Error with hera

Question

[biomagician]

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,

C.

[sonpham]

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.

Answer 1

[biomagician]

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 [e-mail] if you need further support
Index transcripts in: output/genome/celegans/ref/index/hera/transcripts.fasta
Number of sequence  : 58941