CNSistent/example_CLI.sh at main · ICCB-Cologne/CNSistent · GitHub

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#/usr/bin/env bash

# %%
# Version and help
cns -v
cns -h
cns align -h
set -x

mkdir -p ./tests/out

# %%
# Align in gaps in the CNS data
cns align ./tests/in/test_cns_double.tsv --samples ./tests/in/test_samples.tsv --out ./tests/out/test_cns_align.tsv --verbose

# %%
# Infer the aligned regions in the CNS data
cns infer ./tests/out/test_cns_align.tsv --out ./tests/out/test_cns_imp.tsv --verbose

# %%
# Impute the CNS data
cns impute ./tests/in/test_cns_single.tsv --out ./tests/out/test_cns_single_imp.tsv --verbose

# %%
# Calculate portion of the aligned regions in the CNS data
cns coverage ./tests/out/test_cns_align.tsv --out ./tests/out/test_sample_cover.tsv --verbose
cns coverage ./tests/in/test_cns_single.tsv --out ./tests/out/test_sample_single.tsv --verbose

# %%
# Calculate the aneuploidy of the aligned-in CNS data
cns ploidy ./tests/out/test_cns_imp.tsv --samples ./tests/in/test_samples.tsv --out ./tests/out/test_sample_ploidy.tsv --verbose
cns ploidy ./tests/out/test_cns_single_imp.tsv --samples ./tests/out/test_sample_single.tsv --out ./tests/out/test_sample_single.tsv --verbose

# Calculate the aneuploidy of the aligned-in CNS data
cns breakage ./tests/out/test_cns_imp.tsv --samples ./tests/in/test_samples.tsv --out ./tests/out/test_sample_breakage.tsv --verbose
cns breakage ./tests/out/test_cns_single_imp.tsv --samples ./tests/out/test_sample_single.tsv --out ./tests/out/test_sample_single.tsv --verbose

# %%
# Try different segmentations
segment ./tests/out/test_cns_align.tsv --merge 100000 --out ./tests/out/mcs_regions.bed --verbose
segment arms --out ./tests/out/test_segs_arms.bed --verbose
segment bands --out ./tests/out/test_segs_bands.bed --verbose
segment ./tests/out/test_cns_align.tsv --split 1000000 --out ./tests/out/test_segs_1MB.bed --verbose
segment ./tests/out/test_cns_align.tsv --split 1000000 --out ./tests/out/test_segs_1MB_gaps.bed --remove gaps --filter 500000 --verbose
segment arms --out ./tests/out/test_segs_arms_gaps.bed --remove gaps --filter 100000
segment ./data/COSMIC_consensus_genes.bed --out ./tests/out/test_COSMIC_gaps.bed --remove gaps --filter 100000

# %%
# Calculate consisten segmentation
cns aggregate ./tests/out/test_cns_align.tsv --segments ./tests/out/test_segs_1MB.bed --out ./tests/out/test_cns_1MB.tsv --verbose
# Calculate gene selection
cns aggregate ./tests/out/test_cns_imp.tsv --segments ./tests/out/test_COSMIC_gaps.bed --out ./tests/out/test_cns_COSMIC.tsv --verbose --how min
# Calculate single-column segmentation
cns aggregate ./tests/in/test_cns_single.tsv --segments ./tests/out/test_segs_arms_gaps.bed --out ./tests/out/test_cns_arms.tsv --verbose