Results for "files"
Bio-Scripts
Download the gff files from NCBI using bash script/command
...p.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_viral #Read the uerl from file and download FILES=$(pwd)/* for f in $FILES do echo "Processing $f fi...2522 days ago
Reformat the file names with Perl
...::Copy qw(copy);; $| = 1; my %hash; my @files = glob "*.scf"; if (!$ARGV...{code}= $code; } #Chec one by one for (0..$#files){ $files[$_] =~ s/\.scf$//...0]}{code}"."_$pName[1]"."."."scf"; if ( -f "$files[$_].scf" ) { copy("$files[$...2335 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...2331 days ago
Create genome scaffolding with Perl
...############### Program starts here # set default options my @pslFiles = (); my $projOpts = {...=s'); # process remaining command line arguments (hopefully only PSL files) while (@ARGV) { my $argu...2308 days ago
- ...r, you need to open the cmd, navigate to the folder containing the .cpp files using the "cd" command, and t...Change "NewFileName" to w/e you want to name each exe file. The exe files will appear in the same folde...
849 days ago
Perl script to read multi fasta sequence one by one
...int OUT "$key\n$fastaSeq{$key}\n"; } sub readfasta { (my $file)=@_; my %sequence; my $header; my $temp_seq; #suppose fasta files contains multiple sequences;...2220 days ago
Perl script to count the number of files in a directory with regex
..."_A23_","_B34_","_B38_","_E3B2_","_E3T1_","_HPRIM14_","_H158_"); my @files = glob("*.scf *.SCF"); forea...me (@allNames) { my $nName=lc ($name); my $cnt=0; foreach my $file (@files) { #print "$file =~ /$nName/...2237 days ago
Perl script to find coding regions in DNA sequences
...lenames my $filecodontable = $ARGV[0]; my $filesequence = $ARGV[1]; # ope...quence (second file) if (!open(SEQUENCE,"< $filesequence")) { print "dnaloglk...__END__ To test the program, save this two files in your current working direc...2154 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...2123 days ago
- ...no checking for suffix of object files... o checking whether we are...rep -E checking for ANSI C header files... yes checking for sys/type...no checking for suffix of object files... o checking whether we are...anged config.status: executing depfiles commands configure: WARNING:...
2151 days ago
