Andrew Yates 2012

Compile a directory of ATLAS miRNA data files into a tab-delimited matrix intended for use to compute MIC via the reference implementation of MINE.jar.

FILES:

1) __init__.py: module for import
2) test.py: unit tests, run as 
  $ python test.py
3) script.py: shell wrapper around module to execute module tools on the command line
  $ python script.py /path/to/data/dir > miRNA.tab 2> log.txt
----------


Parse sample names from file. Sample name like:
----------
TCGA-A6-2672-01A-01T-0827-13
TCGA-A1-A0SE-01A-11R-A085-13

File name examples:
----------
bcgsc.ca__IlluminaGA_miRNASeq__TCGA-A6-2672-01A-01T-0827-13__mirna_quantification.txt
bcgsc.ca__IlluminaGA_miRNASeq__TCGA-A1-A0SE-01A-11R-A085-13__mirna_quantification.txt

Ignore isoform files named like:
----------
bcgsc.ca__IlluminaGA_miRNASeq__TCGA-A1-A0SH-01A-11R-A085-13__isoform_quantification.txt


File Format (tab delimited):
----------
barcode	miRNA_ID	read_count	reads_per_million_miRNA_mapped	cross-mapped
TCGA-A6-2672-01A-01T-0827-13	hsa-let-7a-1	3613.0	2701.245803	N
TCGA-A6-2672-01A-01T-0827-13	hsa-let-7a-2	7200.0	5383.052804	N
TCGA-A6-2672-01A-01T-0827-13	hsa-let-7a-3	3799.0	2840.308	N

Parse "miRNA_ID" column value as row name, "reads_per_million_miRNA_mapped" as value for associated sample.

e.g., From the example above...
----------
In the resulting compiled, tab-delimited matrix, for the row identified by the variable name "hsa-let-7a-1" in the first column, the value of the column titled by the sample ID "TCGA-A6-2672-01A-01T-0827-13" has the value "2701.245803"