Questions tagged [python]

python is a programming language, widely used in bioinformatics

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7
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2answers
407 views

Is there a standard way to clean a PDB file and re-number its residues?

Is there a pre-existing tool which will tidy up the numbering of a PDB file? Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
3
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2answers
51 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
-1
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1answer
34 views

Problem comparing two fasta files and writing the sequence

I am trying to compare two fasta files to one another, to see if the one contains sequences from the other, in this case if input_file contains sequences from files and then write the sequences to ...
0
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2answers
35 views

Python module for fetching NCBI id for a list of species

I have a list of scientific names of species. Is there a python module that can fetch NCBI taxonomy IDs?
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2answers
65 views

How to efficiently get human gene names from NCBI based on a large list of SNPs

I found a good answer related to my question here: How to get a list of genes corresponding to the list of SNPs (rs ids)? But it says about small number of SNPs. I want to get gene names based on ...
3
votes
2answers
210 views

pvalue calculation of protein-protein network with permutation test

Note: this question has also been asked on Biostars I have performed a network recreation analysis based on the interactions of proteins from String db. I wanted to know if the interactions have ...
2
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3answers
82 views

Modifing a GFF3 file and writting to a new file

I modified the GFF3 file with the below code: ...
1
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1answer
31 views

Adding an attribute to GFF3 file

I failed to add Note=Gene description to mRNA attribute with the below code: ...
1
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1answer
133 views

Calculate molecular mass from chemical formula C9H15N4O8P (e.g.) with rdkit?

Can I calculate the molecular mass from a formula like this C9H15N4O8P in rdkit? I think ...
2
votes
1answer
56 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 ...
3
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2answers
87 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
4
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0answers
153 views

How to find which scales are available in SeqUtil of Biopython?

I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil". ...
5
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2answers
102 views

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

I am trying 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 "...
1
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1answer
91 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 ...
1
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2answers
74 views

Biopython Failure to break out of loop

After qblast, I wanted to print only details from the first 3 BLAST output. Yet, the code below printed the details of every BLAST output. Why can't I break out of the loop to achieve my desired ...
2
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0answers
37 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 ...
3
votes
1answer
34 views

Access workdir defined on command line from within Snakefile

Snakemake provides access to a workflow object within a Snakefile. This allows one to, for example, have dynamic programmatic access to the directory containing the ...
3
votes
2answers
170 views

help with CRCmapper

I'm using CRCmapper on my data. There are several modules in the tool. I've used exactly instructed in the usage. Commands used: ...
8
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1answer
467 views

How GFF3 attributes (9th column) varies from one gene prediction algorithm to another

GFF3 files are in tabular format with 9 fields per line, separated by tabs. The first 8 fields share almost same data structure, but the 9th field varies a lot depending on feature type and gene ...
1
vote
1answer
21 views

semantic similarity measurement for cell line ontologies

I have a set of cell line pairs and I want to know to what extent the pairs are similar based on their ontologies. The problem I have is that I have found a Python library called Fastsemsim, but it ...
3
votes
2answers
101 views

How to do `bedtools intersection` using pandas alone?

I have two pandas Dataframes, using python3.x: ...
3
votes
1answer
28 views

How to select only RNA with Hetero atoms from pdb file with python?

I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
5
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2answers
288 views

What does “fetching by region is not available for SAM files” mean?

I am used to gzip/biopython solutions when dealing with sequencing data, but now I wish to switch to more elegant ...
0
votes
1answer
48 views

Pandas automatically rounds GWAS P-value

I am working with a specific GWAS. If I were to run this on the command line grep <rs_id_of_interest> GWAS.txt I would see the GWAS p-value to be on the ...
0
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2answers
321 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 ...
3
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1answer
97 views

HDF5 and BioSQL solutions

I'm looking at better database/storage solutions for NCBI virus data, with all attributes particularly year and country of isolation, together with structural data, possible antibody data, T-cell data ...
0
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0answers
34 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 ...
4
votes
3answers
464 views

How to compare transcriptomic profiles of two cell types (single cell RNA-seq)?

I found this interesting Single RNA-seq data set in GEO, but I am not sure how to analyze it appropriately. They have deposited transcriptomic profiles of human and mouse pancreatic islets (...
1
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3answers
144 views

Deep learning RNA sequences

Currently I'm working on a project, which combines deep learning with RNA sequences. I'll try to predict pseudotorsion angles [1] from raw rna sequence. The ideas is to train a neural network with raw ...
2
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3answers
147 views

How to reverse complement the DNA sequences for given inverse/reverse coordinates?

I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file. The coordinates of id.txt ...
1
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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 ...
1
vote
3answers
118 views

Calculate the occurrence of motif in sequences (including overlaps) using Python

I need to calculate the occurrences of a motif (including overlaps) in sequences (motif is passed in the first line of standard input and FASTA sequences in subsequent lines). The sequence name starts ...
1
vote
1answer
50 views

How to get Uniprot and swissprot cross references using Biopython

I am struggling to use biopython to gather cross references such as GO annotation from Uniprot/swissprot text files ("DR" in the .txt files) using biopython. From ...
1
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1answer
35 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 ...
9
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5answers
2k views

How do I find identical sequences in a FASTA file?

I want to create a database for a proteomics study. Therefore, the mapping from a given sequence to a protein ID has to be unique. I am wondering whether there is already a built-in function in ...
10
votes
3answers
3k views

Converting a VCF into a FASTA given a reference with Python, R

I am interested in converting a VCF file into a FASTA file given a reference sequence with Python or R. Samtools/BCFtools (Heng Li) provides a Perl script ...
0
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1answer
93 views

filter secondary alignments using pysam

I am new to python and trying to learn. The below is an attempt to filter out secondary reads in a bam using ...
1
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2answers
30 views

Is there a tool to convert a variableStep .wig to fixedStep one?

I have a .wig file in this format: variableStep chrom=chr1 span=20 59965 7 59985 10 60005 10 60025 10 and I would like to format it to something like ...
1
vote
1answer
33 views

Aligned base strand in pysam `pileupcolumn`

Is it possible that on the same pileupcolumn object (i.e a specific aligned base) I find the same base but aligned to different strands? For example, can I find a coverage of 50 'A's that align to ...
0
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0answers
18 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 ...
1
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0answers
52 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.
3
votes
2answers
104 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
vote
2answers
183 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
votes
2answers
453 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. ...
2
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1answer
193 views

Python string editing in Snakemake

I'm running a custom perl script using Snakemake. I use this rule: ...
7
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2answers
326 views

How to write a hash function for canonical kmers?

This question is a follow up from How do kmer counters determine which kmer is 'canonical'?. In that question we learned that kmer counting programs use a 2-bit hash function to internally represent ...
8
votes
3answers
663 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 ...
3
votes
1answer
620 views

Find Patterns in Cluster

I have a heatmap and I would like to find some rectangles. I have already used clustermap. But here, I can not calculate these rectangles. The order of the data should not be changed. This Code is ...
4
votes
2answers
149 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 ...
3
votes
1answer
42 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 ...