core.Mem

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.