Perl script to delete the adjacent repeats !
/usr/bin/perl #Mostly the interview quest...the adjacent repeated character .... $string='ATTTTTTGGC'; # This should be converted to ATGC $string =~ s/(\w)\1/$1/g; print $str...e case when comparing, you could use: $string =~ s/(.)\1/$1/gi #And finall...1577 days ago
Installing ggplot2 and its dependencies on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Download...oud.r-project.org/src/contrib/stringr_1.4.0.tar.gz' Content type...installing *source* package ‘stringi’ ... ** package ‘stringi’ s...D_FORTIFY_SOURCE=2 -g -c stri_stringi.cpp -o stri_stringi.o g++ -...nit.o render.o render_table.o string.o text.o utf8_encode.o utf8_f...1577 days ago
Installing docker for Bioinformatics on Ubuntu !
jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove...runtime for containers Options: --config string Location of client confi...iles (default "/home/jit/.docker") -c, --context string Name of the context to us...1540 days ago
Pack a perl program with their dependencies on Ubuntu !
#Follow steps to create your own executable ./web jit@jit-HP-Pro-3335-MT:~/Downl...assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Sim...1538 days ago
1242 days ago
Perl One-Liner to print only non-uppercase letters
#Go through file and only print words that do not have any uppercase letters. perl -ne 'print unless m/[A-Z]/' dna.fa > dnaOnlyLowercase.fa #To lowercase everything perl -pne 'tr/[A-Z]/[a-z]/' dnaUpperCase.fa >dnawithoutuppercase.fa;1410 days ago
1469 days ago
1367 days ago
Install and set up i-adhore for synteny and wgd analysis ! -- step by step --
#Need to download i-adhore-3.0.01.tar.gz from https://...rc/SvgWriter.cpp: In member function ‘std::__cxx11::string SvgWriter::convertColor(const...gion of size between 0 and 6 [-Wformat-overflow=] string SvgWriter::convertColor(const...1230 days ago
Commandline for paired end reads simulation with BBMap !
(JitMetaENV) ➜ mixedSample git:(main) ✗ /home/urbe/Tools/bbmap/randomreads.sh ref=mixed.fa out=reads_BBMAP250.fq...h=250, mininsert=400, maxinsert=600, gaussian] Writing reference. Executing dna.Fa...1017 days ago