bioinformatics

I want to execute a blastx search application in PHP instead of Linux console text terminal. The actual command line arguments would be ( see definition of refer ): ./blastx -query $input -db ${Sbjct}_db -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv Here's my PHP partial code. exec(' /path/to/blastx -query /path/to/PAO1.fasta -db /path/to/VFDB_setB_pro -evalue 0.0001 -outfmt 6 -out /path/to/output.tsv '); However, when I call exec() function in PHP program there is nothing happened. I also tried another method. It return error code 1. Here is my php exec() content: exec('sh /path/to

I'm trying to use rpy2 to use the DESeq2 R/Bioconductor package in python. I actually solved my problem while writing my question (using do_slots allows access to the r objects attributes), but I think the example might be useful for others, so here is how I do in R and how this translates in python: In R I can create a "DESeqDataSet" from two data frames as follows: counts_data <- read.table("long/path/to/file", header=TRUE, row.names="gene") head(counts_data) ## WT_RT_1 WT_RT_2 prg1_RT_1 prg1_RT_2 ## aap-1 406 311 41 95 ## aat-1 5 8 2 0 ## aat-2 1 1 0 0 ## aat-3 13 12 0 1 ## aat-4 6 6 2 3 ##

I have written a python script to plot the 'Ramachandran Plot' of Ubiquitin protein. I am using biopython. I am working with pdb files. My script is as below : import Bio.PDB import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt phi_psi = ([0,0]) phi_psi = np.array(phi_psi) pdb1 ='/home/devanandt/Documents/VMD/1UBQ.pdb' for model in Bio.PDB.PDBParser().get_structure('1UBQ',pdb1) : for chain in model : polypeptides = Bio.PDB.PPBuilder().build_peptides(chain) for poly_index, poly in enumerate(polypeptides) : print "Model %s Chain %s" % (str(model.id), str(chain.id)), print

I have a data frame, the start of it is below: SM_H1455 SM_V1456 SM_K1457 SM_X1461 SM_K1462 ENSG00000000419.8 290 270 314 364 240 ENSG00000000457.8 252 230 242 220 106 ENSG00000000460.11 154 158 162 136 64 ENSG00000000938.7 20106 18664 19764 15640 19024 ENSG00000000971.11 30 10 4 2 10 Note that there are many more cols and rows. Here's what I want to do: I want to change the name of the columns. The most important information in a column's name, e.g. SM_H1455, is the 4th character of the character string. In this case it's a H. What I want to do is to change the "SM" part to "Control" if the

I've plotted a heat-map like this: ggplot(test, aes(start1, start2)) + geom_tile(aes(fill = logFC), colour = "gray", size=0.05) + scale_fill_gradientn(colours=c("#0000FF","white","#FF0000"), na.value="#DAD7D3") This plots the upper triangle of a heatmap. What i'd like to plot is the very same triangle, but having the hypotenuse as the x-axis . How would I do that? Edit: Added reproducible example library(ggplot2) # dummy data df1 <- mtcars[, c("gear","carb", "mpg")] # normal tile plot gg1 <- ggplot(df1, aes(gear, carb, fill = mpg)) + geom_tile() + xlim(c(1, 10)) + ylim(c(1, 10)) + theme_void()

I'm writing a Clojure implementation of this coding challenge , attempting to find the average length of sequence records in Fasta format: >1 GATCGA GTC >2 GCA >3 AAAAA For more background see this related StackOverflow post about an Erlang solution. My beginner Clojure attempt uses lazy-seq to attempt to read in the file one record at a time so it will scale to large files. However it is fairly memory hungry and slow, so I suspect that it's not implemented optimally. Here is a solution using the BioJava library to abstract out the parsing of the records: (import '(org.biojava.bio.seq.io