Results for "C"
Bio-Scripts
Perl script to count occurrence of a character !
#!/usr/bin/env perl # -*- coding: utf-8 -*- #!/usr/bin/perl use strict; use warnings; my %count_of; whi...t", $_; #my ( $word) = m/(\w+)/; $count_of{$val[13]}++; } for...} keys %count_of ) { print "$word\t$count_of{$word}\n"; }...1952 days ago
- my @tests = ( ["FOO", "BAR"], ["CRATE", "TRACE"], ["CRATE", "CRATE"], ["TRACE", "CRATE"], ["CREATE", "TRACT"], ["DWAYNE", "DUANE"], ); for my $word_pair (@tests) { #Nice way to split the values...
1852 days ago
- Download page https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download Ubuntu / Debian su...d latest BLAST version wget ftp://ftp.ncbi.nlm.nih.gov/blast/executabl...em PATH export PATH=$HOME/tools/BLAST/ncbi-blast-2.8.1+/bin:$PATH
1813 days ago
Palindrome Simulation commands !
...palindromeAssemblySim more allCommands 3315 mutate.sh in= mutant15CH101.fasta out=mutant153CH101....97 3316 mutate.sh in=mutant15CH101.fasta out=mutant153CH101....mplate_pass_FAH31515.faa mutant3CH101.fasta mutant15CH101.fasta...3323 ~/Tools/BWISE/Bwise.py -c 0 -p 4 -K 250 -t 10 -o simPal...1787 days ago
Resume the MIRA assembler run !
mira -r manifest_file Usage: mira [options] manifest_file [manifest_file ...] Options: -c / --cwd= directory Change working directory -r / --resume...1786 days ago
- # Convert FASTQ to FASTA seqtk seq -a IN.fastq > OUT.fasta # Convert FASTQ to FASTA and set bases of quality lower than 20 to N seqtk seq -aQ64 -q20 -n N IN.fastq > OUT.fasta # Download Seqtk https://github.com/lh3/seqtk
1777 days ago
- Map them agaist reference avaga genome using following codes git clone https://github.com/lh3/bwa.git cd bwa; make bwa index ref.fa bwa mem -x pacbio ref.fa pacbio.fq > aln.sam bwa mem -x ont2d ref.fa ont-2D.fq > aln.sam
1777 days ago
- #!/bin/bash cd `pwd` perl ~/apps/SSPACE-1.2_linux-x86_64/SSPACE_v1-2.pl \ -l libraries.txt \ -s Contigs_over200_nocp.fasta \ -k 5 \ -a 0.7 \ -x 1 \ -m 30 \ -o 20 \ -b Rayk31_scaffolds_extension
1774 days ago
Perl script to run in parellel !
...RGV[0]); my %genome=%{$sequence_data_ref}; my $n_processe...m->start and next; my $count = 0; foreach my $chr...pm->finish; } $pm->wait_all_children; sub output_exists...$file=shift; my (%sequence_data); my $file_content...1738 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1667 days ago
