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 (bioinfo)
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/ 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!