Error with hera

Hi,

I get an error when I build the index.

Installation:

git clone https://github.com/bioturing/hera.git output/software/hera
cd output/software/hera/
chmod +x build.sh
./build.sh

Building index:

./output/software/hera/build/hera_build --fasta output/genome/celegans/ref/seq/celegans.fa --gtf output/genome/celegans/ref/annotation/celegans.gtf --outdir output/genome/celegans/ref/index/hera/

Output:

Scan reference sequence ...
Scan gtf file...
Extract transcript sequence
Traceback (most recent call last):
  File "./output/software/hera/build/hera_build", line 195, in <module>
    write_index(total_byte, gene_info)
  File "./output/software/hera/build/hera_build", line 129, in write_index
    fi.write(chr)
TypeError: a bytes-like object is required, not 'str'

My default version of python is 3.

Can you please help me fix this error?

Thanks.

Best,

hera

• 2,018 views • link

updated 9.0 years ago by WouterDeCoster

• written 9.0 years ago by biomagician

Thank you for the bug report and sorry for the inconvenience. We have applied a patch to fix it, and now it should work with both versions of Python. Please get the updated version and it will resolve the problem.

Thank you! BioTuring Algorithm Team.

• 0 views • link

written 9.0 years ago by sonpham

1 answer

Thanks WouterDeCoster: A: Hera: A new tool for RNA-Seq analysis

I have created a conda environment with python 2 and when I activate it and then run the Hera command, it works.

source activate python2env
(python2env) ➜  project ./output/software/hera/build/hera_build --fasta output/genome/celegans/ref/seq/celegans.fa --gtf output/genome/celegans/ref/annotation/celegans.gtf --outdir output/genome/celegans/ref/index/hera/

Scan reference sequence ...
Scan gtf file...
Extract transcript sequence
Hera is a program developed by BioTuring for RNA-Seq analysis.
Please contact info@bioturing.com if you need further support
Index transcripts in: output/genome/celegans/ref/index/hera/transcripts.fasta
Number of sequence  : 58941

• 0 views • link

written 9.0 years ago by biomagician

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