[med-svn] [Git][med-team/kineticstools][upstream] New upstream version 0.6.1+git20200729.e3723e0+dfsg

[Étienne Mollier]

Étienne Mollier pushed to branch upstream at Debian Med / kineticstools


Commits:
cde48152 by Etienne Mollier at 2020-11-25T22:02:53+01:00
New upstream version 0.6.1+git20200729.e3723e0+dfsg
- - - - -


2 changed files:

- kineticsTools/MultiSiteCommon.py
- test/test_integration.py


Changes:

=====================================
kineticsTools/MultiSiteCommon.py
=====================================
@@ -143,7 +143,7 @@ class MultiSiteCommon(object):
     def getContextMeans(self, start, end, sequence):
         meanVector = []
         for pos in range(start, end + 1):
-            ctx = sequence[(pos - self.pre):(pos + self.post + 1)].tostring()
+            ctx = sequence[(pos - self.pre):(pos + self.post + 1)].tostring().decode("ascii")
             if ctx in self.contextMeanTable:
                 meanVector.append(self.contextMeanTable[ctx])
             else:


=====================================
test/test_integration.py
=====================================
@@ -13,10 +13,10 @@ EXPECTED_GFF = """\
 Escherichia_coli_K12\tkinModCall\tmodified_base\t6307\t6307\t34\t-\t.\tcoverage=56;context=CAGATTAGCACGCTGATGCGCATCAGCGACAAACTGGCGGG;IPDRatio=1.92
 Escherichia_coli_K12\tkinModCall\tmodified_base\t6455\t6455\t32\t-\t.\tcoverage=53;context=CCTGCAAGGACTGGATATGCTGATTCTTATTTCACCTGCGA;IPDRatio=1.78
 Escherichia_coli_K12\tkinModCall\tmodified_base\t6512\t6512\t32\t-\t.\tcoverage=55;context=GTAATCACAACTATCGATCAACTCATTCTCATTTTTTGCTA;IPDRatio=1.81
-Escherichia_coli_K12\tkinModCall\tm6A\t6984\t6984\t34\t-\t.\tcoverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;identificationQv=5
-Escherichia_coli_K12\tkinModCall\tm4C\t7111\t7111\t24\t+\t.\tcoverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;identificationQv=4
+Escherichia_coli_K12\tkinModCall\tm6A\t6984\t6984\t34\t-\t.\tcoverage=56;context=TACTGGCGGGTAACGGCACAACCTACATGCCGCTGGAAGGT;IPDRatio=2.02;frac=0.627;fracLow=0.321;fracUp=0.911;identificationQv=5
+Escherichia_coli_K12\tkinModCall\tm4C\t7111\t7111\t24\t+\t.\tcoverage=19;context=GGAGGCCAGGACGCCGCTGCCGCTGCCGCGTTTGGCGTCGA;IPDRatio=2.45;frac=1.000;fracLow=0.370;fracUp=1.000;identificationQv=4
 Escherichia_coli_K12\tkinModCall\tmodified_base\t20051\t20051\t44\t+\t.\tcoverage=19;context=ACGTCAAAGGGTGACAGCAGGCTCATAAGACGCCCCAGCGT;IPDRatio=2.54
-Escherichia_coli_K12\tkinModCall\tm4C\t20296\t20296\t24\t-\t.\tcoverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;identificationQv=9
+Escherichia_coli_K12\tkinModCall\tm4C\t20296\t20296\t24\t-\t.\tcoverage=17;context=GGATGCCGGGCAACAGCCCGCATTATGGGCGTTGGCCTCAA;IPDRatio=1.86;frac=1.000;fracLow=0.379;fracUp=1.000;identificationQv=9
 Escherichia_coli_K12\tkinModCall\tmodified_base\t20449\t20449\t31\t+\t.\tcoverage=18;context=TGTCCGGCGGTGCTTTTGCCGTTACGCACCACCCCGTCAGT;IPDRatio=2.49"""
 
 
@@ -39,6 +39,7 @@ class TestKineticsTools(PbIntegrationBase):
             "--csv", csv_out,
             "--pvalue", "0.001",
             "--identify", "m6A,m4C",
+            "--methylFraction",
             "--reference", ref_set,
             alignments
         ]
@@ -46,6 +47,7 @@ class TestKineticsTools(PbIntegrationBase):
         assert op.isfile(gff_out)
         assert op.isfile(csv_out)
         records = []
+        print(gff_out)
         with open(gff_out, "rt") as gff:
             for line in gff.read().splitlines():
                 if not line.startswith("##"):
@@ -58,4 +60,4 @@ class TestKineticsTools(PbIntegrationBase):
                 csv_records.append(line)
         assert len(csv_records) == 3222
         assert csv_records[1] == \
-            r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33'
+            r'"Escherichia_coli_K12",6214,0,C,8,0.784,0.144,0.631,1.242,33,,,'



View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226

-- 
View it on GitLab: https://salsa.debian.org/med-team/kineticstools/-/commit/cde481528bb724dd09e404cdcb7cdbc33b203226
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