Questions tagged [python]

python is a programming language, widely used in bioinformatics

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1answer
96 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 ...
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1answer
37 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? ...
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1answer
63 views

Creating a tab delimited column [closed]

I have a blast file produced. I executed a blast(x) command outputting both "qeseqid" and ...
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0answers
19 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, ...
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5answers
155 views

How to remove duplicates from a fasta file using python

I am using the following command: ...
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2answers
44 views

How to obtain desired output?

I am working on a project using the following command within nano: ...
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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: ...
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1answer
94 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 ...
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1answer
67 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: ...
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1answer
55 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
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1answer
44 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 ...
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2answers
62 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 ...
2
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1answer
85 views

How do you currently track bugs in python using freely available 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 ...
2
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1answer
60 views

cmapPy exception

I'm trying to read gctx files with cmapPy. This is my code: ...
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0answers
27 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 ...
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1answer
198 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-...
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1answer
218 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
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1answer
79 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 ...
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1answer
170 views

Nonbonded interactions on the GPU

i'm using this command gmx mdrun -deffnm nvt0 -nb gpu but got ...
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2answers
175 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 ...
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2answers
46 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
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1answer
28 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 ...
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0answers
46 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
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1answer
119 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 ...
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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: ...
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1answer
47 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
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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 ...
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0answers
45 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 ...
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0answers
53 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 ...
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1answer
65 views

Truble to run a multiprocessing kmer count script

Hi there I have this code: ...
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0answers
97 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: ...
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2answers
192 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? ...
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2answers
104 views

Interpreting GWAS results with different settings

I did a bunch of GWAS analysis (linear model without covariates) with applying different quality controls. How to choose the optimal settings when filtering for minor allele frequency (maf), Hardy-...
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1answer
74 views

repophlan script to download bacterial genome

I am trying to donwload the microbial genome using the repophlan_get_microbes.py (https://github.com/SegataLab/repophlan) but now it is running more than 10 days and still not finished on slurm HPC. ...
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1answer
49 views

How to get the uniparc ids for all members of uniref cluster in batch request?

I currently use the 'UniProt website REST API' (example) to collect the UniParc IDs of all the members of the given cluster. Fetching each entry individually is very slow though, so I wanted to ask if ...
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0answers
184 views

GTF parser for Python

I found this GTF parser for Python. However, it does not work with Scallop's GTF file: ...
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2answers
42 views

How to refine this distribution comparison script

My data look like this They are compound similarity estimations(the whole file is around 10GB). What I am trying to achieve is to compare the similarity distributions of each compound using the ...
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1answer
223 views

Dealing with duplicate keys

I got the following error: attempting to use to_dict to index a multiple sequence FASTA file with duplicate keys. Are there methods for working around duplicate keys in biopython? I was thinking to ...
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1answer
188 views

Error When Using biocLite as an installer in rpy2 python library

I am running into an error when I tried to run the following lines of code, the error at line 3: ...
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2answers
421 views

Python equivalent to R GRanges and IRanges

Problem: I am trying to convert some codes written in R to Python and part of that conversion process is find classes equivalent to the GRanges and IRanges from the GenomicRanges R package in Python. ...
6
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1answer
335 views

Biohackers Netflix - DNA to binary and video

I'm not sponsored or anything, just interested in their challenge to decipher their DNA code. They encoded their first episode of "Biohackers" video/binary file to DNA code and said if we ...
3
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2answers
229 views

How does DeepVariant construct RGB images from DNA sequences?

DeepVariant is a pipeline to call genetic variants from DNA sequencing data. A major step, before feeding the CNN, is to translate these DNA sequences into images. It's unclear why and how Google ...
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1answer
45 views

GWAS MAC filter Interpretation

I am performing a GWAS analysis and try to understand the influence of the minor allele count filter.Setting the filter to 1 % gave me this plot and I am confused about the same -log10 pvalues around ~...
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1answer
57 views
1
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1answer
120 views

Need a alternative or more complex version of venn diagram in python for matching dna sequences

I am in google colab and I have combined and set up a data frame list of sequences that goes like this Location ID Sequence 1.1 ........ A ........ AAGAGATA 1.2 ........ A........... ...
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2answers
49 views

Transcribing DNA exons and append transcripts into a list

I am trying to find a way to read and transcribe a list of DNA sequences (list of lists) only when the for loop finds a start codon (triplet of the list items) and until it finds a stop codon, over ...
1
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1answer
239 views

Convert VCF to genotype table

How can I convert a VCF file into a genotype table (SNP matrix)? I have this format: ...
1
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1answer
226 views

Split fasta file based on groups in header information and output as separate files

I have a fasta file containing the sequence of a gene across different species. In total there are around 900 samples and 12 species. (Each sequences is over multiple lines and longer than 100bp.) My ...

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