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guigolab / ggsashimi

Command-line tool for the visualization of splicing events across multiple samples
MIT License
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Error: unexpected symbol in " color_list = list(ConAc_A2-11D.sorted" #19

Closed sneha100895 closed 4 years ago

sneha100895 commented 5 years ago

Hi,

I get the following error when using sashimi-plot.py

This is my code python sashimi-plot.py -b /project/uml_frederic_chain/Daphnia/index/ConAc_A2-11D.sorted.bam -c DAPPUscaffold_67:640865-642375 -g /project/uml_frederic_chain/Daphnia/Daphnia_pulex.V1.0.41.exons.gtf --shrink

Could you please help me out in resolving this.

dgarrimar commented 5 years ago

Hi @sneha100895,

In the past I remember that the dash symbol in the file name was giving some problems. Can you try renaming your BAM? If that is the case, we will try to fix the problem in the code.

Best,

sneha100895 commented 5 years ago

Hi @sneha100895,

In the past I remember that the dash symbol in the file name was giving some problems. Can you try renaming your BAM? If that is the case, we will try to fix the problem in the code.

Best,

sneha100895 commented 5 years ago

Hi,

Renaming the BAM file worked!

Thank you.

ghost commented 4 years ago

Hi,

I also have the same question:

sashimi-plot.py -g Homo_sapiens.GRCh38.94.gtf -b 1119TCXSE141816.bam -c chr9:128936582-128940709 -o 1119_TCX.SE_141816

Error: unexpected symbol in " color_list = list(1119TCXSE141816" Execution halted

Could you please help me?

Thank you!

ghost commented 4 years ago

Sorry to bother, I find the answer in #26. The bam file name should not start with a number.