Questions tagged [python]
python is a programming language, widely used in bioinformatics
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questions with no upvoted or accepted answers
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Using dssp after chain extraction
I have a list of PDB IDs with realtive chains IDs that have to be extracted, and then run on dssp.
For the single chain extraction I tried several methods, such as:
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977
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changing blast parameters using NCBIWWW module
I have found a blog post with a script that I would like to use for my current research project: link
The script is incredibly fast and produces a smooth conservation plot. In the blog post, the ...
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How can I use statistics to compare microbial phenotypes?
Note: this question has also been asked on Biostars
I am currently trying to create a theoretical argument that a microbe's phenotype can affect gene expression in their host. I have 5 species of ...
3
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50
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Issue creating CNV plot from WES data
I received Whole Exome Sequencing data from an NGS company (CARIS, specifically). I received R1 and R2 FASTQ files, a BAM file aligned to hg38, and a VCF file.
I used CNVPytor to create a CNV plot (...
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How to concatenate 2 `mdata` of `muon` package?
I used muon(https://github.com/scverse/muon) for single cell Multimodal omics analysis.
How to concatenate 2 mdata from ...
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How are BLAST record scores calculated in biopython
Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
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3
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How to use hgvs to project a variant list on a given protein sequence string?
I have the following protein structural variance list:
...
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3
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1
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How to extract and visualize sequence logos from CNN kernels?
I created a basic CNN architecture using Tensorflow to classify transcription factor binding sites. My aim is to somehow extract and visualize sequence logos from the convolutional kernels. The model ...
3
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Finding common and unique data set by comparing two files based on their column and to split the columns multiple strings to print in output
I have very large sizes tab-delimited .vcf files and want to match these two / or 3 files based on their position and print to a new .csv file
File structures:
File_1: tab-delimited file (.vcf) ...
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2
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How to perform liftover from 38 to 37 in R?
I have some gwas summary statistics in GRCh38 that I want to lift to GRCh37. I am trying to liftover in R using this code:
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Extracting positions from PAF files in order to extract sequences from a Fastq file with Python
I have used Minimap2 to create a paf file by aligning a Fastq file against itself. Now from this Paf file I can see where the reads overlap, and I want to take these positions, and use them to extract ...
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How to make a UMAP for single cell data and color cells by average expression of a list of genes in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.
I did ...
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pyScenic CLI for ctx is giving error: Not a single module loaded
Hi I ran pyScenic's ctx via the command in command prompt:
...
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2
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145
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Drawing synteny using CIRCOS from progressive MAUVE alignment
I am using Mauve app to align two whole genomes. I've aligned these genomes (gbk files) with the progressive Mauve aligner, and I got sp.sslist, sp.xmfa, sp.guide_tree,sp.backbone file, sp.bbcols etc ...
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finding motifs in fasta file with multiple sequences
I am able to find matching motifs on a single sequence, as well as their position as shown below :
...
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Writing to .cif from BioPandas
My question is twofold. First, I've run into an issue working with .cif files and pandas dataframes. With BioPandas, I can read a .pdb file into a dataframe and then go the opposite direction, writing ...
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Naming conventions for kegg nodes with multiple genes
So I'm downloading XML files from Kegg using BioConductor and and I'm running into a problem. If we look at HIF-1 signaling pathway we see the node growth factor (GF) on the left hand side, we can ...
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Is there a way to extract spike sequence from a Sars-CoV-2 complete genome (preferably in Python)?
I have a complete genome sequence of a Sars-CoV-2 variant, but I am only interested in the Spike sequence?
I should note that I am not a biologist (nor bioinformatics).
The complete genome looks like ...
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2
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355
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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 ...
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2
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270
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How to get the GO information for all the human genes?
I would like to retrieve a list of all the human genes and their proteins’ functional classification.
The Gene type attribute on ensembl.org is not specific ...
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2
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Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python
I am writing a Python script to automate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
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working with cutadapt
I'm working with ion torrent data where I apply the program cutadapt.
I'm analyzing ITS seq data, as well as Matk.
When I'm using cutadapt, I search the information for this genes, and built new ...
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2
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Number of reactions per metabolic pathway
What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
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How to get bootstrap support of phylogenetic tree?
I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" ...
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2
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161
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Post ipyrad filtering of SNP loci from GBS, based on SNP quality
I want to use SNPs produced by Ipyrad, which is a python script for RADseq, using maize genome data via RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic ...
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2
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277
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How to measure euclidean distance between points with vtkDelaunay3D package?
I'm working with python vtkDelaunay3D (scipy.spatial.Delaunay) package for a special purpose. Normally the package is used for triangulation/tetrahedralisation.
How do I measure euclidean distance ...
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Why does samtools mpileup sometimes include ref bases (other than ',' or '.')?
This is my first post here. I can think of no way of giving an easily reproducible example, as per the stack ethos. SO apologies in advance and any feedback on question format appreciated.
I have ...
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What are some good miRNA databases?
I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein ...
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Adding step size to cross validation in Python package lifelines
I'm using the Python package lifelines to build a CoxPH model where I reduce the step size to 0.1, like so:
...
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bcbio run not running samples in parallel
Sorry for the cross post but I'm not getting a response on bcbio github:
I'm trying to run bcbio on 20 samples and it's only running one at a time as it steps through the yaml seemingly. I'm using ...
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SNP How to detect regions of erratic pairwise alignment?
I have clusters of DNA sequences that contain some mutations. All the sequences in a cluster should contain the same mutations.
As the mutations aren't known, those clusters of sequences were pairwise-...
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How to use hashsolo for demultiplexing hashtags?
I am trying to use hashsolo and I want to make sure that I have done things correctly.
I did the below:
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GDC API: Obtain the Objective Power (or Magnification) of a WSI file
I've been trying to find out a way to retrieve the Objective Power (or Magnification) of a Whole Slide Image file without downloading it first.
I've seen that some WSI's Objective power might be 40x ...
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84
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From SMILE get Amber force in Python
I have a list of SMILES of small molecules and I want to be able to simulate these molecules with an Amber force field in Python. Currently, I use RDkit to convert the smile into a PDB file:
...
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300
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How to plot average gene expression in scanpy?
I would like to make a UMAP where the cells are colored by the average expression of the bulk signature genes but I am not confident that I did it correctly. I would like to use scanpy for it.
I did ...
- 115
1
vote
1
answer
309
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Reading a Fast5-file with Python
I am trying to extract data from fast5-file with python 3.9.13 in Ubuntu. I have found a library "fast5_research"(This package comprises an API to HDF containers used by the research groups ...
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Visualise multiple disappearing pdb files in Pymol
I have a sequence of pdb files which I want to load in pymol window so that it gives an impression of a video. I am using cmd.load function in a loop and deleting the loaded file in the next step. But ...
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29
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I want to map TFBS on to the sequences from dataset containing 8448 (210 base) sequences. its not giving all the hits I need
I want to map TFBS (transcription factor binding sites) on to the sequences from dataset containing 8448 (210 base) sequences, but it is not giving all the hits I need
...
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1
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Advise on building an effect ML model for predicting important proteins for drug response
I want to create a model to predict proteins which could be associated with drug response in cancer cell lines. I have cell line proteomics data, with compound screening data they have gained for a ...
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1
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AttributeError [in fastStructure's chooseK.py]: module 'vars' has no attribute 'insum'
I've been working with the fastStructure program and am on the step of analyzing model complexity using the provided chooseK.py script. I have been running into the following error:
...
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1
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646
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tensorflow nn_model for DNA sequences: Matrix size-incompatible: In[0]: [2,1], In[1]: [784,300]
Hope anyone can help a beginner here. I'm building a proof-of concept tensorflow classifier for DNA sequences. However, the NN model does not let through train and test vectors saying the matrix size ...
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HGVS python package : How to parse complex insertions?
In HGVS package, how to create more complex variants ?
I just wonder how can I parse more complex insertions such as those :
...
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Converting miRNA names to miRBase version IDs
I have a list of miRNAs IDs (2000-2500) that I want to find miRBase IDs for them. For example:
hsa-miR-106a ---> hsa-miR-106a-5p
hsa-miR-373* --> hsa-miR-373-5p
hsa-miR-33 --> hsa-miR-33a-5p
...
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Download COX1 (COI) gene via biopython using accessions for entire mitochondrial genomes
I have a list of accessions for the the entire mitochondrial genomes for big cats. I need to download the COX1 genes for each of these accessions.
Here is one accession and here is a link to its COX1 ...
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29
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In CIRIquant output, which column shows the expression level of circular?
I am running CIRIquant on Ubuntu 16.04 LTS following the instruction which indicated on https://ciriquant-cookbook.readthedocs.io/en/latest/de.html. I got .GTF file ...
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AttributeError: 'FeatureDB' object has no attribute 'strand'
It appers when a gene has a negative strand then I need to reverse the sequence. Unfortunately, I got the following error:
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646
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How to get a consensus sequence from a nanopore fastq files?
I am new in bioinformatic field. I would like to know a way to generate a consensus sequence from nanopore fastq files (fastq files demultiplexed).
I usually generate a consensus sequence with "...
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813
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Python script to calculate properties of amino acids and storing them in matrix
I want to make a python script that can get as input sequence of N amino acids, and the output is a matrix of Nx6 containing 6 features.
The features are:
Computed volume
Hydrophobicity
Surface ...
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3d model of a protein via nucleotide sequence
I really appreciate @Matteo Ferla's detailed answer to my previous question.
I've already tested several tools to know if a mutation can cause a modification in the function of protein or not. There ...
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