Inreractive SCP / File transfer !
...ename #next line checks if entered value is not null, and if not null it will copy file(s) if ! [ x"$filename" = "x" ]; then #next line prints header echo -n "Copying $filename ....959 days ago
Run Pango on your multifasta file !
...lin/lib/python3.8/site-packages/pangoLEARN/data/decisionTree_v1.joblib Header file: /home/jnarayan/anaconda...3/envs/pangolin/lib/python3.8/site-packages/pangoLEARN/data/decisionTreeHeaders_v1.joblib Designated hash:...896 days ago
Extract fasta header with ids !
#Extract all the fasta header name with certain ids kraken --db ../../../../DATABASE/minikraken_20171019_8GB.tgz out.fa more out.fa_class.txt | grep "227859" | awk '{print $2}...886 days ago
Awk command to keep only short the fasta header !
awk '/^>/ {$0=$1} 1' file.fasta718 days ago
308 days ago
Raku script to find SSRs in fastq file !
...urn @ssrs; } sub process-fastq-file(Str $filename) { my $fh = open $filename, :r; my $line-number = 0; while $fh.readline -> $header { $line-number++;...121 days ago
Python script to convert Multi-line Fasta to Single-line Fasta
...for line in input_file: if line.startswith('>'): # If a header line, write the previous sequence and then the new header if c...104 days ago
Perl script to convert Multi-line Fasta to Single-line Fasta !
...t_sequence = ""; while (my $line = ) { chomp $line; if ($line =~ /^>/) { # If a header line, write the previous sequence and then the new header print $output_fi...104 days ago
Perl script to calculate the basic stats of the assembled genome !
#!/usr/bin/perl use strict; use warnings; use Bio::SeqIO; # Input file containing the genome assembly in FASTA format my $input_file = 'genome_assembly.fasta';...103 days ago
Python script for basic stats of the assembled genome !
...otal_bases = 0 with open(file, 'r') as fh: for line in fh: if line.startswith('>'): continue # Skip header lines line = lin...103 days ago