CheckAgainstReport: Pull an assembly from the NCBI FTP site.

In npcooley/SynExtend: Tools for Comparative Genomics

Pull an assembly from the NCBI FTP site.

Description

This function is designed to work internally to functions within SynExtend so it works on relatively simple atomic vectors and has little overhead checking.

Usage

CheckAgainstReport(FTP_ADDRESS,
                   CHECK_ADDRESS,
                   RETRY = 5L)

Arguments

FTP_ADDRESS	Character; the ftp address of an ncbi assembly.
CHECK_ADDRESS	Character; the ftp address of an ncbi assembly report.
RETRY	Integer; the number of times to retry an assembly download should it not pull correctly.

Details

On occasion, readDNAStringSet fails to completely pull assemblies from the ncbi ftp site. It is not clear why, though it is infrequent but replicable at large scale. CheckAgainstReport checks the captured DNAStringSet against the reported assembly size and string widths.

Value

A DNAStringSet.

Author(s)

Nicholas Cooley [e-mail]

See Also

readDNAStringSet

Examples

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npcooley/SynExtend documentation built on June 8, 2025, 5:24 a.m.