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secastel / phaser

phasing and Allele Specific Expression from RNA-seq
GNU General Public License v3.0
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tabix error due to pandas behavior in python 2.7 #59

Open daniel-munro opened 4 years ago

daniel-munro commented 4 years ago

When I run phaser_expr_matrix.py with the suggested python 2.7, I get this error for every line of the BED file:

[E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?
The offending line was: "10 ENSRNOG00000033508  57185346    57238531    1|0 0|0 [...]

The column order is wrong because the pandas DataFrame is initialized with a dictionary. Pandas documentation says "column order follows insertion-order for Python 3.6 and later." When I run phaser_expr_matrix.py with python3, column order is correct and it runs fine.