From 181336631c96e35f447b8b6a7deaf9d4c198bb40 Mon Sep 17 00:00:00 2001
From: ramonamerong <ramonamerong@live.nl>
Date: Tue, 13 Dec 2022 16:10:58 +0100
Subject: [PATCH] Made insertion motif optional, expanded valid insertion
 sequence check and added support for target site deletions

---
 bin/addsv.py                 | 15 +++++++++------
 bin/bamsurgeon/mutableseq.py |  9 ++++++---
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/bin/addsv.py b/bin/addsv.py
index 965c58d..ebf9872 100644
--- a/bin/addsv.py
+++ b/bin/addsv.py
@@ -528,18 +528,21 @@ def makemut(args, bedline, alignopts):
             assert len(a) > 1 # insertion syntax: INS <file.fa> [optional TSDlen]
             insseqfile = a[1]
             if not (os.path.exists(insseqfile) or insseqfile == 'RND' or insseqfile.startswith('INSLIB:')): # not a file... is it a sequence? (support indel ins.)
-                assert re.search('^[ATGCatgc]*$',insseqfile), "cannot determine SV type: %s" % insseqfile # make sure it's a sequence
+                assert re.search('^[ATGCURYKMSWBDHVNatgcurykmswbdhvn]*$',insseqfile), "cannot determine SV type: %s" % insseqfile # make sure it's a sequence
                 insseq = insseqfile.upper()
                 insseqfile = None
             if len(a) > 2: # field 5 for insertion is TSD Length
                 tsdlen = int(a[2])
 
-            if len(a) > 3: # field 6 for insertion is motif, format = 'NNNN^NNNN where ^ is cut site
-                ins_motif = a[3]
-                assert '^' in ins_motif, 'insertion motif specification requires cut site defined by ^'
+            if len(a) > 3:
+                try:    # field 6 for VAF in case of floating point. This is the end of the fields
+                    svfrac = float(a[3])/cn
+                except: # otherwise is insertion motif, format = 'NNNN^NNNN where ^ is cut site
+                    ins_motif = a[3]
+                    assert '^' in ins_motif, 'insertion motif specification requires cut site defined by ^'
 
-            if len(a) > 4: # field 7 is VAF
-                svfrac = float(a[4])/cn
+                    if len(a) > 4: # field 7 is VAF when field 6 is insertion motif
+                        svfrac = float(a[4])/cn
 
         if action == 'DUP':
             if len(a) > 1:
diff --git a/bin/bamsurgeon/mutableseq.py b/bin/bamsurgeon/mutableseq.py
index a442834..4c996c2 100644
--- a/bin/bamsurgeon/mutableseq.py
+++ b/bin/bamsurgeon/mutableseq.py
@@ -53,10 +53,13 @@ def deletion(self, start, end):
         self.seq = self.seq[:start] + self.seq[end:]
 
     def insertion(self, loc, seq, tsdlen=0):
-        ''' inserts seq after position loc, adds taret site duplication (tsd) if tsdlen > 0 '''
+        ''' inserts seq after position loc, adds target site duplication (tsd) if tsdlen > 0 and deletion if tsdlen < 0'''
         loc = int(loc)
-        tsd = self.seq[loc:loc+tsdlen]
-        self.seq = self.seq[:loc] + tsd + seq + self.seq[loc:]
+        if tsdlen >= 0:
+            tsd = self.seq[loc:loc + tsdlen]
+            self.seq = self.seq[:loc] + tsd + seq + self.seq[loc:]
+        else:
+            self.seq = self.seq[:loc] + seq + self.seq[loc - tsdlen:]
 
     def inversion(self, start, end):
         ''' inverts sequence between start and end, bases at start and end positions are not affected '''