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Questions tagged [bioinformatics]

For programming-related questions related to Bioinformatics. Other questions do not belong here, but might be on-topic at https://bioinformatics.stackexchange.com/.

Bioinformatics is an interdisciplinary scientific field that develops methods and software tools for understanding biological data. Bioinformatics combines computer science, statistics, mathematics, and engineering to study and process various types of biological data.

There is a former Stack Exchange site specific to bioinformatics at Biostars and a new Stack Exchange site dedicated to bioinformatics

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How to get the latest papers from pubmed

This is a bit of a specific question, but somebody must have done this before. I would like to get the latest papers from pubmed. Not papers about a certain subjects, but all of them. I thought to query depending on modification date (mdat). I use…
carl
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How do you generate all possible permutations in python?

I am trying to solve a bioinformatics question. Basically, the user inputs a integer and I output all the possible permutations of A, C, G, T that are length of the imputed integer. The integer can be greater 4. For example: If the user inputs 2, I…
jay a
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Aborting AJAX request in long polling function

I'm implementing an application which can be able to monitor background jobs (BLAST program). I wish that when PID equal 0, then stop the polling process. But in my long-polling example, the polling process continues to run even use abort()…
Penny Liu
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How to transform a range into individual positions

I have a huge "range" data, this data is in GenomicRanges format, if I convert this to data.frame, follows one example: file <- "seqnames start end width strand chr1 2 5 4 * chr2 3 7 5 *" file<-read.table(text=file,header=T) I…
Fpertille
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subset a DNAStringSet by subpattern and remove subpattern in R

I want to subset only the lines that contain the substring and then to remove the substring. I can do the first part, but I do not know how to remove the substring Here is an example library(Biostrings) myseq…
user3067923
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How to excute Fortran program in python for multiple input

I have a Fortran program and want to execute it in python for multiple files. I have 2000 input files but in my Fortran code I am able to run only one file at a time. How should I call the Fortran program in python? My Script: import…
Jone
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Re-use rules and avoid CyclicGraphException with snakemake

I'm writing a pipeline in which a first mapping of reads on a reference genome results in a sam file (rule map_on_genome), and then in a sorted and indexed bam file (rule sam2indexedbam). After processing this bam file (rule small_RNA_seq_annotate),…
bli
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Unable to use add_flags() function in R properly

I am trying to use the add_flags function on the records of a species obtained using rgbif. I am using this vignette So after loading the data frame onto a variable d as per the instructions I try to use add_flags() and I run into a few errors. >…
Djokester
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BioPython: Amino acid Sequence contains 'J' and can't calculate the molecular weight

The data which I am working with comes in an Excel file which has the amino acid sequence on index 1. I'm trying to calculate different attributes based on the sequence using BioPython. The code which I have now: import xlrd import sys from…
Anna Jeanine
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Exporting FCS files from GatingSet

I am trying to gate a flowSet, take the gateSet, and then export it to separate FCS files, which should have only the data I chose to gate. My commands are as follows: Read the FCS files with the names i want s <- read.flowSet(path = path,files =…
Kagestrife
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Find ID coordinates

I have 2 files, 1) A B 2) A,chr1,startA,endA C D B,chr1,startB,endB B A C,chr1,startC,endC D,chr1,startD,endD My desired output, A chr1 startA endA B chr1 startB endB C chr1 startC endC D chr1 startD…
user3224522
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Missing values in lmFit [limma R package]

[This question is specific to bioinformatics. There are posts elsewhere but I couldn't find a satisfactory answer.] If I have a gene/protein expression data with missing values (NA), how does lmFit of the limma package handle these values? Note that…
David C.
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How to change local file path into ARGF for automatically input in Rails

I have my local database file in public folder. I would like to open it in my Rails app without running it manually in a terminal. The command requires ARGF (Gem bio) which will work by In terminal, >> Ruby thiscode.rb database.fasta And in .rb…
Jan
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Find TopHat accepted_hits.bam mapped to transcriptome and genome separetly

I did a tophat/2.0.13 alignment giving both genomic and transcriptome inputs and would like to know how I can find %reads mapped to transcriptome and %ampped to the genome in my accepted_hits.bam output file. Is there a straight forward way of…
Yuka Takemon
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Converting .fasta files to .gff3 files

I'm trying to use Roary to do phylogenetic analysis. It says "Alternatively you can use ncbi-genome-download to pull down the FASTA files and convert them to GFF3 with Prokka." in https://sanger-pathogens.github.io/Roary/ I already have all the…
chiefpika
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