msaexplorer 0.3__py3-none-any.whl

msaexplorer/__init__.py

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+r"""
+# What is MSAexplorer?
+
+MSAexplorer allows the analysis and straight forward plotting of multiple sequence alignments.
+Its focus is to act as a simple python3 extension or shiny app with minimal dependencies and syntax. It's easy
+to set up and highly customizable.
+
+# Usage as a shiny application
+
+The current version of the app is deployed to [GitHub pages](https://jonas-fuchs.github.io/MSAexplorer/app/). This application is serverless, and all
+computation runs through your browser. There is no need to install anything. Enjoy the app!
+
+However, you can also deploy it yourself and host it however you like!
+
+```bash
+git clone https://github.com/jonas-fuchs/MSAexplorer
+cd MSAexplorer
+pip install -r requirements.txt  # installs all dependencies
+shiny run app.py
+```
+
+Now just follow the link provided in your terminal.
+
+
+# Usage as a python3 package
+
+## Installation
+
+Some simple steps are needed at the moment but in the future you will be able to install MSAexplorer via `pip install msaexplorer`.
+
+```bash
+git clone https://github.com/jonas-fuchs/MSAexplorer
+cd MSAexplorer
+pip install .
+```
+
+Now you are able to use MSAexplorer like any package that you would install via `pip`.
+
+## Analysis
+
+The `explore` module lets you load an alignment file and analyze it.
+
+```python
+'''
+a small example on how to use the MSAexplorer package
+'''
+
+from msaexplorer import explore
+
+# load MSA
+msa = explore.MSA('example_alignments/DNA.fasta')
+annotation = explore.Annotation(msa, 'example_alignments/DNA_RNA.gff3')
+
+# you can set the zoom range and the reference id if needed
+msa.zoom = (0, 1500)
+msa.reference_id = 'your_ref_id'
+
+# access functions on what to compute on the MSA
+msa.calc_pairwise_identity_matrix()
+```
+
+Importantly, multiple sequence alignments should have the format:
+
+```
+>Seq1
+ATCGATCGATCGATCG
+>Seq2
+ATCGATCGATCGATCG
+>Seq3
+ATCGATCGATCGATCG
+```
+
+Additionally, you can also read in an annotation in `bed`, `gff3` or `gb` format and connect them to the MSA. Importantly,
+the sequence identifier has to be part of the alignment. All genomic locations are then automatically adapted to the
+alignment.
+
+## Plotting
+
+The plotting `draw` module has several predefined functions to draw alignments.
+
+```python
+'''
+an example demonstrating how to plot multiple sequence alignments
+'''
+# import all packages
+import matplotlib.pyplot as plt
+from msaexplorer import explore
+from msaexplorer import draw
+
+#  load alignment
+aln = explore.MSA("example_alignments/DNA.fasta", reference_id=None, zoom_range=None)
+# set reference to e.g. the first sequence
+aln.reference_id = list(aln.alignment.keys())[0]
+
+fig, ax = plt.subplots(nrows=2, height_ratios=[0.2, 2], sharex=False)
+
+draw.stat_plot(
+    aln,
+    ax[0],
+    stat_type="entropy",
+    rolling_average=1,
+    line_color="indigo"
+)
+
+draw.identity_alignment(
+    aln,
+    ax[1],
+    show_gaps=False,
+    show_mask=True,
+    show_mismatches=True,
+    reference_color='lightsteelblue',
+    color_scheme='purine_pyrimidine',
+    show_seq_names=False,
+    show_ambiguities=True,
+    fancy_gaps=True,
+    show_x_label=False,
+    show_legend=True,
+    bbox_to_anchor=(1,1.05)
+)
+
+plt.show()
+```
+"""
+
+import importlib.metadata, pathlib, tomllib
+
+# get __version__ from pyproject.toml
+source_location = pathlib.Path("__file__").parent
+if (source_location.parent / "pyproject.toml").exists():
+    with open(source_location.parent / "pyproject.toml", "rb") as f:
+        __version__ = tomllib.load(f)['project']['version']
+else:
+    __version__ = importlib.metadata.version("msaexplorer")