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Commit b1213f48 authored by Kautsar, Satria's avatar Kautsar, Satria
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Fix overview screen only shows output from 1 run in the case of multiple runs via --cutoffs

parent a993ac45
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bigscape.py
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......@@ -1340,12 +1340,6 @@ def clusterJsonBatch(bgcs, pathBase, className, matrix, pos_alignments, cutoffs=
pathBase: folder where GCF files will be deposited
"""
numBGCs = len(bgcs)
family_data = { # will be returned, for use in overview.js
"label": className,
"families": [],
"families_similarity": []
}
simDict = {} # dictionary of dictionaries
# Doing this so it only has to go through the matrix once
......@@ -1429,7 +1423,14 @@ def clusterJsonBatch(bgcs, pathBase, className, matrix, pos_alignments, cutoffs=
# Create network
g = nx.Graph()
for cutoff in cutoffs:
results = {}
for cutoff in cutoffs:
family_data = { # will be returned, for use in overview.js
"label": className,
"families": [],
"families_similarity": []
}
print(" Cutoff: {}".format(cutoff))
# first task is to find labels (exemplars) for each node.
# Assign disconnected (singleton) BGCs to themselves
......@@ -1921,7 +1922,9 @@ def clusterJsonBatch(bgcs, pathBase, className, matrix, pos_alignments, cutoffs=
for bgc in familiesDict[family]:
clansFile.write("{}\t{}\t{}\n".format(clusterNames[bgc], clan, family))
return family_data
results[htmlFolder_run] = family_data
return results
def CMD_parser():
......@@ -2803,18 +2806,22 @@ if __name__=="__main__":
# create output directory for network files
network_files_folder = os.path.join(network_folder, run_name)
create_directory(network_files_folder, "Network Files", False)
run_data["networks"] = []
# copy html templates
dir_util.copy_tree(os.path.join(os.path.realpath(os.path.dirname(__file__)), "html_template", "output"), output_folder)
# make a new run folder in the html output & copy the overview_html
network_html_folder = os.path.join(output_folder, "html_content", "networks", run_name)
rundata_networks_per_run = {}
html_subs_per_run = {}
for cutoff in cutoff_list:
network_html_folder_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff)
create_directory(network_html_folder_cutoff, "Network HTML Files", False)
shutil.copy(os.path.join(os.path.realpath(os.path.dirname(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html"))
rundata_networks_per_run[network_html_folder_cutoff] = []
html_subs_per_run[network_html_folder_cutoff] = []
print(rundata_networks_per_run)
# create pfams.js
pfams_js_file = os.path.join(output_folder, "html_content", "js", "pfams.js")
if not os.path.isfile(pfams_js_file):
......@@ -2831,10 +2838,6 @@ if __name__=="__main__":
pfam_json[pfam_code] = pfam_obj
pfams_js.write("var pfams={};\n".format(json.dumps(pfam_json, indent=4, separators=(',', ':'), sort_keys=True)))
# track the sub modules (i.e. allOthers, allNRPS, ...)
html_subs = []
# Try to make default analysis using all files found inside the input folder
print("\nGenerating distance network files with ALL available input files")
......@@ -3011,11 +3014,12 @@ if __name__=="__main__":
# lcsStartA, lcsStartB, seedLength, reverse={True,False}
pa[int(row[1])] = (int(row[-4]), int(row[-3]), int(row[-2]), reverse)
del network_matrix_mix[:]
html_subs.append({ "name" : "mix", "css" : "Others", "label" : "Mixed"})
family_data = clusterJsonBatch(mix_set, pathBase, "mix", reduced_network, pos_alignments,
cutoffs=cutoff_list, clusterClans=options.clans,
clanCutoff=options.clan_cutoff, htmlFolder=network_html_folder)
run_data["networks"].append(family_data)
for network_html_folder_cutoff in family_data:
rundata_networks_per_run[network_html_folder_cutoff].append(family_data[network_html_folder_cutoff])
html_subs_per_run[network_html_folder_cutoff].append({ "name" : "mix", "css" : "Others", "label" : "Mixed"})
del mix_set[:]
del reduced_network[:]
......@@ -3228,12 +3232,14 @@ if __name__=="__main__":
pa[int(row[1])] = (int(row[-4]), int(row[-3]), int(row[-2]), reverse)
del network_matrix[:]
html_subs.append({ "name" : bgc_class, "css" : bgc_class, "label" : bgc_class})
family_data = clusterJsonBatch(BGC_classes[bgc_class], pathBase, bgc_class,
reduced_network, pos_alignments, cutoffs=cutoff_list,
clusterClans=options.clans, clanCutoff=options.clan_cutoff,
htmlFolder=network_html_folder)
run_data["networks"].append(family_data)
for network_html_folder_cutoff in family_data:
rundata_networks_per_run[network_html_folder_cutoff].append(family_data[network_html_folder_cutoff])
if (len(family_data[network_html_folder_cutoff]["families"]) > 0):
html_subs_per_run[network_html_folder_cutoff].append({ "name" : bgc_class, "css" : bgc_class, "label" : bgc_class})
del BGC_classes[bgc_class][:]
del reduced_network[:]
......@@ -3276,19 +3282,20 @@ if __name__=="__main__":
# update family data (convert global bgc indexes into input-only indexes)
for network in run_data["networks"]:
for family in network["families"]:
new_members = []
mibig = []
for bgcIdx in family["members"]:
if bgcIdx in inputClustersIdx:
new_members.append(inputClustersIdx.index(bgcIdx))
else: # is a mibig bgc
clusterName = clusterNames[bgcIdx]
if clusterName in mibig_set:
mibig.append(clusterName)
family["mibig"] = mibig
family["members"] = new_members
for network_key in rundata_networks_per_run:
for network in rundata_networks_per_run[network_key]:
for family in network["families"]:
new_members = []
mibig = []
for bgcIdx in family["members"]:
if bgcIdx in inputClustersIdx:
new_members.append(inputClustersIdx.index(bgcIdx))
else: # is a mibig bgc
clusterName = clusterNames[bgcIdx]
if clusterName in mibig_set:
mibig.append(clusterName)
family["mibig"] = mibig
family["members"] = new_members
# generate overview data
......@@ -3299,11 +3306,14 @@ if __name__=="__main__":
for cutoff in cutoff_list:
# update overview.html
with open(os.path.join("{}_c{:.2f}".format(network_html_folder, cutoff), "run_data.js"), "w") as run_data_js:
run_data_js.write("var run_data={};\n".format(json.dumps(run_data, indent=4, separators=(',', ':'), sort_keys=True)))
html_folder_for_this_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff)
run_data_for_this_cutoff = run_data.copy()
run_data_for_this_cutoff["networks"] = rundata_networks_per_run[html_folder_for_this_cutoff]
with open(os.path.join(html_folder_for_this_cutoff, "run_data.js"), "w") as run_data_js:
run_data_js.write("var run_data={};\n".format(json.dumps(run_data_for_this_cutoff, indent=4, separators=(',', ':'), sort_keys=True)))
run_data_js.write("dataLoaded();\n");
# update bgc_results.js
add_to_bigscape_results_js("{}_c{:.2f}".format(run_name, cutoff), html_subs, os.path.join(output_folder, "html_content", "js", "bigscape_results.js"))
add_to_bigscape_results_js("{}_c{:.2f}".format(run_name, cutoff), html_subs_per_run[html_folder_for_this_cutoff], os.path.join(output_folder, "html_content", "js", "bigscape_results.js"))
pickle.dump(bgc_info,open(os.path.join(cache_folder,'bgc_info.dict'),'wb'))
runtime = time.time()-time1
......
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