CLI Reference¶
For an up-to-date list of subcommands and CLI options refer to stripepy --help.
Subcommands¶
usage: stripepy {call,download,plot,view} ...
stripepy is designed to recognize linear patterns in contact maps (.hic, .mcool, .cool) through the geometric reasoning, including topological persistence and quasi-interpolation.
options:
-h, --help show this help message and exit
--license Print StripePy's license and return.
--cite Print StripePy's reference and return.
-v, --version show program's version number and exit
subcommands:
{call,download,plot,view}
List of available subcommands:
call stripepy works in four consecutive steps:
• Step 1: Pre-processing
• Step 2: Recognition of loci of interest (also called 'seeds')
• Step 3: Shape analysis (i.e., width and height estimation)
• Step 4: Signal analysis
download Helper command to simplify downloading datasets that can be used to test StripePy.
plot Generate various static plots useful to visually inspect the output produced by stripepy call.
view Fetch stripes from the HDF5 file produced by stripepy call.
stripepy call¶
usage: stripepy call [-h] [-n NORMALIZATION] [-b GENOMIC_BELT]
[--roi {middle,start}] [-o OUTPUT_FILE]
[--log-file LOG_FILE] [--plot-dir PLOT_DIR]
[--max-width MAX_WIDTH] [--glob-pers-min GLOB_PERS_MIN]
[-k K] [--loc-pers-min LOC_PERS_MIN]
[--loc-trend-min LOC_TREND_MIN] [-f]
[--verbosity {debug,info,warning,error,critical}]
[-p NPROC] [--min-chrom-size MIN_CHROM_SIZE]
contact-map resolution
positional arguments:
contact-map Path to a .cool, .mcool, or .hic file for input.
resolution Resolution (in bp).
options:
-h, --help show this help message and exit
-n, --normalization NORMALIZATION
Normalization to fetch (default: None).
-b, --genomic-belt GENOMIC_BELT
Radius of the band, centred around the diagonal, where the search is restricted to (in bp, default: 5000000).
--roi {middle,start} Criterion used to select a region from each chromosome used to generate diagnostic plots (default: None).
Requires --plot-dir.
-o, --output-file OUTPUT_FILE
Path where to store the output HDF5 file.
When not specified, the output file will be saved in the current working directory with a named based on the name of input matrix file.
--log-file LOG_FILE Path where to store the log file.
--plot-dir PLOT_DIR Path where to store the output plots.
Required when --roi is specified and ignored otherwise.
If the specified folder does not already exist, it will be created.
--max-width MAX_WIDTH
Maximum stripe width, in bp (default: 100000).
--glob-pers-min GLOB_PERS_MIN
Threshold value between 0 and 1 to filter persistence maxima points and identify loci of interest, aka seeds (default: 0.04).
-k, --k-neighbour K k for the k-neighbour, i.e., number of bins adjacent to the stripe boundaries on both sides (default: 3).
--loc-pers-min LOC_PERS_MIN
Threshold value between 0 and 1 to find peaks in signal in a horizontal domain while estimating the height of a stripe (default: 0.33).
--loc-trend-min LOC_TREND_MIN
Threshold value between 0 and 1 to estimate the height of a stripe (default: 0.25); the higher this value, the shorter the stripe; it is used to avoid overly long stripes when no persistent maximum besides the global one is found.
-f, --force Overwrite existing file(s) (default: False).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).
-p, --nproc NPROC Maximum number of parallel processes to use (default: 1).
--min-chrom-size MIN_CHROM_SIZE
Minimum size, in bp, for a chromosome to be analysed (default: 2000000).
stripepy download¶
usage: stripepy download [-h] [--assembly {hg38,mm10} | --name NAME |
--list-only] [--unit-test | --end2end-test]
[--include-private] [--max-size MAX_SIZE]
[-o OUTPUT_PATH] [-f]
[--verbosity {debug,info,warning,error,critical}]
options:
-h, --help show this help message and exit
--assembly {hg38,mm10}
Restrict downloads to the given reference genome assembly.
--name NAME Name of the dataset to be downloaded.
When not provided, randomly select and download a dataset based on the provided CLI options (if any).
--list-only Print the list of available datasets and return (default: False).
--unit-test Download the test datasets required by the unit tests.
Files will be stored under folder test/data/
When specified, all other options are ignored.
Existing files will be overwritten.
--end2end-test Download the test datasets required by the end2end tests.
Files will be stored under folder test/data/
When specified, all other options are ignored.
Existing files will be overwritten.
--include-private Include datasets used for internal testing (default: False).
--max-size MAX_SIZE Upper bound for the size of the files to be considered when --name is not provided (default: 512.0).
-o, --output OUTPUT_PATH
Path where to store the downloaded file (default: None).
-f, --force Overwrite existing file(s) (default: False).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).
stripepy plot¶
usage: stripepy plot [-h]
{contact-map,cm,pseudodistribution,pd,stripe-hist,hist} ...
options:
-h, --help show this help message and exit
plot_subcommands:
{contact-map,cm,pseudodistribution,pd,stripe-hist,hist}
List of available subcommands:
contact-map (cm) Plot stripes and other features over the Hi-C matrix.
pseudodistribution (pd)
Plot the pseudo-distribution over the given region of interest.
stripe-hist (hist) Generate and plot the histograms showing the distribution of the stripe heights and widths.
stripepy plot contact-map¶
usage: stripepy plot contact-map [-h] [--stripepy-hdf5 STRIPEPY_HDF5]
[--relative-change-threshold RELATIVE_CHANGE_THRESHOLD]
[--coefficient-of-variation-threshold COEFFICIENT_OF_VARIATION_THRESHOLD]
[--highlight-seeds | --highlight-stripes]
[--ignore-stripe-heights] [--cmap CMAP]
[--linear-scale | --log-scale]
[--region REGION] [--dpi DPI] [--seed SEED]
[-n NORMALIZATION] [-f]
[--verbosity {debug,info,warning,error,critical}]
contact-map resolution output-name
positional arguments:
contact-map Path to the .cool, .mcool, or .hic file used to call stripes.
resolution Resolution (in bp).
output-name Path where to store the generated plot.
options:
-h, --help show this help message and exit
--stripepy-hdf5 STRIPEPY_HDF5
Path to the .hdf5 generated by stripepy call.
Required when highlighting stripes or seeds.
--relative-change-threshold RELATIVE_CHANGE_THRESHOLD
Cutoff for the relative change (default: None).
Only used when highlighting architectural stripes.
The relative change is computed as the ratio between the average number of interactions found inside a stripe and the number of interactions in a neighborhood outside of the stripe.
--coefficient-of-variation-threshold COEFFICIENT_OF_VARIATION_THRESHOLD
Cutoff for the coefficient of variation (default: None).
Only used when highlighting architectural stripes.
The coefficient of variation is computed as the ratio between the standard deviation and the mean
of the values inside a stripe. In our case, it is always nonnegative because of the preprocessing step.
--highlight-seeds Highlight the stripe seeds (default: False).
--highlight-stripes Highlight the architectural stripes (default: False).
--ignore-stripe-heights
Ignore the stripes height (default: False).
Has no effect when --highlight-stripes is not specified.
--cmap CMAP Color map used to plot Hi-C interactions (default: fruit_punch).
Can be any of the color maps supported by matplotlib as well as: fall, fruit_punch, blues, acidblues, and nmeth.
--linear-scale Plot interactions in linear scale (default: False).
--log-scale Plot interactions in log scale (default: True).
--region REGION Genomic region to be plotted (UCSC format). When not specified, a random 2.5Mb region is plotted.
--dpi DPI DPI of the generated plot (default: 300; ignored when the output format is a vector graphic).
--seed SEED Seed for random number generation (default: 7606490399616306585).
-n, --normalization NORMALIZATION
Normalization to fetch (default: None).
-f, --force Overwrite existing file(s) (default: False).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).
stripepy plot pseudodistribution¶
usage: stripepy plot pseudodistribution [-h] [--region REGION] [--dpi DPI]
[--seed SEED] [-n NORMALIZATION] [-f]
[--verbosity {debug,info,warning,error,critical}]
stripepy-hdf5 output-name
positional arguments:
stripepy-hdf5 Path to the .hdf5 generated by stripepy call.
output-name Path where to store the generated plot.
options:
-h, --help show this help message and exit
--region REGION Genomic region to be plotted (UCSC format). When not specified, a random 2.5Mb region is plotted.
--dpi DPI DPI of the generated plot (default: 300; ignored when the output format is a vector graphic).
--seed SEED Seed for random number generation (default: 7606490399616306585).
-n, --normalization NORMALIZATION
Normalization to fetch (default: None).
-f, --force Overwrite existing file(s) (default: False).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).
stripepy plot stripe-hist¶
usage: stripepy plot stripe-hist [-h] [--region REGION] [--dpi DPI]
[--seed SEED] [-n NORMALIZATION] [-f]
[--verbosity {debug,info,warning,error,critical}]
stripepy-hdf5 output-name
positional arguments:
stripepy-hdf5 Path to the .hdf5 generated by stripepy call.
output-name Path where to store the generated plot.
options:
-h, --help show this help message and exit
--region REGION Genomic region to be plotted (UCSC format). When not specified, data for the entire genome is plotted.
--dpi DPI DPI of the generated plot (default: 300; ignored when the output format is a vector graphic).
--seed SEED Seed for random number generation (default: 7606490399616306585).
-n, --normalization NORMALIZATION
Normalization to fetch (default: None).
-f, --force Overwrite existing file(s) (default: False).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).
stripepy view¶
usage: stripepy view [-h]
[--relative-change-threshold RELATIVE_CHANGE_THRESHOLD]
[--coefficient-of-variation-threshold COEFFICIENT_OF_VARIATION_THRESHOLD]
[--with-biodescriptors] [--with-header]
[--transform {None,transpose_to_lt,transpose_to_ut}]
[--verbosity {debug,info,warning,error,critical}]
h5-file
positional arguments:
h5-file Path to the HDF5 file generated by stripepy call.
options:
-h, --help show this help message and exit
--relative-change-threshold RELATIVE_CHANGE_THRESHOLD
Cutoff for the relative change (default: 5.0).
The relative change is computed as the ratio between the average number of interactions
found inside a stripe and the number of interactions in a neighborhood outside of the stripe.
--coefficient-of-variation-threshold COEFFICIENT_OF_VARIATION_THRESHOLD
Cutoff for the coefficient of variation (default: None).
The coefficient of variation is computed as the ratio between the standard deviation and the mean
of the values inside a stripe. In our case, it is always nonnegative because of the preprocessing step.
--with-biodescriptors
Include the stripe biodescriptors in the output.
--with-header Include column names in the output.
--transform {None,transpose_to_lt,transpose_to_ut}
Control if and how stripe coordinates should be transformed (default: None).
--verbosity {debug,info,warning,error,critical}
Set verbosity of output to the console (default: info).