pysradb
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saketkc
Package for fetching metadata and downloading data from SRA/ENA/GEO
**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"])...
When I run a command like: pysradb metadata --detailed SRR11085797 the resulting output has inconsistent whitespace. In particular, the "header line" has tab delimiters between columns, but the subsequent data...
Should solve #78, as per the suggestion of @kpj. Requests simply get split up into smaller parts of 150, logic for the rest is untouched. @saketkc would this be something...
**Is your feature request related to a problem? Please describe.** Not sure if it is already implemented, but would it be possible to exclude private/dbgap samples when using the search...
**Describe the bug** In some cases, when using `SRAweb.sra_metadata` with a single run accession, multiple metadata rows are returned. It would seem more sensible to only return the metadata for...
**Describe the bug** My colleague @Rebecza is trying to download a single-cell ATAC-seq dataset and uses pysradb to get some metadata ([seq2science](https://github.com/vanheeringen-lab/seq2science)), and managed to find a JsonDecodeError :bug: ....
Running the colab notebook (https://colab.research.google.com/github/saketkc/pysradb/blob/master/notebooks/02.Commandline_download.ipynb#scrollTo=YQLxy1yzH6dQ) fails on the step `!pysradb srx-to-srr SRX4720625 --detailed | pysradb download` with the error ```The supplied url column "None" cannot be found. Using recommended_url instead....
In the SRA db, in the run info, as well as in the XML, one can see variables such as "GISAID_Accession" and "SARS-CoV-2_diagnostic_pcr_Ct_value_1" for certain samples (below). https://www.ncbi.nlm.nih.gov/sra/?term=SRR15168846 But when...
**Describe the bug** Given SRP319378, when I ask pysradb the SRRs it gives me SRSs instead of SRRs **To Reproduce** Steps to reproduce the behavior: `pysradb srp-to-srr SRP481544` **Desktop** -...
