Regarding Non-available dataset in the package

[saketkc]

Regarding Non-available dataset in the package

[saketkc]

It looks like these GSEs are not yet available in SRAmetadb.sqlite. Unfortunately, I do not have a timeline for when these projects will be accessible through pysradb as it depends on updates upstream.

[saketkc]

Hi @himanshusingh2018, I am going to close this since your query is limited by SRAmetadb.sqlite itself. Please feel free to re-open if you face any difficulty with pysradb. Thanks for using pysradb.

[himanshusingh2018]

Hi @saketkc. Thank you for helping me in the regard. However, I have just one query that can we add any GSE dataset in SRAmetadb.sqlite manually?
Thanks

[saketkc]

In theory, yes. But it will require you to update the records across tables.

Scripts to generate SRAmetadb.sqlite are not public and hence manually adding datasets is not possible, practically.

[himanshusingh2018]

Thank you for your response. Can you suggest me something, where I can get all the datasets available on SRA db? Like we fetch in pysradb...
Thanks

[saketkc]

You can try SRAdbv2: https://github.com/seandavi/SRAdbV2

[himanshusingh2018]

Thank you for your suggestion.

[himanshusingh2018]

Hi Saket,
Is it possible with pysradb to convert list of GSM id into corresponding SRR ID? For example, I want to convert GSM1534712, GSM1534713, GSM1534714 to their SRR Id and want to save the list in any text file.

Thanks
Himanshu

[saketkc]

Yes, you can use gsm-to-srr subcommand for this.

[himanshusingh2018]

I am reading a file then parsing the value of GSM ID in python code.

working code
cmd = "pysradb gsm-to-srr --desc --expand --detailed --db SRAmetadb.sqlite GSM1055806 --saveto gsm_srr_description.txt"
subprocess.call(cmd,shell=True)

I want to extract for multiple GSM ID (which is read from a text file) details. Below is my code. Your help is appreciated.

Its not working. Please help.
list = ['GSM1055806', 'GSM1055807']
cmd = "pysradb gsm-to-srr --desc --expand --detailed --db SRAmetadb.sqlite "+print(*list,spe=" ")+ " --saveto gsm_srr_description.txt"
subprocess.call(cmd,shell=True)

[saketkc]

Hi @himanshusingh2018 ,

With the latest version of pysradb (0.9.6) you should be able to obtain the metadata even if it is not available in the SRAmetadb.sqlite file.

$ pysradb  gse-to-gsm  GSE80990
study_alias experiment_alias experiment_accession
 SRP074240   GSM2946898       SRX3596655         
 SRP074240   GSM2946897       SRX3596654         
 SRP074240   GSM2946896       SRX3596653         
 SRP074240   GSM2946895       SRX3596652         

$ pysradb gsm-to-srr GSM1055806 GSM1055807
experiment_alias run_accession
 GSM1055807       SRR639051   
 GSM1055806       SRR639050   

Please let me know if you face any issue. Thanks!