danillo-alvarenga/tncomp_finder

Composite Transposon Finder

tncomp_finder's Issues

ImportError: Bio.Alphabet has been removed from Biopython.

.Hi, I am facing this error and i followed below instruction also but still unable to solve it.
/TnComp_finder.py
./TnComp_finder.py:247: SyntaxWarning: "is" with a literal. Did you mean "=="?
if character is 'T':
./TnComp_finder.py:249: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif character is 'A':
./TnComp_finder.py:251: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif character is 'C':
./TnComp_finder.py:253: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif character is 'G':
./TnComp_finder.py:255: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif character is 'N':
./TnComp_finder.py:275: SyntaxWarning: "is" with a literal. Did you mean "=="?
if item[3] is '+':
./TnComp_finder.py:278: SyntaxWarning: "is" with a literal. Did you mean "=="?
elif item[3] is '-':
Traceback (most recent call last):
File "./TnComp_finder.py", line 31, in
from Bio.Alphabet import IUPAC
File "/home/bvs/.local/lib/python3.8/site-packages/Bio/Alphabet/init.py", line 20, in
raise ImportError(
ImportError: Bio.Alphabet has been removed from Biopython. In many cases, the alphabet can simply be ignored and removed from scripts. In a few cases, you may need to specify the molecule_type as an annotation on a SeqRecord for your script to work correctly. Please see https://biopython.org/wiki/Alphabet for more information.

Thank you!

Couldn't install

Dear danillo-alvarenga,
Hi, thank you for providing this program.

I would like to try this program, but I couldn't succeed to install it.
I still a beginner in programming, could you please help me with a clear step-by-step?
Currently, I'm using Linux-based.
I already installed blast (conda install blast), prodigal (conda install prodigal) and Python-3.7.0 (by following: wget https://www.python.org/ftp/python/3.7.0/Python-3.7.0.tgz --> tar -xzf Python-3.7.0.tgz --> cd Python-3.7.0/ --> ./configure --> make)
I already downloaded and unzipped the program in the directory that I want.
I created a new environment.
Here is the directory that I want and the files:

cd /data/Ricky/Software/transposone/tncomp_finder-1.0.0
ls
db LICENSE README.md TnComp_finder.py

but when I do

echo 'export PATH=$PATH'$(pwd) >> /data/Ricky/Software/transposone/tncomp_finder-1.0.0/TnComp_finder.py
source /data/Ricky/Software/transposone/tncomp_finder-1.0.0/TnComp_finder.py

it becomes an error and this appeared:

import: unable to open X server ' @ error/import.c/ImportImageCommand/344. import: unable to open X server ' @ error/import.c/ImportImageCommand/344.
import: unable to open X server ' @ error/import.c/ImportImageCommand/344. import: unable to open X server ' @ error/import.c/ImportImageCommand/344.
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
-bash: /data/Ricky/Software/transposone/tncomp_finder-1.0.0/TnComp_finder.py: line 37: syntax error near unexpected token (' -bash: /data/Ricky/Software/transposone/tncomp_finder-1.0.0/TnComp_finder.py: line 37: parser = argparse.ArgumentParser(description="composite transposon finder",'

My questions are:

1. Is the installment of the blast, prodigal, and Python-3.7.0 correct?
2. Is there something wrong with my installation step?

Thank you

Kind regards,
Ricky