Questions tagged [python]

python is a programming language, widely used in bioinformatics

39 questions with no upvoted or accepted answers
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596 views

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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0answers
23 views

MSA (protein) with biopython or something else?

I am very new to bioinformatics (and python in general), but I would like to use python to more efficiently analyse enzymes both in terms of structure and functio, using Jupiter notebook. I would like ...
2
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1answer
54 views

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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0answers
68 views

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 ...
2
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0answers
38 views

Trouble optimizing Five Parameter Logistic (5PL) Standard Curve for ELISA data using Python

I am attempting to write a tool to be used by my lab to automatically generate a 5PL Standard Curve for ELISA data, using an XLSX file template. I am using pandas dataframes to hold the 96 wells as ...
2
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0answers
40 views

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 (kegg, metacyc,reactome..) is more helpful/reliable for ...
2
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1answer
146 views

Is there a way to use BioLemmatizer from Python?

Lemmatization is one of the most important tasks for text normalization in NLP. One of the good lemmatizers I found for biomedical domain is BioLemmatizer. However, it is developed in Java and is ...
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)" ...
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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0answers
103 views

Post ipyrad filtering of SNP loci from GBS, based on SNP quality

I want to use SNPs produced by ipyrad analysis of GBS data in RAxML to examine the monophyly of a highly-variable focal species and its phylogenetic relationships with about 40 congeners. An initial ...
2
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0answers
220 views

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 ...
1
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1answer
29 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 ...
1
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1answer
89 views

Downloading SRA Files from AWS

I want to download the original BAM files that the authors had uploaded to SRA. Normally, I would just use sam-dump, but the files are having issues that seem ...
1
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1answer
36 views

Finding discriminating positions for a sequence alignment column

I don't have any theoretical background in biology, so forgive me if my question is a bit.. well..dumb. I'm trying to use a Monte Carlo approach to find the discriminating position of a given sequence ...
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16 views

Indel quality from mpileup

Could someone please confirm that I understand this correctly? I have the res and qual columns from mpileup and I would like to match them to get the qual per base. It seems that the indel initiation (...
1
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1answer
73 views

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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1answer
128 views

Is there any tool for fuzzy sequence matching?

Note: this question was also asked on biostars are you aware of any tool that is able to perform error-tolerant pattern-matching search on protein FASTA files? For example, I want to know, which ...
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0answers
19 views

the positions computed by ms

I am doing simulations using a program 'ms': https://snoweye.github.io/phyclust/document/msdoc.pdf If you look at page 3 of this pdf, it explains the output produced by ms. The line which starts ...
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0answers
76 views

extracting gene names from pubmed abstracts

I have been extracted number of abstracts from pubmed. now I am having a bunch of abstracts of pubmed articles now from this abstracts I need to extract gene names which are included in abstracts.
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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 ...
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1answer
7 views

Python: How to write duplicate sequences removed from fasta file to new file

I currently am using this code to remove duplicate sequences from the fasta file. However, I would also like to write a new file with only the removed duplicates as well as a count for how many times ...
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43 views

Changing alpha-numeric IDs to numeric only IDs

I need to convert my three text files to the exact formatting of the corresponding example files in order to run my code. I think the formatting error being generated is from the geneID (bold) ...
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0answers
9 views

Could not parse String db protein interaction network PSI-MI XML file with GenerateDS Python parser

I want to get a list of all evidence types for interactions String db finds based on a list of gene names in order to filter in only those pieces of evidence I have confidence in. I downloaded a ...
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25 views

Error in ROSETTA flex ddG tutorial

I'm trying out the ROSETTA flex ddg tutorial (https://github.com/Kortemme-Lab/flex_ddG_tutorial). When running "Example 1" I get an output but with apparently empty folder. When running the "Analysis"...
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22 views

Finding regions between ORFs

I'm doing work on mRNA and need to get predicted mRNA sequences from a genome. I'm working with this genome https://www.ncbi.nlm.nih.gov/nuccore/U00096.3 (E. coli k-12 mg1655). So have a genome ...
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15 views

Chaos game representation to calculate 3 and 4mer result in a blank plot

I need to plot the 3-mer and 4-mer using the Chaos game representation for which I have referred the tutorial available at https://towardsdatascience.com/chaos-game-representation-of-a-genetic-...
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11 views

Finding associated diseases of my collection of diseases extracted from DisGeNET

Goal: I have 101 diseases. (extract from DisGeNET) I want to get associated diseases of these 101 diseases. to validated disease graph that I created. Note: Associated could be measured by jaccard ...
0
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1answer
74 views

How to retrieve dataset names from python statsmodels?

The Python statsmodels library grants access to many R-datasets which can be downloaded e.g. with: ...
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0answers
22 views

No module error when I use ATD script. How can I fix it?

I am using AutoDockTools and I need to prepare receptor and ligand to docking. I want to use AutoDockTools files that are located in Utilities24 folder. But when I try run this scripts by windows ...
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41 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 ...
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43 views

Extract secondary structures and sequences from dssp files

I have a very messy problem and I really need your help. I have a lot of dssp files in a folder. Every dssp file contains informations about proteins. Also, I have a separate file containing two ...
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1answer
70 views

Is there a way to measure cell line similarity using python?

I have a list of cell lines that should be compared against another list of cell lines as pairs. I am trying to find a way in order for me to compare two cells such as MCF7 and 10964c cell lines. I ...
0
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1answer
158 views

Raw Data frame manipulation in python

Using python 3 I need to process qPCR sequencing raw data outputs by searching for the first occurrence of a user defined string and then making a new data frame using all lines after that string. I ...
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43 views

How to compare multiple genetic profiles in Python?

I have hundreds of vcf file where each vcf file contains genome profile for a tissue. A portion of the vcf file is as follows: [ I can read each vcf file into a dataframe. So it would be hundreds of ...
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24 views

How to retrieve the best-scoring Trinity isoform from blastx results

I'm working on a somewhat unusual transcriptome focused on a killer X chromosome. This chromosome has some new genes, with expression levels quite different from their autosomal paralogs. I've found ...
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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 ...
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129 views

How can I calculate and compare intra-cluster correlation for each GO term and pathway?

How can I calculate and compare intra-cluster correlation for each GO term and pathway? I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...
-1
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1answer
58 views

What is the full script to extract sequences from fasta file by using Ids in text file in python 3 and pycharm?

I have a fasta file (gene.fasta)with sequences with names patterns: ...
-1
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1answer
115 views

How to generate ultrametric phylogenetic trees?

I have generated rooted species tree with 1000 bootstraps by RAxML. Further, I need to generate ultrametric tree for the same. Therefore, Please suggest me how to generate ultrametric tree from the ...