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bebatut / enasearch

A Python library for interacting with ENA's API
http://bebatut.fr/enasearch
MIT License
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How do I replicate this URL via this module? #6

Closed tseemann closed 7 years ago

tseemann commented 7 years ago

Below is a manual URL i use to get ENA SRA files from a given project in TSV format.

I have tried to replicate it with enasearch search_data or enasearch retrieve_data but I have failed to get it working.

Any help would be appreciated!

% curl 'http://www.ebi.ac.uk/ena/data/warehouse/filereport?accession=PRJNA275974&result=read_run&download=txt&fields=run_accession,fastq_ftp'

run_accession   fastq_ftp
SRR1922792      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/002/SRR1922792/SRR1922792_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/002/SRR1922792/SRR1922792_2.fastq.gz
SRR1922793      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/003/SRR1922793/SRR1922793_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/003/SRR1922793/SRR1922793_2.fastq.gz
SRR1922794      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/004/SRR1922794/SRR1922794_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/004/SRR1922794/SRR1922794_2.fastq.gz
SRR1922795      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/005/SRR1922795/SRR1922795_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/005/SRR1922795/SRR1922795_2.fastq.gz
SRR1922796      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/006/SRR1922796/SRR1922796_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/006/SRR1922796/SRR1922796_2.fastq.gz
SRR1922797      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/007/SRR1922797/SRR1922797_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/007/SRR1922797/SRR1922797_2.fastq.gz
bebatut commented 7 years ago

Hi @tseemann,

Thanks for using this tool :)

To reproduce your curl with enasearch, you can run the enasearch retrieve_run_report command:

enasearch retrieve_run_report \
   --accession PRJNA275974 \
   --fields run_accession \
   --fields fastq_ftp \
   --file results \

I got as result:

run_accession   fastq_ftp
SRR1922792      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/002/SRR1922792/SRR1922792_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/002/SRR1922792/SRR1922792_2.fastq.gz
SRR1922793      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/003/SRR1922793/SRR1922793_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/003/SRR1922793/SRR1922793_2.fastq.gz
SRR1922794      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/004/SRR1922794/SRR1922794_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/004/SRR1922794/SRR1922794_2.fastq.gz
SRR1922795      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/005/SRR1922795/SRR1922795_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/005/SRR1922795/SRR1922795_2.fastq.gz
SRR1922796      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/006/SRR1922796/SRR1922796_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/006/SRR1922796/SRR1922796_2.fastq.gz
SRR1922797      ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/007/SRR1922797/SRR1922797_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR192/007/SRR1922797/SRR1922797_2.fastq.gz

I hope this will help you :)

Bérénice

tseemann commented 7 years ago

Ok, thank you. I think I was having trouble due to the previous bug #5