Questions tagged [python]

python is a programming language, widely used in bioinformatics

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votes
2answers
135 views

Getting data from fastq by generator

I have a task in a training that I have to read and filter the 'good' reads of big fastq files. I downsampled, got the code working, saving in a python dictionary. But turns out the original files ...
1
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2answers
395 views

Chunk alignment in a name sorted bam for parallel processing

I have a bam file with 1 billion alignment reads of which there are 700 million unique reads. I want to split the alignments into chunks for parallel-processing. Multi-alignments of the same read ...
3
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2answers
2k views

Python - Finding a motif - input: a txt file with 10 sequences and 10 motifs

When I run my BruteForce function with only one input it works and the result is correct. ...
9
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3answers
2k views

Running Snakemake in one single conda env

I have been experimenting a lot lately with Snakemake, I love it. Recently I also switched to using conda (--use-conda) in the way that is advertised. However, I have some issues with it, mostly ...
2
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1answer
374 views

Python string editing in Snakemake

I'm running a custom perl script using Snakemake. I use this rule: ...
4
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2answers
280 views

Plotting coverage of annotation over collection of region

I'm trying to plot "meta" coverage of annotation: i.e. features (eg. gene class) over certain regions. It is similar to read coverage plots over gene body, except my input is two bed files (both in ...
2
votes
2answers
463 views

Calculate molecular mass from chemical formula C9H15N4O8P with Python?

Can I calculate the molecular mass from a formula like this C9H15N4O8P with Python e.g. using rdkit? I think ...
2
votes
1answer
73 views

Drug with as many targets as possible through a system biology graph?

I have 4 pandas data frames containing the following data: affinity_score1: affinity between each couple (Drug-Target) measured using tool1 affinity_score2: affinity between each couple (Drug-Target)...
2
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0answers
100 views

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)" ...
3
votes
1answer
244 views

python does not quit when the input file is too big

I have a script that extracts the set of unique kmer pairs from a kmer dump file (& then using them downstream to guess ploidy). The script seems to work correctly (it's reporting a meaningful ...
1
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0answers
439 views

How to plot a 2D RNA structure in python using dot-bracket input?

I need some help with forgi library for visualisation of RNA secondary structure. I have an RNA sequence and dot-bracket notation of the secondary structure and I would like to plot 2D graph like ...
5
votes
1answer
133 views

How to find all variable-length seqs with an exact 5' and 3' match in a FASTA file

Context I am interested in finding all of the promotors specific to a particular sigma factor. I have identified the -35 and -10 sites from the literature, bold denotes -10, -35, binding sites: <...
2
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1answer
619 views

Snakemake: Cannot find first rule?

Back again with another snakemake query. This time I decided to port my read cleaning and alignment pipeline to snakemake. Repeating the steps from previous question and trying not to make any typo ...
3
votes
1answer
131 views

How to remove frame on RDKit figures?

RDKit can plot molecules, thought the structures are surrounded by an ugly frame with ticks. How can I turn that off and plot the molecules without that frame? Note, the ...
1
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1answer
92 views

Rdkit.Chem.Draw.savefig() creates empty figures

I can draw a molecule in a jupyter notebook with RDKit. Though, when I use the savefig() method only a white canvas is saved. No molecule is saved. ...
1
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1answer
234 views
1
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1answer
132 views

How to separate a microbial strain of MTB resistant and susceptible drugwise?

Im trying to classify my list into three type: XDR - A strain must be resistant to: ...
0
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1answer
806 views

How to get PSSM of protein by protein sequence with python? [closed]

I didn't find way that convert protein sequences in FASTA to PSSM by python, and how to write program in python to find PSSM for our data set ? Maybe better to question how to find PSSM from NCBI ...
4
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2answers
60 views

Group genes by functional categories suming expression values

Using the count of rpkm values from genes in a metagenome sample, I want to group these genes into established categories (for example KEGG or COG). For each sample, my goal is to determine which ...
0
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0answers
30 views

Python module bamtags

Does anyone know this python module, bamtags? I'm using a pipeline (Dovetail Genomics, HiRise) that imports it, but it seems it doesn't exist. It's impossible to install it and there is no ...
3
votes
1answer
67 views

RSVSim insertions from chr1 to chr2

edit explaining python tag I would still rather have a solution based on the RSVSim package in R, but while waiting for someone who might have an answer I wanted to look at other solutions as well. ...
2
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0answers
761 views

Searching for start and stop codons for protein sequencing of contigs

I need to convert contigs into their respective protein sequences given a reference genome (i.e. I need to take a substring, whose position is already known on the string, and I need to locate the ...
2
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1answer
71 views

Store contigs and genome substrings based on mismatches

I have a string, a list of substrings, and a list of positions where substrings are found in string. ...
5
votes
2answers
137 views

How to plot character state changes from a presence-absence matrix on to a phylogeny

I wish to assign character state changes from a presence-absence matrix to a phylogeny. Thus I want to identify the most parsimonious hypothesis for which node and branch a given "mutation" or "change"...
1
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1answer
151 views

AttributeError: module 'scater' has no attribute 'normalize'

I am using rpy2 to run normalization using scran package. After calling computeSumFactors I ...
4
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1answer
116 views

python package for NNI neighbors

I am working on protein sequence data files for reconstructing phylogenetic tree and I need to generate all NNI-neighbours of the tree (two trees are NNI-neighbours if one can be transformed into ...
3
votes
1answer
291 views

How to iterate protein sequences using amino acids?

I was working on certain program using python and I have been using a protein aligned sequence file in two formats, phylip (.phy) and clustal (.aln). Example clustal file: ...
2
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1answer
180 views

Counting the characters in a row using python

I am using python 3 and biopython 1.72. I have been using a protein sequence file in clustal format. ...
3
votes
1answer
688 views

How to automate NCBI genome download

I need to download all the completely assembled cyanobacterial genome's GenBank file(.gbff) from NCBI(RefSeq or INSDC ftp data). For this I think, the steps are: Need to find the completely ...
0
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1answer
139 views

Check if a string is ensembl gene id or not in python

I have many scRNAseq datasets saved as hdf5 files, and when I open them keys sometimes are confused, so I need a way of ...
-1
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1answer
140 views

Convert TPM-normalized matrices back to UMI in python

I want to process a plenty of scRNAseq datasets in python, and I want to run TMM ...
5
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1answer
415 views

Using pysam with cython: htslib/kstring.h not found

I'm trying to learn to use cython to speed up some code based on pysam. My issue is not strictly speaking about bioinformatics, but rather about building tools using a bioinformatics library. I hope ...
0
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2answers
622 views

Python API for working with ENSEMBL genomes

Dear bioinformaticians, I could find two python APIs to mine ENSEMBL genome databases. There is a pyensembl which is more popular and then there is ...
1
vote
1answer
80 views

How to efficiently extract coordinates from a `pybedtools.Interval`?

I'm using pybedtools to process data, and at some point, I loop over a BedTool object and use unpacking to extract coordinates from the ...
0
votes
1answer
153 views

How to calculate Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation from protein (amino acid) sequences?

I want to code Moreau-Broto autocorrelation, Moran autocorrelation, Geary autocorrelation in Python 3.6 from the scratch for amino acid sequences without using any package. Unfortunately, I have not ...
2
votes
1answer
144 views

Plotting Ramachandran Plot from more than one PDB file

I want to plot a Ramachandran Plot for around 5000 PDB files in python that is saved in a folder in my system. I am searching for a way to make it without accessing each file by hard-coding each file ...
2
votes
1answer
463 views

pysam pileup: what reads appear in the pileup?

Cross-posted on Biostars (with no answers currently). I hope that's OK. I thought that iff a read matches the reference at a position, it would appear in the pileup column for that position. But ...
2
votes
1answer
101 views

Download proteomes from NCBI based only on binomial names

I'm trying to download around 2000 proteomes from NCBI, but all I have is the genus and species e.g: lophodermium_seditiosum trichoderma_harzianum Does anyone know ...
0
votes
2answers
409 views

Running python script from terminal: umap issue

Some time ago I asked the question: RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP' It was solved by following the answer in it, however, it is still not ...
3
votes
1answer
205 views

Issues installing Dendropy

I want to perform phylogenetic analysis using Dendropy. I have installed dendropy using command sudo pip install -U dendropy but when I import it in python3.5.1 it ...
6
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1answer
106 views

Generating random BED intervals given constraints

Problem is to generate a random BED interval given the following constraints: minimum start maximum end fixed length maximum ...
3
votes
1answer
687 views

How to extract the protein fasta file from a genbank file?

Let's say I have a genbank file, e.g. the one downloaded from here, that contains entries as ...
14
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1answer
925 views

Biopython Phylogenetic Tree replace branch tip labels by sequence logos

Having recently constructed a lot of phylogenetic trees with the module TreeConstruction from Phylo package from Biopython, I've been asked to replace the branch tip labels by the corresponding ...
4
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1answer
209 views

Finding proteins in a sequence

I have a file with protein sequences, all on a single line, like this: ...
5
votes
2answers
179 views

Is there a Python/R package with the ability to convert an alignment and reference into a CIGAR?

I'm writing a python function from scratch to do this, but I feel like this must exist in some standard bioinformatics library already. In principle, this is a simply regex operation which many must ...
2
votes
2answers
85 views

counting individuals with the present gene and absent gene for each population

I have a folder containing 500 files from different individuals: ...
5
votes
1answer
105 views

How to convert the given mathematical computation (on biological problem) to mathematical fomula, equation?

I have crossposted this question in maths StackExchange. The problem is dominantly mathematical (this question) but the application of the problem is mainly biological. Hoping that people in this ...
1
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1answer
403 views

I need to use my code with fasta format. Can anybody help?

I need some help. I have written a program that simulates protein cleavage but I need to modify it so that it produces fasta formatted output. here is all of my sequence in .fas file ...
7
votes
2answers
1k views

Convert R RNA-seq data object to a Python object

I have done some work in R and would like to try a Python tool. What is a good way to import the data (and its annotations etc) as a Python object? I am particularly interested in converting a ...
3
votes
2answers
213 views

Pepsin digest (cleavage) does not work using RE?

Aim is to code the theoretical peptic cleavage of protein sequences in Python. The cleavage (cutting) rule for pepsin is: 1234^567. This is a position, ...