Questions tagged [python]
python is a programming language, widely used in bioinformatics
597
questions
2
votes
1
answer
134
views
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 ...
CommunityBot
- 1
1
vote
1
answer
63
views
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:
...
CommunityBot
- 1
1
vote
1
answer
93
views
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 ...
CommunityBot
- 1
1
vote
1
answer
421
views
Is there a way to use BioLemmatizer from Python?
Lemmatization is one of the most important tasks for text normalization in natural language processing (NLP), i.e. using deep learning to understand text data.
One of the good lemmatizers I found for ...
CommunityBot
- 1
-1
votes
0
answers
25
views
How can I convert ecat(.v) file to nifti(.nii) file in python?
I want to convert ecat file to nifiti file or ecat file to dicom so I can change it to .nii later. I would like it in python if possible. Do you have any library suggestion? Thank you
2
votes
0
answers
35
views
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:
...
- 2,086
6
votes
2
answers
227
views
BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure
I am using the internal_coords module from BioPython in order to compare dihedral angles of two different conformations of the same protein. The conformations are ...
- 955
3
votes
1
answer
74
views
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 ...
CommunityBot
- 1
2
votes
1
answer
27
views
retrieving past BLAST requests in bioPython
is there any way to retrieve a BLAST request made using the Biopython library using the request's query_id?
Alternatively is it possible to retrieve a query_id before the blast result is complete, and ...
1
vote
0
answers
30
views
0
votes
0
answers
19
views
1
vote
1
answer
41
views
querying gdc metadata issues with resulting fields
I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to ...
CommunityBot
- 1
1
vote
0
answers
25
views
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 ...
- 13.8k
-1
votes
1
answer
19
views
New to DNABERT confused about kmers input
I'm trying to use DNABERT to predict promoter regions. Right now, I have a df with 500k rows, 1st column is the DNA sequence (all different lengths), 2nd column says "promoter" vs. "non-...
- 2,086
1
vote
0
answers
18
views
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:
...
- 11
2
votes
2
answers
240
views
motif searching in a multi-fasta file
I am having trouble trying to search for motifs in a multi fasta file. I have used two techniques one gives me the name of the sequence where the motif is found but doesn't give me the the motif and ...
2
votes
3
answers
547
views
Retrieve ID ligand from PDB file
I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex.
Is there a way to do that ...
- 955
2
votes
1
answer
22
views
BioPython SeqIO fails with Invalid Alphabet found
I am trying to store a GenBank file that could be read by Geneious later.
I found an example how to create the GenBank file here
But now I run into Alphabet issues.
...
M__♦
- 11.9k
0
votes
0
answers
31
views
Error in snakemake when running conda envs in container
I am facing an issue when running snakemake with a container and conda.
Let me explain better.
I am developing a workflow (locally) in snakemake, where some rules use a conda env (defined in /envs/env....
- 123
1
vote
1
answer
646
views
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 ...
CommunityBot
- 1
3
votes
1
answer
558
views
GWAS in python?
A question similar to this has also been asked on Biostars
I understand GWAS is done with R, but are any written in Python?
I'm used to python and java, acclimating to R will take a bit of time and my ...
- 13.8k
1
vote
3
answers
496
views
How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?
I know the algorithm for creating a Hydrogen atom and adding to a residue:
...
- 955
1
vote
0
answers
58
views
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-...
- 181
2
votes
3
answers
103
views
How to merge multiple list into a single dataframe replacing common values with 1 -python
I have multiple lists on python:
...
- 51
3
votes
1
answer
101
views
Generating CIGAR strings for MSA with reference
I have a list containing the results of a MSA:
...
- 181
6
votes
5
answers
6k
views
How to create Phylogenetic Trees from fasta files in Python or R?
I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in Python or R ...
- 106
2
votes
1
answer
555
views
Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"
I am using this script:
...
- 206
2
votes
2
answers
35
views
Compare files with similar names using placeholders/wildcards in Snakemake
In Snakemake I want to use two input files for comparison. The one file has a sample name (e.g. 526846), with an experimental id (e.g. EF_S13' and 'MF_S5'). The file I want to compare it to has the ...
- 301
1
vote
2
answers
220
views
ValueError: count not convert string to float
I'm trying to use a Python script to plot with a rolling window using pandas and seaborn. This code worked for the longest time but now it's giving me an error that I don't know how to fix.
Here is ...
M__♦
- 11.9k
1
vote
1
answer
70
views
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 ...
CommunityBot
- 1
2
votes
1
answer
62
views
How can I develop a snakemake rule for all files in multiple directories?
I am a beginner in snakemake and I'm trying to develop a working flow.
Imagine I have multiple folders and in each folder I have a tumour and normal sample files:
...
- 51
-1
votes
1
answer
87
views
For loop in Python goes wrong
I have mutation status (0,1) for ten genes in ten cancer 3D models
I have also gene expression in these 3D models, like
...
- 2,086
0
votes
1
answer
141
views
How to pack up a Python script in the form a Dockerfile
I have a simple Python script with this header
...
- 1,108
0
votes
1
answer
259
views
Looping over a list of cell models in Python
I have two data sets
Mutations in 10 genes
Gene expression in 18 cancer 3D models
For every (mutation, gene) and gene expression pair we run an ANOVA test
This is my data
...
- 239
2
votes
1
answer
50
views
2
votes
1
answer
244
views
ETE4 manual or improved code description
ETE3 * (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.
ETE4.0.0 ...
M__♦
- 11.9k
2
votes
2
answers
208
views
Blastp MSA to the same length
To generate aligned protein sequence truncate to the same length, I use blastp in biopython for MSA. I have multiple queries and one subject sequence. However, the alignment never returns the same ...
M__♦
- 11.9k
1
vote
1
answer
55
views
different results of RMSD for the same trajectory file
I want to analyze the RMSD of my trajectory files using MdTraj.
I used two different codes for this purpose:
the first code:
...
CommunityBot
- 1
0
votes
1
answer
77
views
Model the effect of treatment on mutation burden
I am struggling a bit to model the following problem. Basically, I would like to model tumor mutation burden (mutations per megabase, a continuous) as a function of treatment (categorical). The ...
CommunityBot
- 1
1
vote
1
answer
309
views
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 ...
CommunityBot
- 1
1
vote
1
answer
30
views
How to access yeast-cyc in a programmatic way to extract the GO terms?
I am a newbie in Bioinformatics, I want to extract the GO terms from yeast-cyc,
which is items in the Go terms tab of this page https://yeast.biocyc.org/gene?orgid=YEAST&id=G3O-29622#tab=GO , not ...
- 695
2
votes
1
answer
59
views
Snakemake and github actions
I am working on a snake-make workflow that follows the guidelines of formatting and linting so that it can be published on the official Snake-make repository.
Whenever I push my code on GitHub, the ...
- 13.8k
2
votes
2
answers
772
views
Biopython - extracting query coverage from XML Blast output
I need to extract (or to calculate precisely) the query coverage from Blast output. I am using NCBIWWW.qblast to query Blast in XML format.
Is it possible to know the query coverage parsing the XML ...
CommunityBot
- 1
4
votes
1
answer
73
views
Can not launch bcftools using python's subprocess module, as it only accepts first command of commands list
I am trying to remove samples from a chromosome vcf file. I wrote a function that takes chromosome number and a list of samples to remove. When I try to run bcftools using subprocess module it only ...
- 2,086
1
vote
1
answer
101
views
BioPython - Retrieve sequence records from pubmed database
I've been assigned a task to fetch sequence records from "pubmed" database:
fetch 30 record of type "fasta" from (pubmed database, with term hemoglobin AND alpha) as a sequence ...
CommunityBot
- 1
-1
votes
1
answer
79
views
Can I perform Expression Analysis on this 10x dataset?
10x Genomics: 20k Human PBMCs is the dataset.
Description of the dataset:
Inputs/Libraries
Human peripheral blood mononuclear cells (PBMCs) of a healthy male donor aged 30-35 were obtained by 10x ...
CommunityBot
- 1
-1
votes
1
answer
37
views
Feature-selection microbiome data to build a model to predict cancer
I want to build a machine learning model to predict colorectal cancer based on 16S rRNA microbiome data (stool samples).
I have filtered the data using filtering approach by Duvallet(removing samples ...
- 37
7
votes
2
answers
531
views
Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?
I have a project to write in Python that requires to write a function that given degenerate DNA sequence (for example: KKGTACACCAG) sequence and a molecular weight interval, returns a list of all ...
- 613
1
vote
2
answers
244
views
Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
M__♦
- 11.9k
2
votes
1
answer
59
views
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 ...
CommunityBot
- 1