GSM with mutiple SRR points to single SRR by pysradb

[mortunco]

GSM with mutiple SRR points to single SRR by pysradb

[saketkc]

Hi @mortunco,

Thanks for the bug report.

The discrepancy seems to be arising from the output at NCBI's SRA interface search end. Please note that your output currently is using the SRAweb interface of pysradb which makes a call to NCBI's web interface for getting the metadata.

I need to figure out the root of the problem. Searching its corresponding SRA id also results in just two hits on the main page.

For now, you can use the database mode so that pysradb will utilize the sqlite file for quering. This is invoked by passing it the --db parameter with the location of the SQLite file:

$ pysradb metadata --db SRAmetadb.sqlite --detailed SRP013728 
study_accession experiment_accession sample_accession run_accession experiment_title                                                  experiment_attribute      sample_attribute                                                                          taxon_id library_selection library_layout library_strategy library_source library_name                               bases      spots    adapter_spec  avg_read_length
 SRP013728       SRX154496            SRS345681        SRR513115     GSM947525: PrEC Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq   GEO Accession: GSM947525  source_name: PrEC || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3   9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947525: PrEC Cells H3K27me3 ChIP-seq   558948700  11178974  None         50.0           
 SRP013728       SRX154496            SRS345681        SRR513116     GSM947525: PrEC Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq   GEO Accession: GSM947525  source_name: PrEC || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3   9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947525: PrEC Cells H3K27me3 ChIP-seq   585244200  11704884  None         50.0           
 SRP013728       SRX154496            SRS345681        SRR513117     GSM947525: PrEC Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq   GEO Accession: GSM947525  source_name: PrEC || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3   9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947525: PrEC Cells H3K27me3 ChIP-seq   590797650  11815953  None         50.0           
 SRP013728       SRX154497            SRS345682        SRR513118     GSM947526: LNCaP Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq  GEO Accession: GSM947526  source_name: LNCaP || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3  9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947526: LNCaP Cells H3K27me3 ChIP-seq  657192700  13143854  None         50.0           
 SRP013728       SRX154497            SRS345682        SRR513119     GSM947526: LNCaP Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq  GEO Accession: GSM947526  source_name: LNCaP || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3  9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947526: LNCaP Cells H3K27me3 ChIP-seq  670278500  13405570  None         50.0           
 SRP013728       SRX154497            SRS345682        SRR513120     GSM947526: LNCaP Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq  GEO Accession: GSM947526  source_name: LNCaP || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3  9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947526: LNCaP Cells H3K27me3 ChIP-seq  672422800  13448456  None         50.0           
 SRP013728       SRX154497            SRS345682        SRR513121     GSM947526: LNCaP Cells H3K27me3 ChIP-seq; Homo sapiens; ChIP-Seq  GEO Accession: GSM947526  source_name: LNCaP || chip antibody manufacturer: Santa Cruz || chip antibody: H3K27me3  9606      ChIP              SINGLE -       ChIP-Seq         GENOMIC        GSM947526: LNCaP Cells H3K27me3 ChIP-seq  674691700  13493834  None         50.0     

I will try to get to the bug in the web mode next week. Thanks once again for reporting this.

[mortunco]

Thank you very much!