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Commit 8a7cd5f7 authored by Louwen, Joris's avatar Louwen, Joris
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remove bgcs_and_modules output, add modules_w_info when querying and making...

remove bgcs_and_modules output, add modules_w_info when querying and making new model so wirte_bgc_mod_fasta gets correct input always
parent e4d342e6
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1 merge request!1iPRESTO refactor
......@@ -328,27 +328,19 @@ def presto_stat_build_subclusters(
mod_file_f = '{}_filtered_modules.txt'.format(
filt_file.split('_filtered_clusterfile.csv')[0])
write_module_file(mod_file_f, modules, bgcs_with_mods)
# todo: assess if this output is necessary
bgcmodfile = '{}_bgcs_with_mods.txt'.format(
filt_file.split('_filtered_clusterfile.csv')[0])
rank_mods = {pair[0]: i + 1 for i, pair in
enumerate(sorted(modules.items(),
key=itemgetter(1)))}
write_bgcs_and_modules(bgcmodfile, f_clus_dict_rem, bgcs_with_mods,
rank_mods)
modules_w_info = q_stat.read_mods(mod_file_f)
else:
# read previously inferred subclusters from file
print("\nReading PRESTO-STAT subclusters from file:",
stat_subclusters_file)
modules = q_stat.read_mods(stat_subclusters_file)
bgcs_with_mods = q_stat.link_all_mods2bgcs(f_clus_dict, list(modules),
cores)
modules_w_info = q_stat.read_mods(stat_subclusters_file)
bgcs_with_mods = q_stat.link_all_mods2bgcs(
f_clus_dict, list(modules_w_info), cores)
out_file = '{}_presto_stat_subclusters.txt'.format(
filt_file.split('_filtered_clusterfile.csv')[0])
print("\nWriting clusters with detected subclusters to", out_file)
q_stat.write_bgc_mod_fasta(bgcs_with_mods, modules, out_file)
q_stat.write_bgc_mod_fasta(bgcs_with_mods, modules_w_info, out_file)
return out_file
......
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