Package core :: Module Mem
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Module Mem

source code

Created 2012


Author: GieseS

Little plotting script which is called in the analysis of different mappings to an artificial reference genome. It produces the following plots:

1) ROC Curve 2) Overview histograms for FP / TP.

Functions [hide private]
array
ReadReferenceSAMfile(ref, compareList, readdic, entries)
Function for reading a complete ReferenceFile into Memory.
source code
dictionary
ReadArtificialSAMfile(art, compareList, RefArray, readdic)
Function for reading a complete ReferenceFile into Memory.
source code
Variables [hide private]
  __package__ = None
Function Details [hide private]

ReadReferenceSAMfile(ref, compareList, readdic, entries)

source code 

Function for reading a complete ReferenceFile into Memory.

Parameters:
  • ref (string) - reference file.ArtRead
  • entries (int) - size for np.array
  • compareList (list) - list containt 1s, where there is a difference in the genomes and 0s where the nucleotides are equal.
  • readdic (dictionary) - dictionary containing read ids and read qualities.
Returns: array
aligned read objects in an array.

ReadArtificialSAMfile(art, compareList, RefArray, readdic)

source code 

Function for reading a complete ReferenceFile into Memory.

Parameters:
  • art (string) - artificial file.
  • RefArray (array) - Results from reading the reference SAM file.
  • compareList (list) - list containt 1s, where there is a difference in the genomes and 0s where the nucleotides are equal.
  • readdic (dictionary) - dictionary containing read ids and read qualities.
Returns: dictionary
aligned read objects from the artificial reference, which where uniquely aligned.