From ce8238452702e68a86181dbbb82e04b4f738a741 Mon Sep 17 00:00:00 2001 From: Shunsuke-1994 Date: Mon, 25 Dec 2023 00:54:23 +0900 Subject: [PATCH] add shape scores --- molcloud/main.py | 5 +- molcloud/rna.py | 30 +- tests/test_shape.fa | 800 ++++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 827 insertions(+), 8 deletions(-) create mode 100644 tests/test_shape.fa diff --git a/molcloud/main.py b/molcloud/main.py index a336eee..4441f77 100644 --- a/molcloud/main.py +++ b/molcloud/main.py @@ -28,6 +28,8 @@ def smiles(smiles_file, output_file, width, background_color, node_size, quiet, @click.argument("fasta-file", type=click.Path(exists=True)) @click.option("--output-file", default="rnacloud.png", type=click.Path(exists=False), help="Path to the output file") @click.option("--width", type=int, default=10, help="Width of the output image") +@click.option("--use-shape", is_flag=True, default=False, help="Use shape information from the fasta file") +@click.option("--cmap", type=str, default="Reds", help="Color map for the shape information") @click.option("--background-color", default="#f5f4e9", help="Background color of the output image") @click.option("--node-size", type=int, default=10, help="Size of the nodes") @click.option("--quiet", is_flag=True, default=False, help="Don't show progress") @@ -44,6 +46,7 @@ def rna(fasta_file, output_file, width, background_color, node_size, quiet): else: fasta_text += line plt.figure(figsize=(width, width)) - plot_rnacloud(fasta_texts, background_color=background_color, + plot_rnacloud(fasta_texts, use_shape=use_shape, cmap=cmap, + background_color=background_color, node_size=node_size, quiet=quiet) plt.savefig(output_file) diff --git a/molcloud/rna.py b/molcloud/rna.py index 424f384..1c40024 100644 --- a/molcloud/rna.py +++ b/molcloud/rna.py @@ -1,4 +1,5 @@ import forgi.graph.bulge_graph as fgb +import matplotlib.pyplot as plt from .lib import * _rna_colors = { @@ -12,8 +13,18 @@ "hydrogen": "#999999" } +unknown_color = "#AAAAAA" + + +def scale(colors): + return (colors - colors.min())/(colors.max() - colors.min()) + +def _fasta_text2graph(fasta_text, use_shape): + if use_shape: + seq, ss, nucleotide_colors = fasta_text.strip().split("\n") + fasta_text = "\n".join([seq, ss]) + nucleotide_colors = scale(np.array(list(map(float, nucleotide_colors.split(","))))) -def _fasta_text2graph(fasta_text): bg = fgb.BulgeGraph.from_fasta_text(fasta_text)[0] G = nx.Graph() residues = [] @@ -21,7 +32,11 @@ def _fasta_text2graph(fasta_text): prev = None for r in bg.define_residue_num_iterator(d): - G.add_node(r, nucleotide=str(bg._seq)[r-1]) + if use_shape: + # print(r, str(bg._seq)[r-1], nucleotide_colors[r-1]) + G.add_node(r, nucleotide=str(bg._seq)[r-1], index = r-1, color_scale=nucleotide_colors[r-1]) + else: + G.add_node(r, nucleotide=str(bg._seq)[r-1], index = r-1) residues += [r] # Add links along the backbone @@ -40,11 +55,12 @@ def _fasta_text2graph(fasta_text): return G -def _colors(G): +def _colors(G, use_shape, cmap): + if use_shape: cmap = plt.get_cmap(cmap) node_colors = [] for n, d in G.nodes(data=True): try: - c = _rna_colors[d["nucleotide"]] + c = cmap(d["color_scale"]) if use_shape else _rna_colors[d["nucleotide"]] except KeyError as e: c = unknown_color node_colors.append(c) @@ -59,16 +75,16 @@ def _colors(G): return node_colors, edge_colors -def plot_rnacloud(fasta_texts, background_color=background_color, node_size=10, quiet=False): +def plot_rnacloud(fasta_texts, use_shape, cmap, background_color=background_color, node_size=10, quiet=False): G = None for fasta_text in tqdm.tqdm(fasta_texts, disable=quiet): - g = _fasta_text2graph(fasta_text) + g = _fasta_text2graph(fasta_text, use_shape) if g is None: continue if G is None: G = g else: G = nx.disjoint_union(g, G) - node_colors, edge_colors = _colors(G) + node_colors, edge_colors = _colors(G, use_shape, cmap) plot_graphs(G, node_colors, edge_colors, background_color, node_size) diff --git a/tests/test_shape.fa b/tests/test_shape.fa new file mode 100644 index 0000000..d559373 --- /dev/null +++ b/tests/test_shape.fa @@ -0,0 +1,800 @@ +>seq_0 +UUCCAGCACCUGAUGUUCGAAUUUAAAUCGGCUCAACGAG +(((.((((.....)))).)))......(((......))). +0.38,0.43,0.43,1.14,0.13,0.36,0.05,0.35,1.89,1.05,1.40,1.73,1.90,0.49,0.16,0.34,0.28,1.24,0.19,0.49,0.22,1.42,1.41,1.88,0.77,1.58,0.98,0.50,0.48,0.03,0.54,1.69,1.62,1.35,1.04,1.48,0.09,0.14,0.19,1.96 +>seq_1 +CCUAGGCCGCUCGUCACGAUUUCCACGUCCGCGGCAUUAG +.(((((((((.(((..........)))...))))).)))) +1.95,0.15,0.13,0.35,0.24,0.33,0.32,0.25,0.29,0.49,0.95,0.06,0.03,0.44,1.84,0.58,1.85,1.53,1.84,1.65,1.86,0.99,0.63,1.83,0.22,0.38,0.07,0.73,0.77,0.59,0.12,0.04,0.25,0.01,0.39,0.89,0.25,0.26,0.23,0.13 +>seq_2 +AGCGACCUUGGUCUAACCUGAUGAUCUCCUGCGAGGAUUU +.....((((((((......))).........))))).... 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