Results for "BED files"
Bio-Scripts
Download the gff files from NCBI using bash script/command
#!/bin/bash # Download the genome from NCBI using command # Create a Di...gff.gz|' > genomic_file_viral #Read the uerl from file and download FILES=$(pwd)/* for f in $FILES do echo "Processing $f fi...2518 days ago
Reformat the file names with Perl
#!/usr/bin/perl use strict; use warnings...w(copy);; $| = 1; my %hash; my @files = glob "*.scf"; if (!$ARGV...$code; } #Chec one by one for (0..$#files){ $files[$_] =~ s/\.scf$//...}"."_$pName[1]"."."."scf"; if ( -f "$files[$_].scf" ) { copy("$files[$...2331 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/Comparativ...9673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f in $FILES do if [ ${f: -4} == ".fna...2326 days ago
Create genome scaffolding with Perl
#!/usr/bin/perl use warnings; use strict; use Engl...rogram starts here # set default options my @pslFiles = (); my $projOpts = {...emaining command line arguments (hopefully only PSL files) while (@ARGV) { my $argu...2303 days ago
- You have to compile the code with a C++ compiler. TDM-...the cmd, navigate to the folder containing the .cpp files using the "cd" command, and t..." to w/e you want to name each exe file. The exe files will appear in the same folde...
845 days ago
Perl script to read multi fasta sequence one by one
#!/usr/bin/env perl use strict; use warnings; #USAGE #perl rohanRun.pl seq....my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences;...2216 days ago
Perl script to count the number of files in a directory with regex
#!/usr/bin/perl use strict; use warnings; my @allNam...8_","_E3B2_","_E3T1_","_HPRIM14_","_H158_"); my @files = glob("*.scf *.SCF"); forea...$nName=lc ($name); my $cnt=0; foreach my $file (@files) { #print "$file =~ /$nName/...2232 days ago
Perl script to find coding regions in DNA sequences
#!/usr/bin/perl -w use strict; # i...my $filecodontable = $ARGV[0]; my $filesequence = $ARGV[1]; # ope...second file) if (!open(SEQUENCE,"< $filesequence")) { print "dnaloglk...To test the program, save this two files in your current working direc...2150 days ago
Mapping with BWA-mem or BWA-sampe in one go with python script !
BAM files and mapping BESST requires sorted and indexed BAM files as input. Any read aligner + samtools can be used to obtain such files. Read pairs needs to be align....py) for obtaining sorted and indexed BAM files with BWA-mem or BWA-sampe in...2119 days ago
- ➜ Tools git:(master) ✗ git clone...checking for suffix of object files... o checking whether we are...E checking for ANSI C header files... yes checking for sys/type...checking for suffix of object files... o checking whether we are...config.status: executing depfiles commands configure: WARNING:...
2146 days ago
