Kozo Nishida kozo2
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| execute pathogen#infect() | |
| syntax on | |
| filetype plugin indent on | |
| inoremap jj <Esc> | |
| inoremap kk <Esc> | |
| inoremap <C-l> <Esc> | |
| nnoremap ; : | |
| nnoremap : ; |
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| sudo aptitude install git-buildpackage | |
| git-pbuilder create | |
| gbp-clone git://anonscm.debian.org/pkg-ruby-extras/ruby-bio.git | |
| cd ruby-bio | |
| sudo apt-get build-dep ruby-bio | |
| git-buildpackage --git-ignore-new --git-biulder='git-pbuilder' | |
| 中略 |
kozo2
/ downloadkgml.py
Last active
December 29, 2015 19:59
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| import requests | |
| ORGANISM = "hsa" | |
| pathways = requests.get('http://rest.kegg.jp/list/pathway/' + ORGANISM) | |
| for line in pathways.content.split('\n'): | |
| pathwayid = line.split('\t')[0].replace('path:', '') | |
| kgml = requests.get('http://rest.kegg.jp/get/' + pathwayid + '/kgml') | |
| f = open(pathwayid + '.xml', 'w') | |
| f.write(kgml.content) |
kozo2
/ KGMLMapper.java
Created
December 5, 2013 19:40
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| package org.cytoscape.keggscape.internal.read.kgml; | |
| import java.util.ArrayList; | |
| import java.util.Arrays; | |
| import java.util.HashMap; | |
| import java.util.List; | |
| import java.util.Map; | |
| import org.cytoscape.keggscape.internal.generated.Entry; | |
| import org.cytoscape.keggscape.internal.generated.Graphics; |
kozo2
/ getCpdNames.py
Created
December 7, 2013 00:42
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| import requests | |
| from sets import Set | |
| import more_itertools | |
| pathways = requests.get('http://rest.kegg.jp/list/pathway') | |
| compounds = [] | |
| for line in pathways.content.split('\n'): | |
| mapid = line.split('\t')[0].replace('path:', '') | |
| cpds = requests.get('http://rest.kegg.jp/link/cpd/' + mapid) |
kozo2
/ gist:7946590
Created
December 13, 2013 16:10
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| [knishida@dhcp255-85]~% cytoscape-unix-3.2.0-SNAPSHOT/cytoscape.sh | |
| _ | |
| ___ _ _| |_ ___ ___ ___ __ _ _ __ ___ | |
| / __| | | | __|/ _ \/ __|/ __|/ _` | '_ \ / _ \ | |
| | (__| |_| | |_| (_) \__ \ (__| (_| | |_) | __/ | |
| \___|\__, |\__|\___/|___/\___|\__,_| .__/ \___| | |
| |___/ |_| | |
| Cytoscape 3.2.0-SNAPSHOT |
kozo2
/ load_kegg.py
Last active
January 1, 2016 17:29
— forked from keiono/load_kegg.py
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| from java.io import File | |
| KEGG_DIR = "/Users/kozo2/kegg/" | |
| CARBOHYDRATE = "Carbohydrate" | |
| pathwayids_for = { CARBOHYDRATE : ["00010", "00020", "00030", "00040", "00051", "00052", "00053", "00500", "00520", "00562", "00620", "00630", "00640", "00650", "00660"] } | |
| ORGANISM = "eco" | |
| loadNetworkTF = cyAppAdapter.get_LoadNetworkFileTaskFactory() |
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| alias l ls -l $* | |
| alias j dired-jump | |
| alias f find-file $1 |
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| import net.liftweb.json.Xml // converts XML to JSON | |
| import com.mongodb.casbah.Imports._ // To put stuff in Mongo | |
| import com.mongodb.casbah.MongoDB // To connect to Mongo | |
| import com.mongodb.util.JSON // To parse JSON into a MongoDBObject | |
| import net.liftweb.json._ // To output Lift JSON as actual JSON | |
| import scala.xml.XML // To load XML | |
| // load the XML | |
| val xml = XML.load("http://www.w3schools.com/xml/note.xml") | |
| // fire up mongo connection |
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| SELECT a #?uniprot_id #?xref_id | |
| WHERE | |
| { | |
| ?id ?label "ConA" . | |
| ?uniprot_id ?p ?id . | |
| ?uniprot_id a <http://purl.uniprot.org/core/Protein> . | |
| # ?uniprot_id <http://www.w3.org/2000/01/rdf-schema#seeAlso> ?xref_id . | |
| # <http://purl.uniprot.org/pfam/PF00139> ?p ?o | |
| # ?xref_id <http://purl.uniprot.org/core/database> <http://purl.uniprot.org/database/Pfam> | |
| } |