Support project file downloads #13
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Good idea! At the CLI level:
$ wort view -d sra PRJEB23372
returns 3 signatures, one for each SRR
Same thing for the API, I might change the response to be a JSON file with download links for each SRR. The CLI would also download this data, but for people accessing the API directly it would be up to them do download the data.
Makes sense/fits your use case?
…On November 9, 2018 7:14:35 PM UTC, Olga Botvinnik ***@***.***> wrote:
Hello,>
I've been using
[bionode-ncbi](https://github.com/bionode/bionode-ncbi/blob/master/lib/bionode-ncbi.js)
to get SRR ids from a `PRJ**` IDs so I don't have to look for each file
individually (example below). Would it be possible to do a similar
query in wort?>
Warmest,>
Olga>
>
```>
(base) >
Fri 9 Nov - 14:01 ~ >
docker run -it bionode/bionode-ncbi bash >
***@***.***:/# bionode-ncbi search sra PRJEB23372 | wc -l>
27>
***@***.***:/# bionode-ncbi search sra PRJEB23372 | head -n 3>
{"uid":"4915577","expxml":{"Summary":{"Title":"Illumina HiSeq 2000
paired end
sequencing","Platform":{"_":"ILLUMINA","instrument_model":"Illumina
HiSeq
2000"},"Statistics":{"total_runs":"1","total_spots":"5615688","total_bases":"1403922000","total_size":"506152479","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"ERA1127236","center_name":"","contact_name":"European
Nucleotide Archive","lab_name":"European Nucleotide
Archive"},"Experiment":{"acc":"ERX2248648","ver":"1","status":"public","name":"Illumina
HiSeq 2000 paired end
sequencing"},"Study":{"acc":"ERP105122","name":"Single-cell
RNA-Sequencing reveals vesicle-mediated communication between mosquito
blood cells"},"Organism":{"taxid":"7165","ScientificName":"Anopheles
gambiae"},"Sample":{"acc":"ERS1996171","name":""},"Instrument":{"ILLUMINA":"Illumina
HiSeq
2000"},"Library_descriptor":{"LIBRARY_NAME":"unspecified","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"Oligo-dT","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"500"}},"LIBRARY_CONSTRUCTION_PROTOCOL":"Smart-seq2"},"Bioproject":"PRJEB23372","Biosample":"SAMEA104371193"},"runs":{"Run":[{"acc":"ERR2192533","total_spots":"5615688","total_bases":"1403922000","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"","createdate":"2018/01/06","updatedate":"2018/01/06"}>
{"uid":"4915578","expxml":{"Summary":{"Title":"Illumina HiSeq 2000
paired end
sequencing","Platform":{"_":"ILLUMINA","instrument_model":"Illumina
HiSeq
2000"},"Statistics":{"total_runs":"1","total_spots":"6481103","total_bases":"1620275750","total_size":"576542121","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"ERA1127236","center_name":"","contact_name":"European
Nucleotide Archive","lab_name":"European Nucleotide
Archive"},"Experiment":{"acc":"ERX2248649","ver":"1","status":"public","name":"Illumina
HiSeq 2000 paired end
sequencing"},"Study":{"acc":"ERP105122","name":"Single-cell
RNA-Sequencing reveals vesicle-mediated communication between mosquito
blood cells"},"Organism":{"taxid":"7165","ScientificName":"Anopheles
gambiae"},"Sample":{"acc":"ERS1996172","name":""},"Instrument":{"ILLUMINA":"Illumina
HiSeq
2000"},"Library_descriptor":{"LIBRARY_NAME":"unspecified","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"Oligo-dT","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"500"}},"LIBRARY_CONSTRUCTION_PROTOCOL":"Smart-seq2"},"Bioproject":"PRJEB23372","Biosample":"SAMEA104371194"},"runs":{"Run":[{"acc":"ERR2192534","total_spots":"6481103","total_bases":"1620275750","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"","createdate":"2018/01/06","updatedate":"2018/01/06"}>
{"uid":"4915579","expxml":{"Summary":{"Title":"Illumina HiSeq 2000
paired end
sequencing","Platform":{"_":"ILLUMINA","instrument_model":"Illumina
HiSeq
2000"},"Statistics":{"total_runs":"1","total_spots":"5274357","total_bases":"1318589250","total_size":"493826312","load_done":"true","cluster_name":"public"}},"Submitter":{"acc":"ERA1127236","center_name":"","contact_name":"European
Nucleotide Archive","lab_name":"European Nucleotide
Archive"},"Experiment":{"acc":"ERX2248650","ver":"1","status":"public","name":"Illumina
HiSeq 2000 paired end
sequencing"},"Study":{"acc":"ERP105122","name":"Single-cell
RNA-Sequencing reveals vesicle-mediated communication between mosquito
blood cells"},"Organism":{"taxid":"7165","ScientificName":"Anopheles
gambiae"},"Sample":{"acc":"ERS1996173","name":""},"Instrument":{"ILLUMINA":"Illumina
HiSeq
2000"},"Library_descriptor":{"LIBRARY_NAME":"unspecified","LIBRARY_STRATEGY":"RNA-Seq","LIBRARY_SOURCE":"TRANSCRIPTOMIC","LIBRARY_SELECTION":"Oligo-dT","LIBRARY_LAYOUT":{"PAIRED":{"NOMINAL_LENGTH":"500"}},"LIBRARY_CONSTRUCTION_PROTOCOL":"Smart-seq2"},"Bioproject":"PRJEB23372","Biosample":"SAMEA104371195"},"runs":{"Run":[{"acc":"ERR2192535","total_spots":"5274357","total_bases":"1318589250","load_done":"true","is_public":"true","cluster_name":"public","static_data_available":"true"}]},"extlinks":"","createdate":"2018/01/06","updatedate":"2018/01/06"}>
```
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Cool! I just showed the first 3 lines for brevity, but there should be 28 total signatures: https://www.ncbi.nlm.nih.gov/Traces/study/?WebEnv=NCID_1_30821840_130.14.18.48_5555_1541797205_1771571446_0MetA0_S_HStore&query_key=4 Are the ids getting aggregated somehow? |
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Hello,
I've been using bionode-ncbi to get SRR ids from a
PRJ**IDs so I don't have to look for each file individually (example below). Would it be possible to do a similar query in wort?Warmest,
Olga
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