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microbio_me_qiime(zipftp, ext = ".zip", parsef = parse_taxonomy_greengenes,
...)
integer
or other single-length vector
that can be coerce
d to an integer;
this function will complete the remainder of the ftp URL hosted at
"ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_494_split_library_seqs_and_mapping.zip"
,
you could simply provide 494
or "494"
as the first (`zipftp`) argument.character
string of the expected
file extension, which also indicates the compression type,
if zipftp
is a study number instead of the full path.
Note that this argument has no effect if zipftp
is the full path,
in which case the file extension is read directly from the downloaded file..biom
file, if present.
This is passed on to import_biom
, but unlike that function
the default parsing function is parse_taxonomy_greengenes
,
rather than parse_taxonomy_default
, because we know
ahead of time that most (or all?) of the taxonomic classifications
in the microbio.me/qiime
repository will be based on
GreenGenes.download.file
. This is mainly for non-standard links to
resources (in this case, a zipped file) that are not being hosted by
phyloseq-class
object if possible, a component if only a
component could be imported, or NULL
if nothing could be imported
after unzipping the file. Keep in mind there is a specific naming-convention
that is expected based on the current state of the
cat
ted to standard out
to help let you know the ongoing status of the current
download and import process.download.file
and url
for details about URL formats --
including local file addresses -- that might work here.
import_biom
import_qiime
# This should return TRUE on your system if you have internet turned on
# and a standard R installation. Indicates whether this is likely to
# work on your system for a URL or local file, respectively.
capabilities("http/ftp"); capabilities("fifo")
# A working example with a local example file included in phyloseq
zipfile = "study_816_split_library_seqs_and_mapping.zip"
zipfile = system.file("extdata", zipfile, package="phyloseq")
tarfile = "study_816_split_library_seqs_and_mapping.tar.gz"
tarfile = system.file("extdata", tarfile, package="phyloseq")
tarps = microbio_me_qiime(tarfile)
zipps = microbio_me_qiime(zipfile)
identical(tarps, zipps)
tarps; zipps
plot_heatmap(tarps)
# An example that used to work, before the QIIME-DB server was turned off by its host.
# # Smokers dataset
# smokezip = "ftp://thebeast.colorado.edu/pub/QIIME_DB_Public_Studies/study_524_split_library_seqs_and_mapping.zip"
# smokers1 = microbio_me_qiime(smokezip)
# # Alternatively, just use the study number
# smokers2 = microbio_me_qiime(524)
# identical(smokers1, smokers2)
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