Results for "Files"
Bio-Scripts
Python script to download covid genome !
...but they require you to sign up import requests import yaml seqs = yaml.load(requests.get("https://www.ncbi.nlm.nih.gov/core/assets/genbank/files/ncov-sequences.yaml").text)...1149 days ago
Install BLAST in Ubuntu/Linux and Window !
...h.gov/blast/executables/blast+/2.7.1/ncbi-blast-2.7.1+-win64.exe #Run this installer using the defaults, it should put BLAST under C:\Program Files\NCBI\blast-2.7.1+1160 days ago
- ...tFile = $seqFile; # Create $outFile name $outFile =~ s/\.fa/\.polyA\.out/; # s/old/new/; #User can process these files as per their need pr...
2929 days ago
Find and replace ambiguous characters in fasta file with Perl and Bioperl
...are repleced with the\n". "specified character. e.g. -m '?' will place ? to the ambigous characters.\n" . "If multiple files are given, sequences in all files are marged. If no \n"....2927 days ago
Converting from Windows-style to UNIX-style line endings with dos2unix
...s2unix amd64 7.3.4-3 [351 kB] Fetched 351 kB in 3s (130 kB/s) Selecting previously unselected package dos2unix. (Reading database ... 177704 files and directories currently ins...1190 days ago
Perl subroutine to read and write files
# Input output (InOut) the file # usage: # @array = InOut('read',$file) # $string = InOut('read',$file) # InOut('write',$file,\$string) # InOut('write',$file,\@a...2879 days ago
Install ATOM editor on Elemantory OS / Ubuntu
...atom amd64 1.54.0 [126 MB] Fetched 845 kB in 4s (219 kB/s) Selecting previously unselected package gconf2-common. (Reading database ... 194272 files and directories currently ins...1189 days ago
Extract fasta sequence from a multifasta file with coordinates
...:Fasta; # Create database from a directory of Fasta files my $db = Bio::DB::Fasta->new('/path/to/fasta/files/'); my @ids = $db->ge...access my $fh = Bio::DB::Fasta->newFh('/path/to/fasta/files/'); while (my $seq = ) {...2545 days ago
Download the genome from NCBI using bash script/command
...tp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_viral #Read the url from file and download FILES=$(pwd)/* for f in $FILES do echo "Processing $f fi...2545 days ago
Unzip all the genome file and remove all fasta header except first one
#!/bin/bash gzip -d *.gz FILES=$(pwd)/* for f in $FILES do echo "Processing $f file..." if [[ $f =~ \.fna$ ]]; then awk ' /^>/ && FNR > 1 {next} {print $0} ' $f | sed '/^>/{s/ /_...2544 days ago
