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saketkc / pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO
https://saketkc.github.io/pysradb
BSD 3-Clause "New" or "Revised" License
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[BUG] ENA search ignores organism when query is specified #143

Closed siebrenf closed 2 years ago

siebrenf commented 2 years ago

Describe the bug pysradb search -d ena ignores --organism when --query is specified.

To Reproduce Organism is used when searching SRA:

pysradb search -d sra -m 1 -O xenopus tropicalis -q development

study_accession experiment_accession    experiment_title        sample_taxon_id sample_scientific_name  experiment_library_strategy     experiment_library_source       experiment_library_selection    sample_accession        sample_alias    experiment_instrument_model     pool_member_spots       run_1_size      run_1_accession    run_1_total_spots       run_1_total_bases
SRP249483 SRX9352396 RPB1 ChIP-seq of X.tropicalis: s11 8364 Xenopus tropicalis ChIP-Seq GENOMIC ChIP SRS6146540 stage11 HiSeq X Ten 44679487 5928734005 SRR12886651 44679487 13403846100

Organism is ignored when searching ENA:

pysradb search -d ena -m 1 -O xenopus tropicalis -q development

study_accession experiment_accession    experiment_title        description     tax_id  scientific_name library_strategy        library_source  library_selection       sample_accession        sample_title    instrument_model        run_accession   read_count      base_count
PRJDB2600 DRX005926 Illumina Genome Analyzer IIx sequencing; RNA-Seq analysis of Oryza sativa cv. Nipponbare root control sample for Developmental Time 0 hour after - replicate 1 Illumina Genome Analyzer IIx sequencing; RNA-Seq analysis of Oryza sativa cv. Nipponbare root control sample for Developmental Time 0 hour after - replicate 1 39947 Oryza sativa Japonica Group RNA-Seq TRANSCRIPTOMIC RANDOM SAMD00012946 Root of rice (Oryza sativa ssp. Japonica cv. Nipponbare) seedling 14 days after germination Illumina Genome Analyzer IIx DRR006601 7518132 571378032

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saketkc commented 2 years ago

Thanks, I will take a look. Also paging @bscrow if he has the bandwidth to debug.

saketkc commented 2 years ago

This should be fixed by #144, thanks once again for reporting!

siebrenf commented 2 years ago

I can confirm both fixes are working for my test set!

Thank you @bscrow for the fixes, and thank you both for the tool! 🚀