Closed romaingroux closed 3 years ago
Hi @romaingroux, thanks for the bug report. I can confirm this is a bug given SRA's webpage does return SRX627421
. Though I am not sure of the origin - given me a couple of days to address this. Apologies.
No problem! Thank you for all :)
I looked into this. It seems, the runs
slot for this SRX627421
:
<Summary><Title>NA12878 P5-C3 Sequencing</Title><Platform instrument_model="PacBio RS">PACBIO_SMRT</Platform><Statistics total_runs="110" total_spots="24522300" total_bases="181073101227" total_size="630384719154" load_done="true" cluster_name="public"/></Summary><Submitter acc="SRA172711" center_name="PacBio" contact_name="Ali Bashir" lab_name=""/><Experiment acc="SRX627421" ver="6" status="public" name="NA12878 P5-C3 Sequencing"/><Study acc="SRP043609" name="Homo sapiens Genome sequencing and assembly"/><Organism taxid="9606" ScientificName="Homo sapiens"/><Sample acc="SRS647947" name=""/><Instrument PACBIO_SMRT="PacBio RS"/><Library_descriptor><LIBRARY_NAME>PB-C3</LIBRARY_NAME><LIBRARY_STRATEGY>WGS</LIBRARY_STRATEGY><LIBRARY_SOURCE>GENOMIC</LIBRARY_SOURCE><LIBRARY_SELECTION>RANDOM</LIBRARY_SELECTION><LIBRARY_LAYOUT> <SINGLE/> </LIBRARY_LAYOUT></Library_descriptor><Bioproject>PRJNA253696</Bioproject><Biosample>SAMN02887092</Biosample> ', 'runs': '',
I am not quite sure why that is the case, but from a second look it does not look like a pysradb bug.
Ok no problem. You can close the issue I guess?
Thanks for having a look :)
Thanks!
Hello,
First of all, I would like to thank you for this package which really does a good job from what I used it.
Second, I don't know whether what I am describing here is i) a
pysradb
bug, ii) coming from the SRA database itself or iii) is a missunderstanding from my side about the SRA (in which case I apologize already).Describe the bug I am trying to obtain all the metadata for
SRP043609
. This project contains two SRX entries :SRX638310
andSRX627421
(according to https://www.ncbi.nlm.nih.gov/sra/?term=SRP043609).My expectations are to retrieve metadata for both SRX entries in the tables returned by the different commands of
pysradb
.I can retrieve all the expected information for
SRX638310
. However, I cannot get anything forSRX627421
.To Reproduce I ran all possible commands :
None of them returns a single line containing
SRX627421
. This is also true if you take anSRX627421
SRR number, saySRR1947646
, and run:Desktop (please complete the following information):