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@@ -11,3 +11,4 @@ script: | |
| - ./test_L.sh | ||
| - ./test_CM.sh | ||
| - ./test_DCC.sh | ||
| - ./test_PRS.sh | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,96 @@ | ||
| #!/usr/bin/env python | ||
| # | ||
| # Calculate the change in the valuses (BC or L) of each residue in a protein over the | ||
| # course of an MD simulation | ||
| # | ||
| # Script distributed under GNU GPL 3.0 | ||
| # | ||
| # Author: David Brown | ||
| # Date: 17-11-2016 | ||
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| from natsort import natsorted | ||
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| from lib.cli import CLI | ||
| from lib.utils import Logger | ||
| from lib.strategies import normalization | ||
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| import numpy as np | ||
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| import sys, argparse, matplotlib | ||
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| matplotlib.use('Agg') | ||
| import matplotlib.pyplot as plt | ||
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| def calc_delta(reference_file, alternative_files, normalizer, generate_plots=False): | ||
| reference = np.loadtxt(reference_file) | ||
| num_nodes = reference.shape[0] | ||
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| label = normalizer.get_label() | ||
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| alternatives = natsorted(alternative_files) | ||
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| log.info("Calculating %s for %d networks...\n" % (label, len(alternatives))) | ||
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| for i, alternative in enumerate(alternatives): | ||
| log.info("Calculating %s (%d/%d)\r" % (label, i + 1, len(alternatives))) | ||
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| title = ".".join(alternative.split(".")[:-1]) | ||
| alternative = np.loadtxt(alternative) | ||
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| difference = alternative - reference | ||
| difference = normalizer.normalize(difference, reference) | ||
| prefix = "%s_%s_delta_%s" % (title, normalizer.get_prefix(), normalizer.matrix_type) | ||
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| np.savetxt("%s.dat" % prefix, difference) | ||
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| if generate_plots: | ||
| node_axis = range(1, num_nodes + 1) | ||
| plt.plot(node_axis, difference) | ||
| plt.axhline(0, color='black') | ||
| plt.title("%s %s" % (title, label), fontsize=18) | ||
| plt.xlabel('Residue Numbers', fontsize=16) | ||
| plt.ylabel(label, fontsize=16) | ||
| plt.savefig("%s.png" % prefix, dpi=300, bbox_inches="tight") | ||
| plt.close() | ||
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| log.info("\n") | ||
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| def get_normalizer(matrix_type, mode): | ||
| type_map = { | ||
| "L": "standard", | ||
| "BC": "plusone" | ||
| } | ||
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| if matrix_type not in type_map: | ||
| log.info("ERROR: --matrix-type must be specified and must be either 'BC' or 'L'") | ||
| sys.exit(1) | ||
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| normalization_mode = mode if mode else type_map[matrix_type] | ||
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| return getattr(normalization, normalization_mode, "standard")(matrix_type) | ||
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| def main(args): | ||
| if args.normalize: | ||
| normalizer = get_normalizer(args.matrix_type, args.normalization_mode) | ||
| else: | ||
| normalizer = normalization.none(args.matrix_type) | ||
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| calc_delta(args.reference, args.alternatives, normalizer, args.generate_plots) | ||
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| log = Logger() | ||
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| if __name__ == "__main__": | ||
| parser = argparse.ArgumentParser() | ||
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| parser.add_argument("--matrix-type", help="The type of values in the matrices i.e. BC or L", default=None) | ||
| parser.add_argument("--reference", help="The reference matrix (.dat)") | ||
| parser.add_argument("--alternatives", help="The alternative matrices (.dat)", nargs="*") | ||
| parser.add_argument("--normalize", help="Normalizes the values", action='store_true', default=False) | ||
| parser.add_argument('--normalization-mode', help="Method used to normalize (default for L = standard, default for BC = plusone)", default=None) | ||
| parser.add_argument("--generate-plots", help="Plot results - without setting this flag, no graph will be generated", action='store_true', default=False) | ||
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| CLI(parser, main, log) |
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