8000 tabix error due to pandas behavior in python 2.7 · Issue #59 · secastel/phaser · GitHub
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tabix error due to pandas behavior in python 2.7 #59

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daniel-munro opened this issue May 24, 2020 · 0 comments
Open

tabix error due to pandas behavior in python 2.7 #59

daniel-munro opened this issue May 24, 2020 · 0 comments

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@daniel-munro
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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.
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