fanc uses subcommands to run all of its analyses. The
fanc command itself can
be used to get an overview of available subcommands, to print the current FAN-C version,
or to set logging and notification parameters that affect all subcommands.
usage: fanc <command> [options] -- Matrix generation -- auto Automatically process an entire Hi-C data set map Map reads in a FASTQ file to a reference genome pairs Process and filter read pairs hic Process, filter, and correct Hic files -- Matrix analysis -- cis-trans Calculate cis/trans ratio of this Hi-C object expected Calculate Hi-C expected values (distance decay) pca Do a PCA on multiple Hi-C objects compartments Calculate AB compartment matrix insulation Calculate insulation scores for Hic object directionality Calculate directionality index for Hic object boundaries Determine domain boundaries compare Create pairwise comparisons of Hi-C comparison maps loops Call loops in a Hic object using FAN-C implementation of HICCUPS aggregate Make aggregate plots with FAN-C -- Other helpers -- fragments In-silico genome digestion sort-sam Convenience function to sort a SAM file by name from-juicer Import a Hi-C object from juicer (Aiden lab) from-txt Import a Hi-C object from a sparse matrix txt format from-cooler Convert a Cooler ( to-cooler Convert a Hic file into cooler format to-juicer Convert a ReadPairs file to Juicer dump Dump Hic file to txt file(s) overlap-peaks Overlap peaks from multiple samples subset Create a new Hic object by subsetting stats Get statistics on number of reads used at each step of a pipeline write-config Write default config file to specified location downsample Downsample contacts from a Hic object upgrade Upgrade objects from old FAN-C versions
|command||Subcommand to run|
|-V, --version||Print version information|
|--verbose, -v||Set verbosity level: Can be chained like “-vvv” to increase verbosity. Default is to show errors, warnings, and info messages (same as “-vv”). “-v” shows only errors and warnings, “-vvv” shows errors, warnings, info, and debug messages.|
|-s, --silent||Do not print log messages to command line.|
|-l, --log-file||Path to file in which to save log.|
|-m, --email||Email address for fanc command summary.|
|--smtp-server||SMTP server in the form smtp.server.com[:port].|
|SMTP sender email address.|
You can set the verbosity level of any
fanc subcommand with the
-v option. Use
more or less v’s for more or less logging output. The default is
corresponds to error, warning, and info messages.
-vvv also displays debug messages,
which might be helpful to identify issues with an analysis.
-v only displays error
and warning messages. To disable logging completely, use the
By default, logging output is sent to
stderr. You can redirect log messages to a file
-l <file name>.
Sometimes it is convenient to be notified by email if a
fanc command finishes,
especially for long-running commands such as
fanc pairs or
fanc map. You can
fanc to send an email when a command finished using
-m <email address>.
You must also specify the SMTP server settings using the options
--smtp-<server|username|password|sender-address>, or you can pre-configure these using
the FAN-C config files.
Many of the more computationally intensive FAN-C commands support the
argument. This instructs the command to copy all input files to a temporary directory
before processing. Similarly, output files will intitially generated in the temporary
directory and only copied to their intended output locations once the command completes.
This can be very effective when your data is located, for example, on a network file
system or a slow external HDD, while your local machine or computing node has access
to a fast SSD. Using
-tmp, and assuming the local machine’s default temporary
directory resides on an SSD, files are copied from their original location to the SSD
at the start of the command, thus avoiding the slow file system access throughout the
remainder of the processing steps.
You can change the default temporary directory by setting the
variable on your local system to a folder of your choice.
FAN-C config files¶
FAN-C supports configuration files, which can be located (in descending order of priority)
- in the current directory, named
- in a path specified by the Unix environment variable
- in the user’s home folder (named
- in the
.configfolder in a user’s home directory, called
Settings made in one config file are overridden by settings in a file with higher priority.
You can write the default config file to a location of your choice using
usage: fanc write-config [-h] [-f] [config_file]
|config_file||Output file for default configuration.|
|-f, --force||Force overwrite of existing config file.|
An explanation of the different settings can be found as comments in the default config file. The file is written in YAML
NumExpr ThreadPool configuration¶
FAN-C uses PyTables for fast querying of most of its storage classes. Condition-based queries in PyTables, which are used, for example, to find regions and pixels in certain matrix subsets, rely on the NumExpr package. NumExpr can be multi-threaded, and FAN-C uses the default NumExpr ThreadPool configuration (typically 8 threads). There is generally no need to change this preset, but if you want to optimise every single aspect of your pipeline, you may want to take a look at this NumExpr help page .