I'd like to use ScaleHD to analyse some Illumina amplicon sequencing of a trinucleotide repeat region.



I’m using a conda environment in MacOS and installed ScaleHD using pip install scalehd. I think I’ve installed all the dependencies suggested by the developer. But when I try to run it I get a syntax error.

$ ScaleHD -v -c ~/analysis/ScaleHD/config_mf.xml -j "hello_documentation" -o ~/analysis/ScaleHD/output
Traceback (most recent call last):
  File "/Users/michaelflower/opt/anaconda3/envs/bioinfo/bin/ScaleHD", line 5, in <module>
from ScaleHD.sherpa import main
  File "/Users/michaelflower/opt/anaconda3/envs/bioinfo/lib/python3.6/site-packages/ScaleHD/sherpa.py", line 115
except Exception, e:
SyntaxError: invalid syntax

I’ve read around a bit and seen it could be a problem with how the ScaleHD.sherpa file has written the ‘except’ – stackoverflow.com/questions/14908789/whats-wrong-with-my-except. But I'm not sure what can be done about it?

I’ve provided sample R1 and R2 fastq file, the config file and reference files I’m using here:

Here’s how I’ve set up the directory:

$ tree analysis/ScaleHD/
|-- config.xml
|-- config_mf.xml
|-- data_dir
|   |-- ciosi41CAG_S4_L001_R1_001.fastq
|   `-- ciosi41CAG_S4_L001_R2_001.fastq
|-- output
`-- ref
    |-- 4k-HD-INTER.fa
    `-- 4k-HD-Reverse.fasta

I'd be very grateful for any help getting this up and running. Thanks!

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