Reformat the multifasta for sequence length !
#awk oneliner to reformat the multifasta sequences awk '!/^>/ {printf "%s", $0; n = "\n"} /^>/ {print n $0; n = ""}' file.fasta | fold -w 1001433 days ago
Bash script to handle Multifasta files
#Convert all lowercase residues to uppercase in a FASTA sequence file $ awk 'BEGIN{F...pper($0)}else{print $1}}' input.fasta > output.fasta #Rearrange...0);} END {printf("\n");}' input.fasta |\ >awk -F '\t' '{printf("%d...printf ">";} print $0; }' input.fasta > output.fasta #Match FAST...1398 days ago
Print the screenshot of read coverage remotely !
#Chrom_2:9700000-9760000 ASCIIGenome -ni --fasta A_vaga.NDPD.fasta -r Chrom_2:9700000-9760000 -x "save >> test.pdf" A_vaga.NDPD.fasta.out.sam.bam.sorted.bam1324 days ago
1244 days ago
Perl script to check perl modules and download NCBI, BUSCO, Taonomy, Silva databases !
use strict; use warnings; use ExtUtils::Installed; use LW...release_138_1/Exports/SILVA_138.1_LSUParc_tax_silva.fasta.gz'; my $silva_LSU_fileName = 'SILVA_138.1_LSUParc_tax_silva.fasta.gz'; my $silva_LSU_code =...1201 days ago
Corona variant calling steps !
#!/bin/bash FILE_PATH="data/trimmed_fastq_small/" find "$FILE_PATH" -name "*.fasta" | while IFS= read -r my_fi...e") basename=$(basename "$my_file" .fasta) echo $basename mkdir...name.bcf -f data/ref_genome/sequences.fasta results/bam/$basename.sorted....1086 days ago
Perl onliner to print fasta headers !
#Save all your fasta in seq.fa and run the following ... perl -ne 'print if /^>/' seq.fa #Print header with line number perl -ne 'print "$. $_" if /^>/ ' seq.fa1037 days ago
Python script to read FASTA and FASTQ file !
# !/usr/bin/env python3 # -*- coding: utf-8 -*- from pysam import FastxFile def read_fasta_q_file(fasta_q_file): """Parse FASTA/...Args: fasta_q_file (str): Path to FASTA/Q file. """ with...1017 days ago
Tadpole is 250x faster than SPADes assembler !
...s are not supported. Specifically, it allows 1-31, multiples of 2 from 32-62, multiples of 3 from 63-93, etc. Pleas...ented) dump= Write kmers and their counts. fastadump=t Write kmers and counts as fasta versus 2-column tsv. mincoun...1017 days ago
Run multiple bash command in screen !
#login to screen screen -r 123 #bash.sh srun --partition=compute --nodes=1 --ntasks-per-node=40 --pty bash.sh #Run and check the status in screen contol +A +D1003 days ago