From d93f7a0db56b38f6957b8faa75d3e927f9918b2c Mon Sep 17 00:00:00 2001 From: Jens Luebeck Date: Fri, 5 Jan 2024 09:47:22 -0800 Subject: [PATCH] increment version --- README.md | 17 ++++++++++------- amplicon_classifier.py | 2 +- 2 files changed, 11 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a92ba2e..1f04569 100644 --- a/README.md +++ b/README.md @@ -121,13 +121,16 @@ This two-column file reports the `sample_name` and the number of ecDNA identifie #### ****`[output_prefix]_ecDNA_context_calls.tsv`**** This two column file reports the ecDNA feature name (sample_amplicon_ecDNA_number), and a classification of the ecDNA focal amplification genome context. The possibilities for ecDNA context classification are -- Simple circular simple background: A simple cycle with minimal rearrangements in the surrounding genome. Likely not derived from chromothripsis. -- Simple circular complex background: A simple cycle however there are genomic rearrangements in the vicinity outside the ecDNA region. -- BFB-like: possibly derived from a BFB. -- Two-foldback: being flanked by two foldback-like SVs. Likely not derived from chromothripsis. -- Heavily rearranged unichromosomal: from a heavily rearranged genome on one chromosome. Possibly due to chromothripsis. -- Heavily rearranged multichromosomal: from a heavily rearranged genome involving multiple chromosomes. Possibly due to chromothripsis and chromoplexy. -- Unknown: Does not match any of the classes above. + +| Column name | Contents | +|-------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| Simple circular simple background | A simple ecDNA cycle with minimal rearrangements in the surrounding genome. Likely not derived from chromothripsis. | +| Simple circular complex background | A simple ecDNA cycle however there are genomic rearrangements in the vicinity outside the ecDNA region. | +| BFB-like | ecDNA possibly derived from a BFB. | +| Two-foldback | ecDNA being flanked by two foldback-like SVs. Likely not derived from chromothripsis, but possibly from [ODIRA](https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002016). | +| Heavily rearranged unichromosomal | ecDNA from a heavily rearranged genome on one chromosome. Possibly due to chromothripsis. | +| Heavily rearranged multichromosomal | ecDNA from a heavily rearranged genome involving multiple chromosomes. Possibly due to chromothripsis and chromoplexy. | +| Unknown | Does not match any of the classes above. | #### Amplicon bed files, annotated cycles, and SV summaries Additionally, there are three directories created by `amplicon_classifier.py`. They are diff --git a/amplicon_classifier.py b/amplicon_classifier.py index 1f99b41..89d60b6 100755 --- a/amplicon_classifier.py +++ b/amplicon_classifier.py @@ -1,6 +1,6 @@ #!/usr/bin/env python3 -__version__ = "1.1.0" +__version__ = "1.1.1" __author__ = "Jens Luebeck (jluebeck [at] ucsd.edu)" import argparse