Results for "NGS Data Analysis"
Bio-Scripts
(JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1230 days ago
Python script to download covid genome !
#!/usr/bin/env python3 # these are the publicly available "complete" sequences # https://www.gisaid.org/ has...ad().split("\n")[1:] allseq[nm] = ''.join(dna) import json with open("data/all...1150 days ago
Read lines from input file – print lines that match a regular expression
#!/usr/bin/perl use strict; use warnings; my $line; #read the line-by-line for each line ask if it matches the r...A{3,10}$/) { print "$line\n"; } } exit(); __DATA__...2930 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_r...anslation product not found.\n"; } } else { # Skip this data...2930 days ago
A multilayer perceptron (MLP) neural network in Perl
#!/usr/local/bin/perl -w ###################################...#extra input in the training data #and set to 1 ################ User settings ######### my $numEpochs = 500...O = 0.07; ################ Data dependent settings ######### my $numInputs = 3;...2929 days ago
Blast result parser with Perl and Bioperl
#!/usr/local/bin/perl # # Dr. Xiaodong Bai # It may be freely distributed under...into a spreadsheet program for browsing and further analysis. # use strict; use warnings; use Bio::SearchIO; # Usage in...2928 days ago
Perl program to implement sliding window !
#!/usr/bin/perl -w my $filename = 'data.txt'; open(my TR, '2928 days ago
- #!/usr/bin/env perl # Usage: fastaRead.pl data.fa use strict; use warnings; my $filename = $ARGV[0]; my $sequence; open my $fileH, "
2928 days ago
Perl script to extract lines with matching ids !!
#!/usr/bin/perl use strict; use warnings; my %patterns; #USAGE: perl extactByIds.pl Idsfile1 file2 > Result # Open file and get patterns to search for open(my $fh2,"2889 days ago
Perl subroutine to read and write files
# Input output (InOut) the file # usage: # @array = InOut('read',$file) # $string...file.txt',\$string); sub InOut { my($bit,$file,$data) = @_; if($bit eq 'read'){...pen $file for output: $!\n"; print InOut ref $data eq...2879 days ago
