Hi Thomas, Sorry for not getting back to you earlier on this. Opening/closing each file inside the loop (i.e. at the beginning/end of each iteration) instead of opening all files before entering the loop would indeed address the problem. I'll look into this and will let you know. Cheers, H.
On 02/15/2016 05:42 AM, Thomas Lin Pedersen wrote:
Hi (mostly Herv?) I?m running into problems trying to run fasta.index() from Biostrings on a list of 4700 files, as the limit on open files are reached. Is it possible to continuously open and close the connections in the C code to circumvent this? I expect this problem also arises with readXStringSet..? I know dealing with such a high number of files in one chunk is probably an edge case, so I can understand if this is not something you wish to change the code for... with best wishes Thomas Lin Pedersen
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Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319