Open acvill opened 3 years ago
Just wanted to write and say that my colleague was able to replicate these errors, so I have more confidence that what I'm seeing is not a problem with my environment / installation.
I have met the same errors. The raw_input and xrange in python script metaron are not difined when I tested the example data. Have you solved these problems? I will be much appreciated if you can give me some suggestions.
I have met the same errors. The raw_input and xrange in python script metaron are not difined when I tested the example data. Have you solved these problems? I will be much appreciated if you can give me some suggestions.
Sorry, QI-cy, I have not solved these problems, and I am still unable to implement MetaRon. If you're looking for alternatives, I can suggest POEM, though its outputs are annoying to parse.
Thank you so much for you suggestion. POEM looks great to me and I will try it. Best wishes, Lu Qian ------------------ Original ------------------ From: "Albert @.>; Date: Tue, Sep 28, 2021 11:25 PM To: @.>; Cc: @.>; @.>; Subject: Re: [zaidissa/MetaRon] contaminating python2 code in python3 build? (#3)
I have met the same errors. The raw_input and xrange in python script metaron are not difined when I tested the example data. Have you solved these problems? I will be much appreciated if you can give me some suggestions.
Sorry, QI-cy, I have not solved these problems, and I am still unable to implement MetaRon. If you're looking for alternatives, I can suggest POEM, though its outputs are annoying to parse.
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English ArabicHebrewPolish
BulgarianHindiPortuguese CatalanHmong DawRomanian Chinese SimplifiedHungarianRussian Chinese TraditionalIndonesianSlovak CzechItalianSlovenian DanishJapaneseSpanish DutchKlingonSwedish EnglishKoreanThai EstonianLatvianTurkish FinnishLithuanianUkrainian FrenchMalayUrdu GermanMalteseVietnamese GreekNorwegianWelsh Haitian CreolePersian
any update on this?
any update on this?
Nothing from me. If I ever get MetaRon to work, I'll be sure to post my solution here.
I would love to use this too but ran into the same problems.
if you modify the main metaron script to make the following changes:
on line 444 change "wb" to "w" (as well as any other write lines)
search and replace xrange with range
surround all calls to map() with list, like list(map())
You will also have to remove any "region" lines from your gff file as it doesn't handle those well.
Then it will run on python3.
However there are weird issues with parsing gff files so it still doesn't run completely...
Congratulations on your recent publication in BMC Genomics. I would like to use MetaRon, but there appears to be conflicting information between the MetaRon paper and this repository. The paper states that MetaRon requires Python 3, but the installation prerequisites in this repository state Python 2.7 is needed. Further, your most recent commit is named "python3", so I went ahead with a Python 3 installation.
After resolving an indentation issue...
... the
--help
option now works.But running both the example data and my own data through the
op
process lead to additional errors.Error 1
It seems like this error with
writer.writerows()
is documented in StackOverflow: TypeError: a bytes-like object is required, not 'str' in python and CSVNote that my config.txt file reads:
NNPP2.2_path=/home/metaron/NNPP2.2/bin/fa2TDNNpred-PRO.linux
which points to my local installation of NNPP2.2. I've confirmed that the standalone NNPP2.2 program works fine.
In the absence of a config file, I see a second error that also looks to be caused by python3 trying to compile python2 code:
Error 2
Again, StackOverflow: How do I use raw_input in Python 3
So, should metaron-2.0 be compiled and run in a python2 environment, despite the documentation in the paper and elsewhere that metaron is written in python3?