treesak 1.53.3__py3-none-any.whl

TreeSAK/ALE7.py

@@ -0,0 +1,126 @@
+import os
+import argparse
+
+
+ALE7_usage = '''
+=============================== ALE7 example commands ===============================
+
+# get presence/absence of interested functions in reconstructed ancestral genomes
+
+TreeSAK ALE7 -6 ALE6_op_dir -fun ko.txt -node internal_node.txt -o Fun_PA.txt
+TreeSAK ALE7 -6 ALE6_op_dir -fun K01995,K01995 -node 359,466,470 -o Fun_PA.txt
+TreeSAK ALE7 -6 ALE6_op_dir -fun arCOG07811,K01995 -node 359,466,470 -o Fun_PA.txt
+
+# needed input files:
+-6: annotation_COG/annotation_KEGG
+
+=====================================================================================
+'''
+
+
+def sep_path_basename_ext(file_in):
+
+    f_path, f_name = os.path.split(file_in)
+    if f_path == '':
+        f_path = '.'
+    f_base, f_ext = os.path.splitext(f_name)
+
+    return f_name, f_path, f_base, f_ext[1:]
+
+
+def ALE7(args):
+
+    ale6_op_dir        = args['6']
+    interested_fun_txt = args['fun']
+    interested_gnm_txt = args['node']
+    op_txt             = args['o']
+
+    op_txt_name, op_txt_path, op_txt_base, op_txt_ext = sep_path_basename_ext(op_txt)
+    op_txt_pct = '%s/%s_percentage.%s' % (op_txt_path, op_txt_base, op_txt_ext)
+
+    if os.path.isdir(ale6_op_dir) is False:
+        print('%s not found, program exited!' % ale6_op_dir)
+        exit()
+
+    interested_fun_set = set()
+    if os.path.isfile(interested_fun_txt) is False:
+        if ',' in interested_fun_txt:
+            interested_fun_set = interested_fun_txt.split(',')
+        else:
+            interested_fun_set.add(interested_fun_txt)
+    else:
+        for each_fun in open(interested_fun_txt):
+            interested_fun_set.add(each_fun.strip().split()[0])
+
+    node_desc_dict = dict()
+    interested_node_set = set()
+    if os.path.isfile(interested_gnm_txt) is False:
+        if ',' in interested_gnm_txt:
+            interested_node_set = interested_gnm_txt.split(',')
+        else:
+            interested_node_set.add(interested_gnm_txt)
+    else:
+        for each_node in open(interested_gnm_txt):
+            each_node_split = each_node.strip().split()
+            node_id = each_node_split[0]
+            interested_node_set.add(each_node.strip().split()[0])
+            if len(each_node_split) >= 2:
+                node_desc = each_node_split[1]
+                node_desc_dict[node_id] = node_desc
+
+    interested_fun_list_sorted = sorted(list(interested_fun_set))
+    interested_gnm_list_sorted = sorted(list(interested_node_set))
+
+    op_txt_handle = open(op_txt, 'w')
+    op_txt_pct_handle = open(op_txt_pct, 'w')
+    if len(node_desc_dict) == 0:
+        op_txt_handle.write('ID\t' + '\t'.join(interested_fun_list_sorted) + '\n')
+        op_txt_pct_handle.write('ID\tPercentage\n')
+    else:
+        op_txt_handle.write('ID\tDescription\t' + '\t'.join(interested_fun_list_sorted) + '\n')
+        op_txt_pct_handle.write('ID\tDescription\tPercentage\n')
+    for each_node in interested_gnm_list_sorted:
+
+        node_desc            = node_desc_dict.get(each_node, 'na')
+        node_annotation_cog  = '%s/annotation_COG/%s_COG.txt'   % (ale6_op_dir, each_node)
+        node_annotation_kegg = '%s/annotation_KEGG/%s_KEGG.txt' % (ale6_op_dir, each_node)
+
+        node_fun_set = set()
+        if os.path.isfile(node_annotation_cog):
+            for each_line in open(node_annotation_cog):
+                node_fun_set.add(each_line.strip().split()[0])
+        if os.path.isfile(node_annotation_kegg):
+            for each_line in open(node_annotation_kegg):
+                node_fun_set.add(each_line.strip().split()[0])
+
+        fun_pa_list = []
+        for each_fun in interested_fun_list_sorted:
+            if each_fun in node_fun_set:
+                fun_pa_list.append('1')
+            else:
+                fun_pa_list.append('0')
+
+        fun_presence_pct = fun_pa_list.count('1')*100/len(fun_pa_list)
+        fun_presence_pct = float("{0:.2f}".format(fun_presence_pct))
+        if len(node_desc_dict) == 0:
+            op_txt_handle.write('%s\t%s\n' % (each_node, '\t'.join(fun_pa_list)))
+            op_txt_pct_handle.write('%s\t%s\n' % (each_node, fun_presence_pct))
+        else:
+            op_txt_handle.write('%s\t%s\t%s\n' % (each_node, node_desc, '\t'.join(fun_pa_list)))
+            op_txt_pct_handle.write('%s\t%s\t%s\n' % (each_node, node_desc, fun_presence_pct))
+    op_txt_handle.close()
+    op_txt_pct_handle.close()
+
+    print('Results exported to %s and %s' % (op_txt, op_txt_pct))
+    print('Done!')
+
+
+if __name__ == '__main__':
+
+    ALE7_parser = argparse.ArgumentParser()
+    ALE7_parser.add_argument('-6',      required=True,                          help='ALE6 output directory')
+    ALE7_parser.add_argument('-fun',    required=True,                          help='interested functions')
+    ALE7_parser.add_argument('-node',   required=True,                          help='interested internal nodes')
+    ALE7_parser.add_argument('-o',      required=True,                          help='output directory')
+    args = vars(ALE7_parser.parse_args())
+    ALE7(args)