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[BUG] gsm_to_srx false positives (reanalysis) #165

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Maarten-vd-Sande opened this issue Jul 22, 2022 · 1 comment
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[BUG] gsm_to_srx false positives (reanalysis) #165

Maarten-vd-Sande opened this issue Jul 22, 2022 · 1 comment
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@Maarten-vd-Sande
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Describe the bug

Not sure if it's a bug on the pysradb side or SRA. But I seem to get some false positives:

import pysradb
db_sra = pysradb.SRAweb()
db_sra.gsm_to_srx(["GSM1155957"])

  experiment_alias experiment_accession
3       GSM1621354            SRX893751
4       GSM1621353            SRX893750
5       GSM1621352            SRX893749
6       GSM1621351            SRX893748
7       GSM1155957            SRX298000

Could be because the other GSM numbers are a re-analysis of the previous?
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM1155957

@Maarten-vd-Sande Maarten-vd-Sande added the bug Something isn't working label Jul 22, 2022
@saketkc
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saketkc commented Jul 23, 2022

That is correct - the results reflect what we see on the search page: https://www.ncbi.nlm.nih.gov/gds/?term=GSM1155957 We could handle this internally, but for now I would recommend subsetting based on exact string match.

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