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{ | |
"metadata": { | |
"name": "Create and manipulate molecules." | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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{ | |
"metadata": { | |
"name": "Create and manipulate secondary structures." | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
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{ | |
"metadata": { | |
"name": "Create and manipulate tertiary structures" | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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{ | |
"metadata": { | |
"name": "PyRNA Cookbook" | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
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#!/bin/bash | |
echo "Start..." | |
rm -f ~/results.txt | |
mkdir -p ~/Data/nematostella_vectensis | |
cd ~/Data/nematostella_vectensis |
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wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.2.26+-x64-linux.tar.gz" | |
tar -xzvf ncbi-blast-2.2.26+-x64-linux.tar.gz | |
ncbi-blast-2.2.26+/bin/blastn -remote -query your_fasta_file.fasta -out blast_results.txt -db nr | |
grep "^>" blast_results.txt | wc -l | |
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cat gene_ids.txt | xargs -I % wget -qO %.fasta "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=%&rettype=fasta" |
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wget -qO - "http://www.ncbi.nlm.nih.gov/genome/genomes/167?&subset=complete&limit=refseq" | grep 'title="chromosome">Chr' | sed -E 's/.+(NC_.+|NZ_.+)/\1/' | cut -d \< -f 1 |
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wget -r ftp://anonymous:anonymous@ftp.ncbi.nih.gov/genomes/Arabidopsis_thaliana/CHR_I/ |
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wget -qO - "http://rfam.sanger.ac.uk/family/browse" | grep ">RF" | tr -d ' ' | cut -d \> -f 2 | cut -d \< -f 1 |
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