Conda
See the ‘activating the conda environment’ section below to access this
software.
plotsr-0.5.4
Plotsr generates high-quality visualisation of synteny and structural
rearrangements between multiple genomes. For this, it uses the genomic
structural annotations between multiple chromosome-level assemblies.
See the readme for examples and
to get example data.
syri
syri is included in the conda
environment so that the alignmetns can be done.
Activating the conda environment
Check out a node with qrsh and run:
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bash
source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
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And then run your commands as usual. To use over SGE, include the source line
above in a shell script prior to your commands, e.g.
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$ cat run_plotsr.sh
#!/usr/bin/env bash
source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
plotsr ...
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And then run SGE_Batch -c 'bash ./run_plotsr.sh' -r sge.plotsr ....
Making activation easier
If you have had conda set up for a while, e.g. using the instructions in this
post, then you can
run (only necessary once):
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bash
conda config --append envs_dirs /local/cluster/conda-envs/envs
conda config --append pkgs_dirs /local/cluster/conda-envs/pkgs
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and then you can activate the env using conda activate plotsr-0.5.4.
Location and version
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$ source /local/cluster/conda-envs/envs/plotsr-0.5.4/activate.sh
$ which plotsr
/local/cluster/conda-envs/envs/plotsr-0.5.4/bin/plotsr
$ plotsr --version
0.5.4
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help message
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$ plotsr --help
usage: Plotting structural rearrangements between genomes [-h] [--sr SR]
[--bp BP] --genomes
GENOMES
[--markers MARKERS]
[--tracks TRACKS]
[--chrord CHRORD]
[--chrname CHRNAME]
[-o O] [--itx]
[--chr CHR]
[--reg REG] [--rtr]
[--nosyn] [--noinv]
[--notr] [--nodup]
[-s S] [--cfg CFG]
[-R] [-f F] [-H H]
[-W W] [-S S] [-d D]
[-b {agg,cairo,pdf,pgf,ps,svg,template}]
[-v]
[--log {DEBUG,INFO,WARN}]
[--version]
Input/Output files:
--sr SR Structural annotation mappings (syri.out) identified by
SyRI (default: None)
--bp BP Structural annotation mappings in BEDPE format
(default: None)
--genomes GENOMES File containing path to genomes (default: None)
--markers MARKERS File containing path to markers (bed format) (default:
None)
--tracks TRACKS File listing paths and details for all tracks to be
plotted (default: None)
--chrord CHRORD File containing reference (first genome) chromosome IDs
in the order in which they are to be plotted. File
requires one chromosome ID per line. Not compatible
with --chr (default: None)
--chrname CHRNAME File containing reference (first genome) chromosome
names to be used in the plot. File needs to be a TSV
with the chromosome ID in first column and chromosome
name in the second. (default: None)
-o O Output file name. Acceptable format: pdf, png, svg
(default: plotsr.pdf)
Data filtering:
--itx Use inter-chromosomal plotting mode (experimental)
(default: False)
--chr CHR Select specific chromosome on reference (first genome)
and plots them in the given order. Not compatible with
--chrord. Can be used multiple time to select more than
one chromosomes. (default: None)
--reg REG Plots a specific region. Use as:
GenomeID:ChromosomeID:Start-End. Not compatible with
--chr and -R. (default: None)
--rtr When using --reg, plot all SRs that are within the
boundaries of the homologous regions. For highly zoomed
regions, this could result in visually disconnected
alignments. (default: False)
--nosyn Do not plot syntenic regions (default: False)
--noinv Do not plot inversions (default: False)
--notr Do not plot translocations regions (default: False)
--nodup Do not plot duplications regions (default: False)
-s S minimum size of a SR to be plotted (default: 10000)
Plot adjustment:
--cfg CFG Path to config file containing parameters to adjust
plot. (default: None)
-R Join adjacent syntenic blocks if they are not
interrupted by SRs. Using this would decrease gaps in
the visualisation. (default: False)
-f F font size (default: 6)
-H H height of the plot (default: None)
-W W width of the plot (default: None)
-S S Space for homologous chromosome (0.1-0.75). Adjust this
to make more space for annotation markers/texts and
tracks. (default: 0.7)
-d D DPI for the final image (default: 300)
-b {agg,cairo,pdf,pgf,ps,svg,template}
Matplotlib backend to use (default: agg)
-v Plot vertical chromosome (default: False)
optional arguments:
-h, --help show this help message and exit
--log {DEBUG,INFO,WARN}
Log-level (default: WARN)
--version show program's version number and exit
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software ref: https://github.com/schneebergerlab/plotsr
software ref: https://github.com/schneebergerlab/syri
research ref: https://doi.org/10.1093/bioinformatics/btac196