miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
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Add function and test unit for function to read BAM file #8

Closed lpantano closed 6 years ago

lpantano commented 7 years ago

Introduce a test unit to read the example GTF file at here: https://github.com/miRTop/mirtop/blob/dev/data/aligments/let7-perfect.bam

The output should be a nested dict like the following:

Initial function already implemented here:
https://github.com/miRTop/mirtop/blob/dev/mirtop/bam/bam.py#L34

The unit test should be included here: https://github.com/miRTop/mirtop/blob/dev/test/test_functions.py#L22

extra: this line should be optional: https://github.com/miRTop/mirtop/blob/dev/mirtop/bam/bam.py#L65. Need a parameter in the command line to turn it on and off.