fixed kmer analysis - bug was due to making a ref dict

mitenjain · Jul 3, 2014 · 4f0a2cf · 4f0a2cf
1 parent a3da28d
commit 4f0a2cf
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Showing 2 changed files with 5 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1 +1,3 @@
 tests/output/*
+testLog.txt
+testJobTree*
diff --git a/nanopore/analyses/kmerAnalysis.py b/nanopore/analyses/kmerAnalysis.py
@@ -46,9 +46,10 @@ def convert_sam_record(self, record, target):
     def run(self, kmer_size=5):
         """Run karen's pipeline.
         """
-        self.ref = dict(fastaRead(open(self.referenceFastaFile, "r")))
+        self.ref = getFastaDictionary(self.referenceFastaFile)
         outf = open(os.path.join(self.getLocalTempDir(), "tab_delim_align"), "w")
-        sam = pysam.Samfile(self.samFile, "r" )
+	outf = open(os.path.join(self.outputDir, "test"), "w")
+	sam = pysam.Samfile(self.samFile, "r" )
         for record in sam:
             rseq = self.ref[sam.getrname(record.tid)]
             seq, ref = self.convert_sam_record(record, rseq)