extended fields).
Next steps
If you have any idea how this could be fixed / fine-tuned, that would be awesome! If for example it could not be "easily" fixed e.g. because how the reference database is constructed, then I would suggest to update the display of the results to something like this:
thanks for reporting this! The latest commit (above) in develop should address this for srp-to-gse command. I will have to see if there are any other commands that run into issues because of such edge cases.
Hi,
Every now and then, when I am given "GSE" accession number and I wish to convert it to "SRP", I receive with empty output, this for example happened to me Today for
GSE209835
:while usually, this command should produce output like this:
The problematic nature of this issue is that If only one GSE is being converted at a time, one can immediately see that it was not converted. However, when say dozens of GSE numbers are simultaneously converted, then the one that is "missing" is simply missing, and its sometimes hard to spot it (one would have to check if the number of accession numbers in query and output is matching and if not, then which one is missing. E.g. this command shows this behavior:
At the same time, its not that those metadata are not at all in the database, because if I for example find SRP number, which for the example
GSE209835
isSRP388275
, then I can find other types of metadata, e.g.:Moreover, if I instead run this type of command
pysradb search --query 'SRP388275' --detailed | grep "GSE209835"
I can see that theGSE209835
is "hidden" in the metadata (at least the extended fields).Next steps
If you have any idea how this could be fixed / fine-tuned, that would be awesome! If for example it could not be "easily" fixed e.g. because how the reference database is constructed, then I would suggest to update the display of the results to something like this:
This kind of output format would simplify post-processing and mitigate omitting of the datasets for bulk analyses.
Desktop (please complete the following information):
All the best, Wojciech
PS. Once again thank you for your amazing tool, it elevates all kinds of work related with reprocessing of public data to another level!