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bebatut / enasearch

A Python library for interacting with ENA's API
http://bebatut.fr/enasearch
MIT License
22 stars 6 forks source link

Write TSV to stdout when --result is not provided #12

Closed tseemann closed 7 years ago

tseemann commented 7 years ago

It seems to output it in internal Python stringified manner. I would expect STDOUT to behave the same as --result FILENAME. This would be very convenient for Unix pipes.

% enasearch retrieve_run_report --accession PRJNA275974 --fields run_accession --fields fastq_ftp

# expected TSV but got __string__

('run_accession\tfastq_ftp\n'
 'SRR1922792\t'
 '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\n'
 'SRR1922793\t'
 '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\n'
 'SRR1922794\t'
 '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\n'
 'SRR1922795\t'
 '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\n'
 'SRR1922796\t'
 '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\n'
 'SRR1922797\t'
 '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\n')
bebatut commented 7 years ago

Should be fixed with #17 

$ enasearch retrieve_run_report --accession PRJNA275974 --fields run_accession --fields 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