Comments (8)
Hi @fgypas,
The correct usage is:
pysradb download -p SRP083135
Can you post the error message you get when you run the above command?
Thanks!
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Hi @saketkc
Thank you for the response.
I get the following error message:
File "miniconda3/envs/pysradb/bin/pysradb", line 10, in
sys.exit(parse_args())
File "miniconda3/envs/pysradb/lib/python3.8/site-packages/pysradb/cli.py", line 1044, in parse_args
download(args.out_dir, args.db, args.srx, args.srp, args.skip_confirmation)
File "miniconda3/envs/pysradb/lib/python3.8/site-packages/pysradb/cli.py", line 139, in download
sradb.download(
File "miniconda3/envs/pysradb/lib/python3.8/site-packages/pysradb/sradb.py", line 1249, in download
srapaths = self._srapath_url(df.study_accession.unique()[0])
File "miniconda3/envs/pysradb/lib/python3.8/site-packages/pysradb/sradb.py", line 1174, in _srapath_url
raise Exception("Unable to run srapath.")
Exception: Unable to run srapath.
Foivos
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Thanks @fgypas. I confirm this is a bug and is arising because of pysradb
relying on srapath
to get the new URLs. I will have a temporary fix soon.
Thanks once again and sorry that pysradb
is not completely useful for your use case at the moment.
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Hi @saketkc,
could you please provide me some information on how to store the result which we get from
"pysradb metadata SRP063732 --desc --expand" into pandas dataframe
Thanks in advance
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Hi @deepthi888, You can save the output to a tab separated file by doing:
pysradb metadata SRP063732 --desc --expand --saveto SRP063732.tsv
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Hi @saketkc,
could you please provide me information on how to fetch the name of the organism by giving project id and also how to get the count of runs and experiments of each project
I tried with this "pysradb metadata SRP063732 --desc --expand --detailed" but it fetched all the attributes information except name of the organism.
Thanks in advance
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@deepthi888 Can you please open a separate issue for your question?
Thanks!
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Hi @fgypas,
I can confirm that v0.9.9 of pysradb fixes this.
Please let me know if you run into any issues and thanks a lot for your patience!
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Related Issues (20)
- Filtering results by instrument type HOT 3
- [ENH] Super useful package!
- [BUG] cannot download a single experiment from command line HOT 1
- [BUG] aspera HOT 3
- [BUG] Metadata download not only for the provided accession number HOT 3
- [BUG] aspera HOT 3
- [BUG] gse-to-srp error HOT 1
- [BUG] Download error HOT 1
- [BUG] download error HOT 2
- [BUG]Downloading issue HOT 1
- fastq's URLs are empty HOT 2
- Not all attributes are being exported HOT 6
- [BUG] missing run-related entries for experiments with high number of runs
- [BUG] Metadata download only for a few run accessions, not for all the run accessions of the study HOT 4
- [BUG] srp-to-srr giving SRSs as result HOT 3
- could you expend to support European Nucleotide Archive data HOT 1
- [BUG] All arrays must be of the same length
- [ENH] geo_download_links error handling HOT 1
- Incosistencies with retrieving SRX data from different archives HOT 1
- Specific srp seems to cause metadata download to freeze
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