# HG changeset patch
# User mmonot
# Date 1513764817 18000
# Node ID b9e4dea1c49a8b59184b4d25c56bb79b96df68ca
# Parent  fab295449424a271ed94f3e0c44182c1288e2f9b
Uploaded

diff -r fab295449424 -r b9e4dea1c49a phageterm/._.DS_Store
Binary file phageterm/._.DS_Store has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/._PhageTerm.py
Binary file phageterm/._PhageTerm.py has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/._PhageTerm.xml
Binary file phageterm/._PhageTerm.xml has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/._READ_ME.txt
Binary file phageterm/._READ_ME.txt has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/.__modules
Binary file phageterm/.__modules has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/PhageTerm.py
--- a/phageterm/PhageTerm.py	Thu Jul 13 09:29:44 2017 -0400
+++ b/phageterm/PhageTerm.py	Wed Dec 20 05:13:37 2017 -0500
@@ -46,7 +46,7 @@
 usage = """\n\nUsage: %prog -f reads.fastq -r phage_sequence.fasta [-n phage_name -p reads_paired -s seed_lenght -d surrounding -t installation_test -c nbr_core -g host.fasta (warning increase process time)]
     
     Program: PhageTerm - Analyze phage termini and packaging mode using reads from high-throughput sequenced phage data
-    Version: 1.0.8
+    Version: 1.0.9
     Contact: Julian Garneau <julian.garneau@usherbrooke.ca>
     Contact: David Bikard <david.bikard@pasteur.fr>
     Contact: Marc Monot <marc.monot@pasteur.fr>
diff -r fab295449424 -r b9e4dea1c49a phageterm/PhageTerm.xml
--- a/phageterm/PhageTerm.xml	Thu Jul 13 09:29:44 2017 -0400
+++ b/phageterm/PhageTerm.xml	Wed Dec 20 05:13:37 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="PhageTerm" name="PhageTerm" version="1.0.8">
+<tool id="PhageTerm" name="PhageTerm" version="1.0.9">
     <description>Determine Bacteriophage Termini and Packaging Mode using randomly fragmented NGS data.</description>
     <requirements>
         <requirement type="package" version="2.7">python</requirement>
diff -r fab295449424 -r b9e4dea1c49a phageterm/READ_ME.txt
--- a/phageterm/READ_ME.txt	Thu Jul 13 09:29:44 2017 -0400
+++ b/phageterm/READ_ME.txt	Wed Dec 20 05:13:37 2017 -0500
@@ -7,7 +7,7 @@
 VERSION
 =======
 
-Version 1.0.8
+Version 1.0.9
 
 
 INTRODUCTION
diff -r fab295449424 -r b9e4dea1c49a phageterm/_modules/.___init__.py
Binary file phageterm/_modules/.___init__.py has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/_modules/._functions_PhageTerm.py
Binary file phageterm/_modules/._functions_PhageTerm.py has changed
diff -r fab295449424 -r b9e4dea1c49a phageterm/_modules/functions_PhageTerm.py
--- a/phageterm/_modules/functions_PhageTerm.py	Thu Jul 13 09:29:44 2017 -0400
+++ b/phageterm/_modules/functions_PhageTerm.py	Wed Dec 20 05:13:37 2017 -0500
@@ -756,13 +756,8 @@
         elif ( dist_peak < 20 and dist_peak > 2 ) or ( dist_peak_over < 20 and dist_peak_over > 2 ):
             Redundant = 0
             Permuted  = "No"
+            P_class, P_type    = typeCOS(plus_significant["Position"][0], minus_significant["Position"][0], gen_len/2 )
             P_seqcoh, packstat = sequenceCohesive("COS", refseq, [((plus_significant["SPC"][0]),(plus_significant["Position"][0])-1)], [((minus_significant["SPC"][0]),(minus_significant["Position"][0])-1)], gen_len/2)
-            if plus_significant["Position"][0] < minus_significant["Position"][0] and abs(plus_significant["Position"][0]-minus_significant["Position"][0]) < ( gen_len / 2 ):
-                P_class = "COS (5')"
-                P_type  = "Lambda"
-            else:
-                P_class = "COS (3')"
-                P_type  = "HK97"
         # DTR
         elif ( dist_peak <= 1000 ) or ( dist_peak_over <= 1000 ):
             Redundant = 1
@@ -885,20 +880,35 @@
     """Return cohesive sequence for COS phages."""
     if Packmode != 'COS':
         return '', Packmode
-    gen_len = nbr_lim*2
     PosPlus = picMaxPlus[0][1]
     PosMinus = picMaxMinus[0][1]
-    if abs(PosMinus - PosPlus) < nbr_lim:
-        seqcoh = refseq[min(PosPlus, PosMinus):max(PosPlus,PosMinus)+1]
-        if len(seqcoh) > ( 0.1 * gen_len ):
-            return '', "OTHER"
-        return seqcoh, Packmode
+
+    SC_class, SC_type = typeCOS(PosPlus, PosMinus, nbr_lim)
+
+    if SC_class == "COS (5')":
+        if abs(PosMinus - PosPlus) < nbr_lim:
+            seqcoh = refseq[min(PosPlus, PosMinus):max(PosPlus,PosMinus)+1]
+            return seqcoh, Packmode
+        else:
+            seqcoh = refseq[max(PosPlus,PosMinus)+1:] + refseq[:min(PosPlus, PosMinus)]
+            return seqcoh, Packmode
+
+    elif SC_class == "COS (3')":
+        if abs(PosMinus - PosPlus) < nbr_lim:
+            seqcoh = reverseComplement(refseq[min(PosPlus, PosMinus)+1:max(PosPlus,PosMinus)])
+            return seqcoh, Packmode
+        else:
+            seqcoh = refseq[max(PosPlus,PosMinus)+1:] + refseq[:min(PosPlus, PosMinus)]
+            return seqcoh, Packmode
     else:
-        seqcoh = refseq[max(PosPlus,PosMinus)+1:] + refseq[:min(PosPlus, PosMinus)]
-        if len(seqcoh) > ( 0.1 * gen_len ):
-            return '', "OTHER"
-        return seqcoh, Packmode
+        return '', Packmode
 
+def typeCOS(PosPlus, PosMinus, nbr_lim):
+    """ Return type of COS sequence."""
+    if PosPlus < PosMinus and abs(PosPlus-PosMinus) < nbr_lim:
+        return "COS (5')", "Lambda"
+    else:
+        return "COS (3')", "HK97"
 
 ### IMAGE Functions
 def GraphCov(termini_coverage, picMaxPlus, picMaxMinus, phagename, norm, draw, hybrid = 0):
@@ -1271,9 +1281,7 @@
     """Export the phage sequence reorganized and completed if needed."""
     if test_run:
         return
- 
     seq_out = ""
-
     # Mu-like
     if Mu_like:
         if P_orient == "Forward":
@@ -1295,19 +1303,25 @@
 
     # COS
     elif isinstance(P_left, int) and isinstance(P_right, int):
-        # Genome
-        if abs(P_left-P_right) > len(refseq)/2:
-            seq_out = refseq[min(P_left,P_right)-1:max(P_left,P_right)]
-        else:
-            seq_out = refseq[max(P_left,P_right):] + refseq[:min(P_left,P_right)-1]
         # Cos or DTR
-        if P_class == "COS (5')":
-            seq_out = P_seqcoh + seq_out
-        elif P_class == "COS (3')":
+        if P_class == "COS (3')":
+            if abs(P_left-P_right) > len(refseq)/2:
+                seq_out = refseq[min(P_left,P_right)-1:max(P_left,P_right)]
+            else:
+                seq_out = refseq[max(P_left,P_right)-1:] + refseq[:min(P_left,P_right)]
             seq_out = seq_out + P_seqcoh
         else:
-            seq_out = P_seqcoh + seq_out + P_seqcoh
-
+            # Genome
+            if abs(P_left-P_right) > len(refseq)/2:
+                seq_out = refseq[min(P_left,P_right)-1:max(P_left,P_right)]
+            else:
+                seq_out = refseq[max(P_left,P_right):] + refseq[:min(P_left,P_right)-1]
+            # COS 5'
+            if P_class == "COS (5')":
+                seq_out = P_seqcoh + seq_out
+            # DTR
+            else:
+                seq_out = P_seqcoh + seq_out + P_seqcoh
     # PAC
     elif isinstance(P_left, int) or isinstance(P_right, int):
         if P_orient == "Reverse":