Questions tagged [python]

python is a programming language, widely used in bioinformatics

Filter by
Sorted by
Tagged with
0
votes
1answer
30 views

MemoryError w/ matrix | Smith-Waterman Algorithm Python

I am implementing my own version of the Smith-Waterman algorithm. This works perfectly fine with 2 genomes of 100 chars each. However, I want to run this ...
1
vote
0answers
26 views

Load balancing numerous single-threaded processes with Snakemake on the grid

I'm familiar with running Snakemake in a DRMAA-enabled grid environment. (Most often, I write Python programs as wrappers and invoke the workflow via Snakemake's Python API.) Typically, I'm running ...
0
votes
1answer
32 views

Common gene naming conventions and how to convert between them

I have two questions, one is a direct question about some RNA expression data. The other is more broad, but motivated by the first. I have downloaded an expression set for a class project and I am ...
0
votes
2answers
79 views

Remove Redundant Sequences from FASTA file with Biopython reducing memory footprint

I need help with my Biopython code, I am kind of new to Python and Biopython so please don't be harsh on me. Everything started from here: Remove duplicated sequences in FASTA with Python I answered ...
1
vote
0answers
36 views

Error during File conversion

Conversion of a multi-entry sdf to a multi-entry pdb file with open babel results in the loss of the compound names in the resulting PDB file. Why do you think this might occur and how can I resolve ...
1
vote
1answer
20 views

Create a NHX phylogeny format with r or python

I need help to add information in my phylogenetic tree on each branch. I have two pieces of information at my disposal: 1 ) A phylogenetic tree in newick format : <...
2
votes
0answers
36 views

Snakemake fails because it cannot create logs inside a read-only Singularity Container

I am using Snakemake from inside a Singularity container. Because of that, the directory that Snakemake wants to log to cannot be created, and I get an ...
3
votes
2answers
79 views

Create new range based from existing range (python)

I have a pyranges object that I am looking to iterate over. For each range, I would like to "resize" it to its centre (so start+end/2) and save that into ...
0
votes
0answers
23 views

Reliably create female and male individuals in a -ped file for plink

For a study I need some kind of "decoy" GWAS-data. For this I created a panel with some genes, the same ones as in the real data. From NCBI I fetch some of their SNPs and create my own ...
1
vote
1answer
58 views

How can I use pandas agg here to avoid iteration?

can anyone help me improve this pandas code? ...
1
vote
1answer
42 views

How to convert a SDF molecular structure file to a pandas dataframe with Python?

What is the best python tool to convert a SDF file to a structured data frame (pandas.DataFrame). Similar to Molconvert from ChemAxon? SDF can have different datafields for each compound which I would ...
0
votes
0answers
16 views

How to fetch all protein sequences from c3.ai Covid datalake?

I want to download ALL currently known protein sequences for all SARS-CoV-2 strains. I am not sure how up ...
1
vote
1answer
324 views

What changed wwith Python in WDL change from draft 2 to version 1?

I'm updating my WDL from draft 2 (whichs works fine) to version 1. I'm stuck with a Py snippet ...
0
votes
1answer
58 views

OpenAPI-Generator Python Client Instructions Examples

Trying to learn a little bit of Python and Biopython I ended up figuring out what a Rest API is when the RCSB PDB repository released its new Rest API. I tried to retrieve info from the PDB repository ...
-1
votes
2answers
62 views

How can I convert Protein ID to PDB ID?

I have a list of Protein ID such as Q9S9U6, A2XLL2, Q06402. What name is this ID? UniProtKB ID? And how can I get PDB ID from this list? Is its PDB ID only one? I'm using Python. Get a list of PDB ids ...
0
votes
0answers
31 views

How can I get properties from each one letter amino acid?

Im using python and wish to get properties from each one letter amino acid? I mean M(Met) => Density:1.340, MW:149.21... The RDkit methods atom.GetSymbol(), atom.GetDegree() permit this and I am ...
0
votes
1answer
41 views

Loop Pymol command get_area

I want to select multiple residues from different PDB files loaded on the same pymol session. select resi LIG get_area sele How do I loop the above command to ...
1
vote
1answer
28 views

Segment cell organelles with pixellib

I've got some images of cell organelles and I really want to avoid labeling them by hand. The images all look something like the image below. Is there already an existing model specifially for cells? ...
-4
votes
1answer
59 views

Creating a tab delimited column [closed]

I have a blast file produced. I executed a blast(x) command outputting both "qeseqid" and ...
1
vote
0answers
18 views

Detecting Allelic Imbalance

I am interested in detecting allelic imbalance for a credible set of SNPs. Currently, I am looking for some packages, hopefully, for Python, that can assist with this. I am aware of this R package, ...
1
vote
5answers
123 views

How to remove duplicates from a fasta file using python

I am using the following command: ...
0
votes
2answers
42 views

How to obtain desired output?

I am working on a project using the following command within nano: ...
0
votes
2answers
48 views

How to fix NameError?

I am working on a project and am having issues with the following code that I have written in nano: ...
2
votes
1answer
77 views

Survival analysis using CoxPH - Effect of covariates

Hi and sorry for the long post in advance, I'm doing a survival analysis of lung cancer patients using Python's lifelines package. According to the documentation, the function ...
0
votes
1answer
45 views

How to concatenate two fasta sequences by py

I have three backbone and i want to concatenate 70 sequence into these backbone. such like: fasta file 1: ...
1
vote
1answer
37 views

Is there a Python program that is able to show convergent and divergent evolution on a phylogenetic tree?

I was wondering if there was a Python program that detects convergent and divergent evolution on a tree. I am also curious if it is just better to look at a phylogenetic tree and conclude what is ...
1
vote
1answer
42 views

Is there a simple command for outputting a tab delimited columns?

I am working on a fasta file and am writing my command in nano within command-line and executing using python, also within a command line. My objective is to get my command to provide me with a tab ...
0
votes
2answers
56 views

creating a tab delimited file

I am working on a project using a fasta file. I am writing my command in nano within command-line and executing using python, also within my command-line. I would like my command to provide me with a ...
0
votes
1answer
49 views

How do you currently track bugs/assign bioinformatics bugs using freely available bioinformatics software/websites?

I am starting a project using Python to track, archive, assign and manage bioinformatics bugs. This software will be able to be integrated into project management software or stand alone. How do you ...
1
vote
1answer
53 views

cmapPy exception

I'm trying to read gctx files with cmapPy. This is my code: ...
0
votes
0answers
23 views

Opening gctx files

I installed cmapPy but I don't know how to use it to read gctx files. I read the documentation. If anyone knows how to do it with cmapPy or any faster method your help would be greatly appreciated. I ...
1
vote
1answer
123 views

How to predict with the pre-trained DNABERT model?

I was curious to give DNA BERT a try. This is a BERT (Bidirectional Encoder Representations from Transformers) model that was trained on short (k=3,4,5, or 6) k-...
1
vote
1answer
118 views

I want to write python program to cut a DNA sequence at an EcoRI restriction site and print the two fragments after cutting

Seq = AAAAAAAAAAATTTTTTTTTTTGAATTCCCCCCCCCCCGGGGGGGGGGG Restriction site = GAATTC I want to cut the sequence at GA/ATTC I tried split method in python but It does not cut at GA/ATTC. Please help
1
vote
1answer
72 views

Find CRISPR PAM-sites with python

I am a college student and just started bioinformatics. I am trying to write a script (not for school) that finds all potential NGG and TTTN protospacer adjacent motif sequences in a genome string. I ...
0
votes
1answer
142 views

Nonbonded interactions on the GPU

i'm using this command gmx mdrun -deffnm nvt0 -nb gpu but got ...
1
vote
2answers
103 views

How to sort multiple FASTA files based on their content?

I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate these files into different locations based on ...
0
votes
2answers
42 views

How to sort multiple FASTA files based on their content? [duplicate]

So I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate these files into different locations based ...
0
votes
1answer
20 views

How can I add for several bed files the header : track type=narrowPeak name=“narrowPeak” preferably in python ,can handle with R

I want to create custom tracks from these files I can add the line : track type=narrowPeak name=“narrowPeak” manually by opening it with text editor: track type=narrowPeak name=“narrowPeak” but I ...
0
votes
0answers
39 views

Python/Biopython - Replace amino acid residue on MSA with “z” from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
4
votes
1answer
105 views

Are there computational tools to extract features of DNA sequences?

I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc. I have found the generateFeatures.py script from the PyFeat repo, but is there ...
0
votes
0answers
20 views

skbio “ValueError: Tree must be rooted” when using tree generated from SILVA's ACT

I'm trying to compute unweighted unifrac distances between samples. To do that, I generated a tree using SILVA's Alignment, Classification and Tree Service. I read the tree in using: ...
0
votes
1answer
38 views

.cif .pdb conversion with python

can you please give me an advice how to convert .cif files into .pdb preferably using python? Thanks in advance! Best, Balint Biro
0
votes
0answers
7 views

How to generate variant DNA sequence from an HGVS-formatted variant?

I'm parsing clinvitae using the python hgvs module. For each variant, I want to generate the variant DNA sequence in a 500 bp radius around the variant position. I don't see a way to generate the ...
1
vote
0answers
34 views

project ideas for a final year CS undergrad/CS masters student [closed]

I am enrolled in an online undergrad CS program in Canada and also Georgia Tech OMSCS where I finished computational photography and AI for Robotics. I also have some deep learning programming ...
0
votes
0answers
29 views

GWAS phenotype data format and preprocessing

I have a set of different phenotypes which I want to use for a GWAS analysis (general linear model). I have a couple of questions and uncertainty about the phenotype data input. I have control and ...
2
votes
1answer
49 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
3
votes
0answers
66 views

Using dssp after chain extraction

I have a list of PDB IDs with realtive chains that are to be extracted, and the run on dssp. For the single chain extraction I tried several methods, such as: ...
1
vote
2answers
166 views

How to run Jupyter script on Slurm HPC

Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it? ...

1
2 3 4 5 6