script for reporting gaps

Author: ranwez

OTHER_SCRIPTS/REPORT_GAP/input_aligned.fasta

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+> seq 1
+ ACT---NCT
+> seq2
+ACTACTA!T

OTHER_SCRIPTS/REPORT_GAP/input_nonaligned.fasta

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+> seq 1
+ ACTRCT
+> seq2
+ACTactAT

OTHER_SCRIPTS/REPORT_GAP/insert_gaps.py

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+import sys
+
+def insert_gaps(aligned_file, unaligned_file):
+    unaligned_seqs = {}
+    with open(unaligned_file, "r") as unaligned:
+        seq_name = ""
+        seq = ""
+        for line in unaligned:
+            if line.startswith(">"):
+                if seq_name:
+                    unaligned_seqs[seq_name] = seq
+                seq_name = line.strip()
+                seq = ""
+            else:
+                seq += line.strip()
+        if seq_name:
+            unaligned_seqs[seq_name] = seq
+    
+    with open(aligned_file, "r") as aligned:
+        seq_name = ""
+        for line in aligned:
+            if line.startswith(">"):
+                seq_name = line.strip()
+                print(line.strip())
+            else:
+                aligned_seq = line.strip()
+                unaligned_seq = unaligned_seqs.get(seq_name, "")
+                i = 0
+                res = []
+                for char in aligned_seq:
+                    if char == "-" or char == "!":
+                        res.append(char)
+                    else:
+                        res.append(unaligned_seq[i])
+                        i += 1
+                print("".join(res))
+
+if len(sys.argv) != 3:
+    print("Usage: python insert_gaps.py input_aligned.fasta input_nonaligned.fasta")
+    sys.exit(1)
+
+aligned_file = sys.argv[1]
+unaligned_file = sys.argv[2]
+
+insert_gaps(aligned_file, unaligned_file)
+

OTHER_SCRIPTS/REPORT_GAP/output.fasta

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+> seq 1
+ACT---RCT
+> seq2
+ACTactA!T