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-> Small performance improvement - Varna "line" and "radiate" now computing in parallel #24

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9 changes: 7 additions & 2 deletions utils/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -296,8 +296,13 @@ def prob_to_secondary_structure(ensemble_outputs, label_mask, seq, name, args, b

if args.plots:
try:
subprocess.Popen(["java", "-cp", base_path + "/utils/VARNAv3-93.jar", "fr.orsay.lri.varna.applications.VARNAcmd", '-i', output_path + name + '.ct', '-o', output_path + name + '_radiate.png', '-algorithm', 'radiate', '-resolution', '8.0', '-bpStyle', 'lw', '-auxBPs', tertiary_bp], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0]
subprocess.Popen(["java", "-cp", base_path + "/utils/VARNAv3-93.jar", "fr.orsay.lri.varna.applications.VARNAcmd", '-i', output_path + name + '.ct', '-o', output_path + name + '_line.png', '-algorithm', 'line', '-resolution', '8.0', '-bpStyle', 'lw', '-auxBPs', tertiary_bp], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0]
varna_command = ["java", "-cp", base_path + "/utils/VARNAv3-93.jar", "fr.orsay.lri.varna.applications.VARNAcmd", '-i', output_path + name + '.ct', '-resolution', '8.0', '-bpStyle', 'lw', '-auxBPs', tertiary_bp]

radiate_process = subprocess.Popen(varna_command + ['-o', output_path + name + '_radiate.png', '-algorithm', 'radiate'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE)
line_process = subprocess.Popen(varna_command + ['-o', output_path + name + '_line.png', '-algorithm', 'line'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE)

radiate_process.communicate()[0]
line_process.communicate()[0]
except:
print('\nUnable to generate 2D plots;\nplease refer to "http://varna.lri.fr/" for system requirments to use VARNA')

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