File input and output¶
As part of the Immcantation suite of tools, the alakazam
package includes a set of
built-in functions capable of reading and writing tab-delimited database files created by
Change-O into R data.frames. However, due to
differences in how certain values and sequences are handled, alakazam::readChangeoDb
and
alakazam::writeChangeoDb
will not properly read in AIRR
formatted files. These files should instead be loaded using the functions included
in the airr
package (airr::read_rearrangement
and airr::write_rearrangement
).
You can read more about how we use both data standards here and here. Please note that the default file format for all functions in Immcantation is the AIRR-C format as of Immcantation v4.0.0, which corresponds to alakazam v1.0.0.
Reading data¶
Small example databases for both the Change-O format (ExampleDbChangeo
) and the AIRR format (ExampleDb
)
are included in the alakazam
package. For specific details about the latter, visit the
AIRR Community documentation site.
# Set the file paths from inside the package directory
# These files are smaller versions of the example databases previously mentioned
changeo_file <- system.file("extdata", "example_changeo.tab.gz", package="alakazam")
airr_file <- system.file("extdata", "example_airr.tsv.gz", package="alakazam")
# Read in the data
db_changeo <- alakazam::readChangeoDb(changeo_file)
db_airr <- airr::read_rearrangement(airr_file)
Writing data¶
# Write the data to a tab-delimited file
alakazam::writeChangeoDb(db_changeo, "changeo.tsv")
airr::write_rearrangement(db_airr, "airr.tsv")