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: -- GitLab