pysradb

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fastq's URLs are empty

2

**Describe the bug** The columns "ena_fastq_http", "ena_fastq_http" and "ena_fastq_http" are all NA. I tested the code in several environments, and no change. (the data does exist in the same path...

NomiCentarix

**Describe the bug** Missing run-related data for experiments having many runs. When I run `pysradb metadata SRP245574`, certain rows have missing entries for `run_accession`, `run_total_spots`, `run_total_bases`. I don't think this...

masarunakajima

Data download is interrupted after a few minutes

7

**Describe the bug** Not sure what's happening but for the last few days, I'm struggling to download data using pysradb. This used to work no problem a couple of weeks...

sert23

[BUG] Download error

1

**Describe the bug** When I download the file using the following command, no error is reported, but the file content is empty, only the corresponding SRX folder. **To Reproduce** pysradb...

tzhu-bio

[BUG] aspera

3

Following my previous issue - I still don't get the fastq files with aspera, only empty folders, with the following code: ``` from pysradb.sraweb import SRAweb SRA_OUR_DIR = "/data/NCBI_data/" db...

NomiCentarix

[BUG] cannot download a single experiment from command line

1

**Describe the bug** Running pysradb from command line to download a single experiment SRX results into the program hanging forever. **To Reproduce** Steps to reproduce the behavior: `pip install git+https://github.com/saketkc/pysradb`...

marcomoretto

[BUG] gse-to-srp error

1

Hello, I have list of GEO study accession IDs and need to extract SRA meta data. And I got several studies returned error message. Does anyone know what causes this...

sumin5784

Not a bug report or an enhancement package, but simply a note of thanks for a super useful tool!

pmagwene

Possible missing keys in esearch response results

1

https://github.com/saketkc/pysradb/blob/0286ba9cf3d0f6e97b6d08baccf0bd36e11c650c/pysradb/sraweb.py#L340 I can't reproduce this, but I had a random event of: ``` File "/Users/aaaaaa/.venv/lib/python3.11/site-packages/pysradb/sraweb.py", line 339, in get_efetch_response n_records = int(esearch_response["esearchresult"]["count"]) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^ KeyError: 'count' ``` line numbers are off...

andrewdavidsmith

[ENH] Include data processing steps, reference to which the reads were aligned or if possible lab protocol into the main table

1

**Is your feature request related to a problem? Please describe.** I was wondering whether it is possible to also retrieve data processing description that is present in the sample's records...

ajandria