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{ | |
"metadata": { | |
"name": "PyRNA Cookbook" | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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{ | |
"metadata": { | |
"name": "Create and manipulate tertiary structures" | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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{ | |
"metadata": { | |
"name": "Create and manipulate secondary structures." | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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{ | |
"metadata": { | |
"name": "Create and manipulate molecules." | |
}, | |
"nbformat": 3, | |
"nbformat_minor": 0, | |
"worksheets": [ | |
{ | |
"cells": [ | |
{ |
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#!/usr/bin/env python | |
import xml.etree.ElementTree as ET | |
import sys, urllib, urllib2 | |
eutils_base_url = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/" | |
def get_ids(taxid): | |
accession_numbers =[] | |
retstart = 0 |
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#!/bin/bash | |
query=$1 | |
genome_ids=$(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) | |
for genome_id in $genome_ids | |
do | |
wget -qO - "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$genome_id&rettype=gb&retmode=xml" > genome.xml | |
gene_ids=$(xmllint --xpath "//GBFeature[GBFeature_key[.='CDS'] and GBFeature_quals/GBQualifier[GBQualifier_name[.='product'] and GBQualifier_value[contains(.,\"$query\")]]]" genome.xml | grep "GI:" | sed -E 's/.+GI:(.+)<.+/\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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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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cat gene_ids.txt | xargs -I % wget -qO %.fasta "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=%&rettype=fasta" |