{"id":20083744,"url":"https://github.com/y9c/cfutils","last_synced_at":"2025-10-27T08:38:23.318Z","repository":{"id":62561560,"uuid":"133211617","full_name":"y9c/cfutils","owner":"y9c","description":"🧬 Chromatogram File Utils, a package that integrates trace visualization, mutation calling and quality control for Sanger sequencing 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Releases](https://img.shields.io/pypi/v/cfutils.svg)](https://pypi.python.org/pypi/cfutils)\n[![Downloads](https://static.pepy.tech/badge/cfutils)](https://pepy.tech/project/cfutils)\n\n**Chromatogram File Utils**\n\nFor Sanger sequencing data visualizing, alignment, mutation calling, and trimming etc.\n\n## Demo\n\n![plot chromatogram with mutation](https://raw.githubusercontent.com/y9c/cfutils/master/data/plot.png)\n\n\u003e command to generate the demo above\n\n```bash\ncfutils mut --query ./data/B5-M13R_B07.ab1 --subject ./data/ref.fa --outdir ./data/ --plot\n```\n\n## How to use?\n\n- You can have mutation detection and visualization in one step using the command line.\n\n```bash\ncfutils mut --help\n```\n\n- You can also integrate the result matplotlib figures and use it as a python module.\n\nAn example:\n\n```python\nimport matplotlib.pyplot as plt\nimport numpy as np\n\nfrom cfutils.parser import parse_abi\nfrom cfutils.show import plot_chromatograph\n\nseq = parse_abi(\"./data/B5-M13R_B07.ab1\")\npeaks = seq.annotations[\"peak positions\"][100:131]\n\nfig, axes = plt.subplots(2, 1, figsize=(12, 6), sharex=True)\nplot_chromatograph(\n    seq,\n    region=(100, 130),\n    ax=axes[0],\n    show_bases=True,\n    show_positions=True,\n    color_map=dict(zip(\"ATGC\", [\"C0\", \"C2\", \"C1\", \"C4\"])),\n)\naxes[1].bar(peaks, np.random.randn(len(peaks)), color=\"0.66\")\nplt.show()\n```\n\n![plot chromatogram in_matplotlib](https://raw.githubusercontent.com/y9c/cfutils/master/data/matplotlib_example.png)\n\n## How to install?\n\n### form pypi\n\n_(use this way ONLY, if you don't know what's going on)_\n\n```bash\npip install --user cfutils\n```\n\n### manipulate the source code\n\n- clone from github\n\n```bash\ngit clone git@github.com:y9c/cfutils.git\n```\n\n- install the dependence\n\n```bash\nmake init\n```\n\n- do unittest\n\n```bash\nmake test\n```\n\n## ChangeLog\n\n- Reverse completement the chromatogram file. (Inspired by Snapgene)\n- build as python package for pypi\n- fix bug that highlighting wrong base\n- replace blastn with buildin python aligner\n\n## TODO\n\n- [ ] call mutation by alignment and plot Chromatogram graphic\n- [ ] add a doc\n- [x] change xaxis by peak location\n- [ ] fix bug that chromatogram switch pos after trim\n- [x] wrap as a cli app\n- [ ] return quality score in output\n- [ ] fix issue that selected base is not in the middle\n- [ ] fix plot_chromatograph rendering bug\n\n- [ ] add projection feature to make align and assemble possible\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fcfutils","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fy9c%2Fcfutils","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fy9c%2Fcfutils/lists"}