Results for "Open Source"
Bio-Scripts
...um groupinstall -y 'Development Tools' sudo yum install -y expat-devel openssl-devel mysql-devel libxml2-...ERL_BASE="$HOME/perl" mkdir -p $PERL_BASE cd $PERL_BASE # Download source tarball into a subfolder name...2134 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has m...xt').read().split("\n")[1:] allseq[nm] = ''.join(dna) import json with open("...1126 days ago
- #!/usr/local/bin/perl -w # Can be easily modified to run any command on every seque...terns/polyA.pat"; # Go to sequence directory and open it (i.e, read contents) chdi..."Cannot change to $myDir: $!"; # Go to $myDir opendi...
2906 days ago
Parse a genbank file using regular expressions
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot open $gb_report for reading: $!"; # Flag for multiline translation; 1 means translation "in progre...2907 days ago
Perl script to Mutate a DNA Sequence
#!/usr/local/bin/perl -w # This script randomly mutates the DNA sequence and generates 10 success...NA SEQUENCE:= "; $dnafilename = ; chomp $dnafilename; unless ( open(DNAFILE, $dnafilename) ) { print "Cannot open f...2906 days ago
Perl script to count the number of Adenine, Thymine, Guanine and Cytosine in your DNA Sequence
#!/usr/local/bin/perl -w # While executing this script it asks for the file name of...$dna_filename = ; chomp $dna_filename; unless ( open(DNAFILE, $dna_filename) ) {...rry the file does not exist!!! \n"; print "Cannot open f...2906 days ago
Retrieve NCBI GenBank records with a range of accession numbers
#!/usr/bin/perl #FILE: ncbi_search.pl #AUTH: Paul Stothard (paul.stothard@gmail.co...$count ) { $retmax = $count; } open( my $OUTFILE, ">" . $param{outputFile} ) or die("Error: Cannot open $...2906 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w #################################################### #MLP neural network in Perl Original source code by Phil Brierley #Trans...2906 days ago
Extract a random sequence from a file
#!/usr/local/bin/perl -w use strict; use warnings; use autodie; use List::Util qw/ shuffle /; my $outputfile = 'randomoutput.txt'; open m...2905 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under GNU General Public...my $in = Bio::SearchIO->new(-format => 'blast', -file => $infile); open (OUT,">$outfile") or die "Cannot open $...2905 days ago
