Questions tagged [python]
python is a programming language, widely used in bioinformatics
641 questions
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Mapping specific Gene Ontology terms to broader PANTHER pie chart categories
I'm working with the PANTHER DB API to analyze gene functions and want to categorize specific molecular functions into broader PANTHER pie chart categories for visualization.
What I've done:
Used ...
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Reading clustal format alingments
I am trying to make a python script that allows me to get an already generated alignment from clustal W online, introducing the sequences of a set of primers and getting an HTML with all the sequences ...
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How do I get a dataset of NRPS Enzymes from antiSMASH?
I need a dataset of Non-Ribosomal Peptide Synthetases (NRPSs) for my research. I think it should be there on antiSMASH but unfortunately after trying many types of queries (here) I was not able to get ...
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1
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Getting organism information from the ENA API
I have been generating Snakemake sample tables from a GEO identifier (GSExxxxxx) directly by making requests to the NCBI and ENA APIs. It works, but with some caveats (explained in this open question: ...
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Understanding NCBI eutils API results
I have made a Python function that can turn an NCBI GEO identifier (GSExxxxxx) into an ENA bioproject accession using the NCBI API. I need this to get sample tables which I then feed into Snakemake. ...
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Inquiry about using EMBOSS MATCHER with Python
I am new to Bioinformatics and want to know if this is possible. I have a .txt file with a series of 50 gene sequences and I want to know if I can find the identity of them iteratively through a ...
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Why is Biotite not returning correct hbonds count?
According to HBPLUS, 5i55.pdb has 44 hydrogen bonds.
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How can I group mitochondrial heteroplasmy into bins based on age
I have mitochondrial heteroplasmy data obtained from ddPCR that I am trying to group into age bins. One bin edge has to be 0. I would like to dynamically choose all the other bin edges.
Each bin ...
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Install DCA and its dependencies
I am trying to install DCA but it fails due to dependency issues. The package is no longer being maintained. Following are the commands I need to run:
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Still Having Trouble Integrating LinearFold with Arnie's bpps.py – KeyError 'linearfold_v' & Import Issues Despite Proper Configuration
I am modifying bpps.py in the Arnie Python package to integrate LinearFold for RNA secondary structure predictions. However, I keep encountering "KeyError: '...
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Issues Configuring Arnie with LinearFold, LinearPartition, and bpps.py – ViennaRNA Path and RNAfold Execution Errors
I am trying to configure Arnie to work with LinearFold, LinearPartition, and ensure that bpps.py integrates properly. However, I’ve encountered multiple issues regarding ViennaRNA path detection, ...
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How do I convert data from an excel sheet into .json format properly according to a template?
I am an undergraduate student trying to understand the working of Apta-MCTS (https://pmc.ncbi.nlm.nih.gov/articles/PMC8232527/). I believe that initially, I have to run the preprocess.py file first ...
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pycoQC: N50 is zero (or null). overflow encountered in scalar add
We ran into an issue with pycoQC this week that we spent a stupid amount of time resolving. Someone reported a related issue on the ...
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vSNP step2 no output
I am running vSNP step 2 and it is saying that the process completed and that it saved the VCF files in default files but I can't find any output. I'm not getting any errors either. Here is my script:
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Arnie (RNA Folding) Not Detecting ViennaRNA Even After Modifying utils.py
I'm trying to use the Arnie Python package for RNA folding with ViennaRNA and LinearFold. However, even after modifying utils.py to include debugging statements and manually add ViennaRNA, Arnie does ...
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