offtracker 2.10.5__zip → 2.10.6__zip
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {offtracker-2.10.5/offtracker.egg-info → offtracker-2.10.6}/PKG-INFO +1 -1
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/_version.py +2 -2
- {offtracker-2.10.5 → offtracker-2.10.6/offtracker.egg-info}/PKG-INFO +1 -1
- {offtracker-2.10.5 → offtracker-2.10.6}/scripts/offtracker_analysis.py +1 -1
- {offtracker-2.10.5 → offtracker-2.10.6}/scripts/offtracker_plot.py +2 -2
- {offtracker-2.10.5 → offtracker-2.10.6}/LICENSE.txt +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/MANIFEST.in +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/README.md +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/X_offplot.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/X_offtracker.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/X_sequence.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/__init__.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/snakefile/Snakefile_QC.smk +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/snakefile/Snakefile_offtracker.smk +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/1.1_bed2fr.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/1.3_bdg_normalize_v4.0.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/bedGraphToBigWig +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/hg38.chrom.sizes +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/mm10.chrom.sizes +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/offtracker_blacklist_hg38.merged.bed +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/offtracker_blacklist_mm10.merged.bed +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker.egg-info/SOURCES.txt +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker.egg-info/dependency_links.txt +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker.egg-info/requires.txt +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/offtracker.egg-info/top_level.txt +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/scripts/offtracker_candidates.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/scripts/offtracker_config.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/scripts/offtracker_qc.py +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/setup.cfg +0 -0
- {offtracker-2.10.5 → offtracker-2.10.6}/setup.py +0 -0
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@@ -1,4 +1,4 @@
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__version__ = "2.10.
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__version__ = "2.10.6"
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# 2023.08.11. v1.1.0 adding a option for not normalizing the bw file
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# 2023.10.26. v1.9.0 prerelease for v2.0
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# 2023.10.27. v2.0.0 大更新，还没微调
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@@ -33,4 +33,4 @@ __version__ = "2.10.5"
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# 2025.04.25. v2.8.0 修复了 offtracker candidates 会把小写序列转换成 N 的 bug
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# 2025.05.22. v2.9.0 翻新部分代码结构
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# 2025.06.05. v2.10.0 增加了QC模块。保留了负数score的记录，并在plot时显示为红字。增加了 "--ignore_chr" 用于跳过common chr过滤。
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# 2025.06.17. v2.10.
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# 2025.06.17. v2.10.6 修复翻新代码结构导致的bug
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@@ -27,7 +27,7 @@ def main():
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parser.add_argument('--exp' , type=str, default='all', nargs='+', help='A substring mark in the name of experimental samples. The default is to use all samples other than control' )
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parser.add_argument('--control' , type=str, default='none', nargs='+', help='A substring mark in the name of control samples. The default is no control. "others" for all samples other than --exp.' )
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parser.add_argument('--fdr' , type=int, default=0.01, help='FDR threshold for the final result. Default is 0.01.')
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parser.add_argument('--score' , type=int, default=
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parser.add_argument('--score' , type=int, default=1.9, help='Track score threshold for the final result. Default is 1.9.')
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parser.add_argument('--smooth' , type=int, default=1, help='Smooth strength for the signal.')
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parser.add_argument('--window' , type=int, default=3, help='Window size for smoothing the signal.')
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parser.add_argument('--binsize' , type=int, default=100, help='Window size for smoothing the signal.')
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full_seq = gRNA + PAM
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df_result = pd.read_csv(args.result)
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n_pos = len(df_result)
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# n_pos = len(df_result)
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xoffplot.offtable(df_result, full_seq, length_pam = len(PAM), col_seq='target', threshold=2,
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title=f'{outname}
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title=f'{outname}',
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savefig=dir_savefig)
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return f'The plot is saved as {dir_savefig}'
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{offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/offtracker_blacklist_hg38.merged.bed
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{offtracker-2.10.5 → offtracker-2.10.6}/offtracker/utility/offtracker_blacklist_mm10.merged.bed
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