How to download only viridiplantae miRNA from miRBase~ Bioinformatics Made Simple.com

How to download only viridiplantae miRNA from miRBase

There is no direct way to download the organism specific miRNA from miRBase database. So I extracted the miRNA of viridiplantae plant from miRBase using some unix command. Steps are as follows

Download the information regarding organisms from HERE.
Download the mature miRNA sequence from HERE
Extract both files in same directory
Download the fasta dereplicating python script from HERE
Now run the bash script given from the same directory

#!/bin/bash
#script to extact plant mirna from mirbase database

# convert fasta to tab
awk 'BEGIN{RS=">"}{gsub("\n"," ",$0); print ">"$0}' mature.fa >mature.tab


#extract the organisms belong to Viridiplantae. You can extract the miRNA for other
# organism too by changing the word "Viridiplantae"
grep Viridiplantae organisms.txt >plants_mirbase.txt

# extract name of plants
awk '{ print $3 " " $4 }' plants_mirbase.txt >plant_name.txt

#extract mirna for plants
grep -f plant_name.txt mature.tab >plant_mirna.tab

#convert tab to fasta
awk '{print ""$1" "$2" "$3" "$4" "$5"\n"$6}' plant_mirna.tab > plant_mirna.rna

#convert RNA to DNA
sed '/^[^>]/ y/uU/tT/' plant_mirna.rna  >plant_mirna.fasta


#dereplicate mirna file
python derep.py -i plant_mirna.fasta

#cleaning fasta header
cat derep_plant_mirna.fasta | awk -F ';' '{print $1}' >plant_mature_mirna_unique.fasta


rm mature.tab
rm plants_mirbase.txt
rm plant_mirna.tab
rm plant_mirna.rna
rm plant_name.txt
rm derep_plant_mirna.fasta

echo mature mirna from all plants are in plant_mirna.fasta!!!
echo unique mature mirna from all plants are in plant_mature_mirna_unique.fasta!!!
echo all job done!!!

Basically the above bash script extract the miRNA from plant deposited to miRBase database and save them to a file plant_mirna.fasta. In second part, it remove the duplicate miRNAs and save them in another file plant_mature_mirna_unique.fasta.

How to remove duplicate sequences from FASTA file HERE