[Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)

Cook, Malcolm MEC at stowers.org
Thu Feb 14 15:22:41 CET 2013

Dear Rasko,

Thanks for the quick response and acknowledgement and attempted fix for my issue.

I find that the matter is improved as results are returned, but I am now getting a new warning message for each file:

	1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
		  incomplete final line found by readTableHeader on 'http://www.ebi.ac.uk/ena/data/view/reports/sra/fastq_files/SRR345569'
I do not know if the problem is limited to my few accessions, but my guess is that it is widespread.

Looking at the report, I see that there is an extra unneeded trailing tab in the header line of 'http://www.ebi.ac.uk/ena/data/view/reports/sra/fastq_files/SRR345569'

When I remove it by hand I can read the file in R with importText.

So, I think your solution is to review the code that writes these files and fix the part that writes this extra tab character.

In the meantime, I have a variety of workarounds, but I and others will appreciate your restoring the old format tab for tab if possible.



 .-----Original Message-----
 .From: datasubs at ebi.ac.uk [mailto:datasubs at ebi.ac.uk]
 .Sent: Thursday, February 14, 2013 6:54 AM
 .To: Cook, Malcolm
 .Cc: bioc-devel at r-project.org; zhujack at mail.nih.gov
 .Subject: RE: [Bioc-devel] SRAdb listSRAfile returns empty datatable with filetype='fastq' (rasko) (SUB#832914)
 .Dear Malcolm,
 .We have reverted minor differences in the reports for submitted and fastq files
 .that were unintentionally introduced yesterday. We have compared the current
 .reports with the previously deployed ones and have not found any further
 .Could you please let me know if the problem persists, and in case it does, could
 .you please send example accessions manifesting the problem?
 .Kind Regards,
 .Rasko Leinonen
 .European Nucleotide Archive (ENA)

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