--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RaGOO/ragoo_utilities/get_ragoo_stats.py	Mon Jul 26 18:22:37 2021 +0000
@@ -0,0 +1,55 @@
+import argparse
+
+parser = argparse.ArgumentParser(description='Summary stats about contig scaffolding with RaGOO.')
+parser.add_argument("index", metavar="<contigs.fasta.fai>", type=str, help="Samtools fasta index file for input contigs. If chimera breaking mode was used, this must be"
+                                                                           "the index file of the chimera broken contigs, which can be found in ragoo_output/chimera_break."
+                                                                           "The correct file to use is the file with the .intra.chimera.broken.fa suffix.")
+parser.add_argument("groupings", metavar="<groupings.fofn>", type=str, help="file of file names for all *_groupings.txt produced by RaGOO. Single column with full path to each grouping file.")
+
+args = parser.parse_args()
+contigs_index = args.index
+grouping_fofn = args.groupings
+
+remaining_ctg = []
+all_ctg_len = dict()
+with open(contigs_index) as f:
+    for line in f:
+        L1 = line.split('\t')
+        all_ctg_len[L1[0]] = int(L1[1])
+        remaining_ctg.append(L1[0])
+
+grouping_files = []
+with open(grouping_fofn) as f:
+    for line in f:
+        grouping_files.append(line.rstrip())
+
+num_ctg_localized = 0
+num_bp_localized = 0
+
+for group_file in grouping_files:
+    with open(group_file) as f:
+        for line in f:
+            L1 = line.split('\t')
+            header = L1[0].rstrip()
+            num_ctg_localized += 1
+            num_bp_localized += all_ctg_len[header]
+            assert header in remaining_ctg
+            remaining_ctg.pop(remaining_ctg.index(header))
+
+num_ctg_unlocalized = 0
+num_bp_unlocalized = 0
+for ctg in remaining_ctg:
+    num_ctg_unlocalized += 1
+    num_bp_unlocalized += all_ctg_len[ctg]
+
+print('%r contigs were localized by RaGOO' %(num_ctg_localized))
+print('%r bp were localized by RaGOO' %(num_bp_localized))
+print('%r contigs were unlocalized by RaGOO' %(num_ctg_unlocalized))
+print('%r bp were unlocalized by RaGOO' %(num_bp_unlocalized))
+
+print('%r %% of contigs were localized by RaGOO' %((num_ctg_localized/(num_ctg_localized + num_ctg_unlocalized))*100))
+print('%r %% of bp were localized by RaGOO' %((num_bp_localized/(num_bp_localized + num_bp_unlocalized))*100))
+
+
+
+