From ed1e9168fd47aeaea39573dc3ba63e34984ed29c Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Tue, 29 May 2018 15:51:20 +0200
Subject: [PATCH]  bug fix for the test on Mu packaging

---
 _modules/functions_PhageTerm.py |  3 ++-
 _modules/main_utils.py          | 12 +++++++++++-
 2 files changed, 13 insertions(+), 2 deletions(-)

diff --git a/_modules/functions_PhageTerm.py b/_modules/functions_PhageTerm.py
index ea44ef4..3610616 100644
--- a/_modules/functions_PhageTerm.py
+++ b/_modules/functions_PhageTerm.py
@@ -57,7 +57,8 @@ from reportlab.lib.units import inch
 from reportlab.lib import colors
 from reportlab.lib.utils import ImageReader
 
-from utilities import reverseComplement,changeCase,hybridCoverage,applyCoverage,correctEdge
+from utilities import reverseComplement,hybridCoverage,applyCoverage,correctEdge
+from common_readsCoverage_processing import picMax
 
 
 
diff --git a/_modules/main_utils.py b/_modules/main_utils.py
index 7eba44e..c3542e9 100644
--- a/_modules/main_utils.py
+++ b/_modules/main_utils.py
@@ -255,9 +255,19 @@ class InputDerivedDataArgs:
         if fparms.virome:
             self.refseq_liste, self.refseq_name, refseq_rejected = ["N" * self.mean_virome], ["Test_virome"], 0
         # HOST sequence recovery
+        # # HOST sequence recovery
+        # if len(refseq_liste) == 1 and host != "":
+        #     hostseq = genomeFastaRecovery(host, limit_reference, edge, 1)
+        #     if len(hostseq[0]) != 0 and len(hostseq[0]) < len(refseq_liste[0]):
+        #         print "\nHost length < Phage length : removing host sequence."
+        #         hostseq = ""
+        # else:
+        #     hostseq = ""
+        #     if len(refseq_liste) > 1:
+        #         print "\nWARNING: Host analysis impossible with multiple fasta input\n"
         if len(self.refseq_liste) == 1 and inputRaw.host != "":
             self.hostseq = genomeFastaRecovery(inputRaw.host, fparms.limit_reference, fparms.edge, 1)
-            if len(self.hostseq[0]) != 0 and len(self.hostseq[0]) < len(self.refseq_liste[0]):
+            if len(self.hostseq[0]) != 0 and len(self.hostseq[0]) > len(self.refseq_liste[0]):
                 print "\nHost length < Phage length : removing host sequence."
                 self.hostseq = ""
         else:
-- 
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