| Next changeset 1:adf18db4c14a (2017-03-25) |
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Commit message:
planemo upload for repository https://github.com/eteriSokhoyan/galaxytools/tree/master/tools/GraphClust/Plotting commit 057c2fd398055dc86eb2c00d8a74f301d5c231d9-dirty |
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added:
MotifFinderPlot.py MotifFinderPlot.xml test-data/RESULTS.zip test-data/motif_plot.png |
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| diff -r 000000000000 -r edcf58ab7552 MotifFinderPlot.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MotifFinderPlot.py Wed Feb 22 16:53:29 2017 -0500 |
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| @@ -0,0 +1,60 @@ +#!/usr/bin/env python + +import matplotlib +matplotlib.use('Agg') +from matplotlib import pyplot as plt +import matplotlib.patches as mpatches +from collections import defaultdict +import glob +import pandas as pd +import itertools +import seaborn as sns + + +def plot_bar(ranges, colors, orig_names, cluster_nums): + fig, ax = plt.subplots() + for i, k in enumerate(sorted(ranges.keys())): + ax.broken_barh(ranges[k], (i-0.25, 0.5), facecolors=colors[k]) + + ax.set_xlim(0) + ax.set_xlabel('position in sequence') + ax.set_yticklabels(['']+[k+'-'+orig_names[k] for k in sorted(ranges.keys())]) + ax.grid(True) + fig.suptitle('Structure motif prediction\nRegions with same color are prediticted to have similar structures') + # Add the legend + patches = [mpatches.Patch(color=cluster_nums[lab], label=lab) for lab in sorted(cluster_nums)] + ax.legend(handles=patches, loc='best') # , bbox_to_anchor=(1, 0.5), loc='center left') + plt.savefig("motif_plot.png", bbox_inches='tight') + + +def parse_clusters(): + currentdir_files = sorted(list(glob.glob('*'))) + print ("currentdir_files are: ", currentdir_files) + print ("RESULTS_files are: ", sorted(list(glob.glob('RESULTS/*')))) + + cluster_files = sorted(list(glob.glob('RESULTS/*.cluster.all'))) + if len(cluster_files) == 0: + raise RuntimeError('Expected cluster.all search path is empty:{}'.format(cluster_files)) + palette = itertools.cycle(sns.color_palette("Set2", len(cluster_files))) + + + ranges = defaultdict(list) + colors = defaultdict(list) + orig_names = defaultdict(list) + cluster_nums = defaultdict(list) + for cluster_file in cluster_files: + cluster_color = next(palette) + df_cluster = pd.read_csv(cluster_file, sep='\s+', header=None) + for irow, row in df_cluster.iterrows(): + seq, start, end, strand = row[0].split("#") + ranges[seq].append((int(start), int(end)-int(start)+1)) + colors[seq].append(cluster_color) + assert row[1] == 'RESULT' + cluster_nums['cluster-{}'.format(row[2])] = cluster_color + assert row[9] == 'ORIGHEAD' + orig_names[seq] = row[10] + return ranges, colors, orig_names, cluster_nums + + +my_ranges, my_colors, my_orig_names, my_cluster_nums = parse_clusters() +plot_bar(my_ranges, my_colors, my_orig_names, my_cluster_nums) |
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| diff -r 000000000000 -r edcf58ab7552 MotifFinderPlot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/MotifFinderPlot.xml Wed Feb 22 16:53:29 2017 -0500 |
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| @@ -0,0 +1,35 @@ +<tool id="motifFinderPlot" name="Motif_Finder_Plot" version="0.1"> + <requirements> + <!-- <requirement type="package" version="2.0.0">matplotlib</requirement> --> + <!-- <requirement type="package" version='0.19.2'>pandas</requirement> --> + <requirement type="package" version='0.7.1'>seaborn</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command> + <![CDATA[ + unzip $RESULTS -d "RESULTS" &> /dev/null && + python '$__tool_directory__/MotifFinderPlot.py' +]]> + </command> + <inputs> + <param type="data" name="RESULTS" format="zip" /> + </inputs> + <outputs> + <data name="motif_plot" format="png" from_work_dir="motif_plot.png" label="motif_plot" /> + </outputs> + <tests> + <test> + <param name="RESULTS" value="RESULTS.zip" ftype="searchgui_archive"/> + <output name="motif_plot" file="motif_plot.png" ftype="png" compare="sim_size" /> + </test> + </tests> + <help> + <![CDATA[ + + ]]> + </help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r edcf58ab7552 test-data/RESULTS.zip |
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| Binary file test-data/RESULTS.zip has changed |
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| diff -r 000000000000 -r edcf58ab7552 test-data/motif_plot.png |
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| Binary file test-data/motif_plot.png has changed |
