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mimakaev committed 41190a1

Added sample metadata for fragmentHiC test

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Files changed (3)

src/hiclib/fragmentHiC.py

         plt.title("strands2, side 2")
         plt.plot(myrange, np.bincount(
             dists2[self.strands1 == False])[:length])
-
-
-class experimentalFeatures(HiCdataset):
-    "This class contain some dangerous features that were not tested."
-    def splitFragmentsBystrands(self):
-        """Splits fragments: those with strands = 1 gets location += 1.
-        This is totally safe!
-        This might be fun if you want to analyze two sides of the
-        fragment separately, but unnecessary otherwise"""
-        f1 = self.fragids1
-        f1 += ((f1 % self.fragIDmult) % 2)
-        f1[self.strands1 == 1] += 1
-        f2 = self.fragids2
-        f1 += ((f2 % self.fragIDmult) % 2)
-        f2[self.strands1 == 1] += 1
-        self.rebuildFragments()

src/hiclib/mapping.py

         os.remove(unmapped_fastq_path)
 
 
+
 def _find_rfrags_inplace(lib, genome, min_frag_size, side):
     '''Private: assign mapped reads to restriction fragments by
     their 5' end position.
         if not sam_paths:
             raise Exception('No SAM/BAM files with \'%s\' basename are found.' % sam_basename)
 
+
         for sam_path in sam_paths:
+
             samfile = pysam.Samfile(sam_path)
 
             # Make Bowtie's chromosome tids -> genome_db indices dictionary.

tests/fragmentHiC/sampleMetadata

Binary file added.