zakandrewking

Visual Studio Code (1.76.1, undefined, desktop)
Jupyter Extension Version: 2023.2.1200692131.
Python Extension Version: 2023.4.1.
Workspace folder /Users/zak/repos/test
warn 13:48:48.940: Exception while attempting zmq : No native build was found for platform=darwin arch=arm64 runtime=electron abi=106 uv=1 armv=8 libc=glibc node=16.14.2 electron=19.1.11
    loaded from: /Users/zak/.vscode/extensions/ms-toolsai.jupyter-2023.2.1200692131/out/node_modules/zeromq

User belongs to experiment group 'jupyterEnhancedDataViewer'
User belongs to experiment group 'jupyterTest'
debug 13:48:49.017: Updating cache with Python kernels 

zakandrewking

import contextlib
import os
import sys

# Suppress stdout http://stackoverflow.com/a/17753573
class DummyFile(object):
    def write(self, x): pass
@contextlib.contextmanager
def no_stdout(std_channel, dest_filename):
    old_std_channel = os.dup(std_channel.fileno())

zakandrewking

import requests
import re

response = requests.post(
    'http://bigg.ucsd.edu/advanced_search_external_id_results',
    data={'database_source': 'kegg.compound', 'query': 'C00234'}
)

try:
    print re.search(r'/models/universal/metabolites/([^"]+)', response.text).group(1)

zakandrewking

# inputs
# model, old_gene, new_gene

for reaction in model.genes.get_by_id(old_gene).reactions:
    reaction.gene_reaction_rule = re.sub(r'\b' + old_gene + r'\b', new_gene, 
                                         reaction.gene_reaction_rule)
remove_genes(model, [g for g in model.genes if len(g.reactions) == 0])

zakandrewking

# http://stackoverflow.com/questions/15288891/how-can-i-serve-files-with-utf-8-encoding-using-python-simplehttpserver
python -c "import SimpleHTTPServer; m = SimpleHTTPServer.SimpleHTTPRequestHandler.extensions_map; m[''] = 'text/plain'; m.update(dict([(k, v + ';charset=UTF-8') for k, v in m.items()])); SimpleHTTPServer.test();"

zakandrewking

 diff <(jq -S '.' s_cerevisiae.iMM904.all_reactions.json) <(jq '.' 2007179_map.json -S) | less

zakandrewking

# http://ck.kennt-wayne.de/2013/sep/emacs-using-ctags-for-javascript-and-rails

--langdef=js
--langmap=js:.js
--regex-js=/([A-Za-z0-9._$]+)[ \t]*[:=][ \t]*\{/\1/,object/
--regex-js=/([A-Za-z0-9._$()]+)[ \t]*[:=][ \t]*function[ \t]*\(/\1/,function/
--regex-js=/function[ \t]+([A-Za-z0-9._$]+)[ \t]*\(([^)])\)/\1/,function/
--regex-js=/([A-Za-z0-9._$]+)[ \t]*[:=][ \t]*\[/\1/,array/
--regex-js=/([^= ]+)[ \t]*=[ \t]*[^"]'[^']*/\1/,string/
--regex-js=/([^= ]+)[ \t]*=[ \t]*[^']"[^"]*/\1/,string/

zakandrewking

#!/bin/bash
# Put this in .git/hooks/post-checkout, and chmod +x
/Users/zaking/.emacs.d/etags.sh -js -py -!/bin/ -!/lib/ -!escher.*

zakandrewking

tax_id	Org_name	GeneID	CurrentID	Status	Symbol	Aliases	description	other_designations	map_location	chromosome	genomic_nucleotide_accession.version	start_position_on_the_genomic_accession	end_position_on_the_genomic_accession	orientation	exon_count	OMIM	
511145	Escherichia coli str. K-12 substr. MG1655	5625560	0	live	aaaD	b4634ECK4439, ylcF	pseudo				NC_000913.3	581354	581662	plus	0		
511145	Escherichia coli str. K-12 substr. MG1655	7751645	0	live	aaaE	b4693ECK1135, JW1135, ymfN	pseudo				NC_000913.3	1204404	1205537	plus	0		
511145	Escherichia coli str. K-12 substr. MG1655	947748	0	live	aaeA	b3241ECK3230, JW3210, yhcQ	p-hydroxybenzoic acid efflux system component				NC_000913.3	3388194	3389126	minus	0		
511145	Escherichia coli str. K-12 substr. MG1655	947747	0	live	aaeB	b3240ECK3229, JW3209, yhcP	p-hydroxybenzoic acid efflux system component				NC_000913.3	3386221	3388188	minus	0		
511145	Escherichia coli str. K-12 substr. MG1655	947760	0	live	aaeR	b3243ECK3232, JW3212, qseA, yhcS	transcriptional regulator for

zakandrewking

import json

# save a single flux vector as JSON
flux_dictionary = {'asdf': 2}
with open('out.json', 'w') as f:
    json.dump(flux_dictionary, f)
    flux_dictionary = {'asdf': 2}
    
# save a flux comparison as JSON
flux_comp = [{'GAPD': 3}, {'GAPD': 4}]