cd work

mkdir src

cd src

curl ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip -O

unzip edirect.zip

cd edirect
ls

./setup.sh

Trying to establish local installations of any missing Perl modules
(as logged in /Users/adu/work/src/edirect/setup-deps.log).
Please be patient, as this step may take a little while.
Entrez Direct has been successfully downloaded and installed.
In order to complete the configuration process, please execute the following:
  echo "source ~/.bash_profile" >> $HOME/.bashrc
  echo "export PATH=\${PATH}:/Users/adu/work/src/edirect" >> $HOME/.bash_profile
or manually edit the PATH variable assignment in your .bash_profile file.

echo "export PATH=\${PATH}:/Users/adu/work/src/edirect" >> $HOME/.bash_profile

esearch -help

esearch -db databaseName -query queryString

esearch -db pubmed -query "opsin gene conversion"

esearch -db pubmed -query "opsin gene conversion" | elink -related

esearch -db pubmed -query "opsin gene conversion" | \
  elink -related | \
  elink -target protein

esearch -db pubmed -query "lycopene cyclase" |
  efetch -format abstract

esearch -db protein -query "lycopene cyclase" |
  efetch -format fasta

esearch -db pubmed -query "opsin gene conversion" |
  elink -related |
  efilter -query "tetrachromacy"

efilter -days 60 -datetype PDAT
  efilter -mindate 1990 -maxdate 1999 -datetype PDAT

"Tager HS [AUTH] AND glucagon [TIAB]"

Mac-mini:work adu$ esearch -db pubmed -query "Tager HS [AUTH] AND glucagon [TIAB]"
<ENTREZ_DIRECT>
  <Db>pubmed</Db>
  <WebEnv>NCID_1_123525658_130.14.22.76_9001_1555050683_279099027_0MetA0_S_MegaStore</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>24</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

"alcohol dehydrogenase [PROT] NOT (bacteria [ORGN] OR fungi [ORGN])"

Mac-mini:work adu$ esearch -db protein -query "alcohol dehydrogenase [PROT] NOT (bacteria [ORGN] OR fungi [ORGN])"
<ENTREZ_DIRECT>
  <Db>protein</Db>
  <WebEnv>NCID_1_123764783_130.14.18.97_9001_1555052879_1098401792_0MetA0_S_MegaStore</WebEnv>
  <QueryKey>1</QueryKey>
  <Count>8402</Count>
  <Step>1</Step>
</ENTREZ_DIRECT>

esearch -db protein -query "NP_567004 [ACCN]" |
  elink -related |
  efilter -query "28000:30000 [MLWT]" |
  elink -target structure |
  efilter -query "0:2 [RESO]"

Mac-mini:work adu$ esearch -db protein -query "NP_567004 [ACCN]" |   elink -related |   efilter -query "28000:30000 [MLWT]" |   elink -target structure |   efilter -query "0:2 [RESO]"
Retrying elink, step 2: callMLink: Timeout waiting for response from MegaLink server (3)
Retrying elink, step 2: callMLink: Timeout waiting for response from MegaLink server (3)
Retrying elink, step 2: callMLink: Timeout waiting for response from MegaLink server (3)
ERROR in link output: callMLink: Timeout waiting for response from MegaLink server (3)
WebEnv: NCID_1_123813944_130.14.22.76_9001_1555053764_1622274016_0MetA0_S_MegaStore
URL: dbfrom=protein&db=protein&query_key=1&WebEnv=NCID_1_123813944_130.14.22.76_9001_1555053764_1622274016_0MetA0_S_MegaStore&cmd=neighbor_history&linkname=protein_protein
Result: <?xml version="1.0" encoding="UTF-8" ?>
<!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD elink 20101123//EN" "https://eutils.ncbi.nlm.nih.gov/eutils/dtd/20101123/elink.dtd">
<eLinkResult>
<LinkSet>
  <DbFrom>protein</DbFrom>
  <IdList>
    <Id>18410104</Id>
  </IdList>
  <LinkSetDbHistory>
    <DbTo>protein</DbTo>
    <LinkName>protein_protein</LinkName>
  <ERROR>callMLink: Timeout waiting for response from MegaLink server (3)</ERROR>
  </LinkSetDbHistory>
  <WebEnv>NCID_1_123813944_130.14.22.76_9001_1555053764_1622274016_0MetA0_S_MegaStore</WebEnv>
</LinkSet>
</eLinkResult>
ERROR in filt input: callMLink: Timeout waiting for response from MegaLink server (3)
ERROR in link input: callMLink: Timeout waiting for response from MegaLink server (3)
<ENTREZ_DIRECT>
  <Error>callMLink: Timeout waiting for response from MegaLink server (3)</Error>
</ENTREZ_DIRECT>
ERROR in filt input: callMLink: Timeout waiting for response from MegaLink server (3)

esearch -db protein -query "amyloid* [PROT]" |
  elink -target pubmed |
  esearch -db gene -query "apo* [GENE]" |
  elink -target pubmed |
  esearch -query "(#3) AND (#6)" |
  efetch -format docsum |
  xtract -pattern DocumentSummary -element Id Title

Mac-mini:work adu$ esearch -db protein -query "amyloid* [PROT]" |
>   elink -target pubmed |
>   esearch -db gene -query "apo* [GENE]" |
>   elink -target pubmed |
>   esearch -query "(#3) AND (#6)" |
>   efetch -format docsum |
>   xtract -pattern DocumentSummary -element Id Title
20301340  Alzheimer Disease Overview
28987665  Altered spontaneous brain activity pattern in cognitively normal young adults carrying mutations of APP, presenilin-1/2 and APOE ε4.
28252024  Evolution of complexity in the zebrafish synapse proteome.
28071753  De novo assembly, annotation, and characterization of the whole brain transcriptome of male and female Syrian hamsters.
27626380  High-throughput discovery of novel developmental phenotypes.
27535807  Sex-specific characterization and evaluation of the Alzheimer's disease genetic risk factor sorl1 in zebrafish during aging and in the adult brain following a 100 ppb embryonic lead exposure.
27234028  Alzheimer's disease risk genes in wild-type adult zebrafish exhibit gender-specific expression changes during aging.
27189481  Gene evolution and gene expression after whole genome duplication in fish: the PhyloFish database.
26871637  Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing.
26614614  Multi-tissue transcriptome profiles for coho salmon (Oncorhynchus kisutch), a species undergoing rediploidization following whole-genome duplication.
26469318  RFX transcription factors are essential for hearing in mice.
26319212  Transcriptome sequencing and development of an expression microarray platform for liver infection in adenovirus type 5-infected Syrian golden hamsters.
26107351  Annotation of the Protein Coding Regions of the Equine Genome.
25852190  Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy.
25765076  Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes.
25319552  A new rhesus macaque assembly and annotation for next-generation sequencing analyses.
24952961  A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain.
24709693  Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.
24705354  The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease.
24658140  The mammalian-membrane two-hybrid assay (MaMTH) for probing membrane-protein interactions in human cells.
24402279  Elephant shark genome provides unique insights into gnathostome evolution.
23962925  Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii.
23258410  Comparative analysis of bat genomes provides insight into the evolution of flight and immunity.
23236062  Sequencing, annotation, and characterization of the influenza ferret infectome.
23149746  Genome sequences of wild and domestic bactrian camels.
23127152  Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote.
20301414  Early-Onset Familial Alzheimer Disease
22751099  The yak genome and adaptation to life at high altitude.
22134011  A preliminary sketch of horn cancer transcriptome in Indian zebu cattle.
22002653  Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques.
21993625  Genome sequencing reveals insights into physiology and longevity of the naked mole rat.
21857902  Transcriptome sequencing of the blind subterranean mole rat, Spalax galili: utility and potential for the discovery of novel evolutionary patterns.
21484476  Major chimpanzee-specific structural changes in sperm development-associated genes.
21048031  Single nucleotide polymorphisms of matrix metalloproteinase 9 (MMP9) and tumor protein 73 (TP73) interact with Epstein-Barr virus in chronic lymphocytic leukemia: results from the European case-control study EpiLymph.
20875843  Cloning, sequencing and expression in the dog of the main amyloid precursor protein isoforms and some of the enzymes related with their processing.
20433749  Salmo salar and Esox lucius full-length cDNA sequences reveal changes in evolutionary pressures on a post-tetraploidization genome.
20403183  Transcriptome sequencing and development of an expression microarray platform for the domestic ferret.
20237496  New genetic associations detected in a host response study to hepatitis B vaccine.
19946888  Defining the membrane proteome of NK cells.
19820115  BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum.
19393038  A whole-genome assembly of the domestic cow, Bos taurus.
19199708  Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT).
18362917  The genome of the model beetle and pest Tribolium castaneum.
17145712  PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences.
16710414  The DNA sequence and biological annotation of human chromosome 1.
16335952  Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.
16141072  The transcriptional landscape of the mammalian genome.
16136131  Initial sequence of the chimpanzee genome and comparison with the human genome.
16109975  The zebrafish gene map defines ancestral vertebrate chromosomes.
15642098  Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis.
15489334  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
15202933  Insertion of the amyloid precursor protein into lipid monolayers: effects of cholesterol and apolipoprotein E.
15169875  Identification and verification of novel rodent postsynaptic density proteins.
15164054  The DNA sequence and comparative analysis of human chromosome 10.
15164053  DNA sequence and analysis of human chromosome 9.
15057824  The DNA sequence and biology of human chromosome 19.
14702039  Complete sequencing and characterization of 21,243 full-length human cDNAs.
14681463  PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries.
12665801  Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides.
12537572  Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.
12520002  BayGenomics: a resource of insertional mutations in mouse embryonic stem cells.
12477932  Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.
12454917  Genetic and genomic tools for Xenopus research: The NIH Xenopus initiative.
12040188  A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.
11247302  Disabled-2 colocalizes with the LDLR in clathrin-coated pits and interacts with AP-2.
11230166  Toward a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs.
11181995  The sequence of the human genome.
10731132  The genome sequence of Drosophila melanogaster.
8858135 Regulation of tumor necrosis factor-and Fas-mediated apoptotic cell death by a novel cDNA TR2L.
7542371 Expression in mouse embryos and in adult mouse brain of three members of the amyloid precursor protein family, of the alpha-2-macroglobulin receptor/low density lipoprotein receptor-related protein and of its ligands apolipoprotein E, lipoprotein lipase, alpha-2-macroglobulin and the 40,000 molecular weight receptor-associated protein.

esearch -db structure -query "insulin [TITL]" |
  elink -target pubmed -label struc_cit |
  esearch -db protein -query "insulin [PROT]" |
  elink -target pubmed -label prot_cit |
  esearch -query "(#struc_cit) AND (#prot_cit)" |
  efetch -format uid

Mac-mini:work adu$ esearch -db structure -query "insulin [TITL]" |
>   elink -target pubmed -label struc_cit |
>   esearch -db protein -query "insulin [PROT]" |
>   elink -target pubmed -label prot_cit |
>   esearch -query "(#struc_cit) AND (#prot_cit)" |
>   efetch -format uid
25423173
15299880
9235985
9141131
8421693
1433291
1772633
2025410
2905485

// Swift 2
class Foo: NSObject, NSCopying {
	override func isEqual(_ x: AnyObject?) -> Bool { ... }
	func copyWithZone(_ zone: NSZone?) -> AnyObject { ... }
}

// Swift 3
class Foo: NSObject, NSCopying {
	override func isEqual(_ x: Any?) -> Bool { ... }
	func copy(with zone: NSZone?) -> Any { ... }
}

// Swift 2
struct State {
	var name: String
	var abbreviation: String
	var population: Int
	var asPropertyList: [NSObject: AnyObject] {
		var result: [NSObject: AnyObject] = [:]
		// Implicit conversions turn String into NSString here…
		result["name"] = self.name
		result["abbreviation"] = self.abbreviation
		// …and Int into NSNumber here.
		result["population"] = self.population
		return result
	}
}
let california = State(name: "California",
					   abbreviation: "CA",
					   population: 39_000_000)
NSNotification(name: "foo", object: nil,
			   userInfo: california.asPropertyList)

// Swift 2
struct State {
	var name: String
	var abbreviation: String
	var population: Int
	var asPropertyList: NSDictionary {
		var result = NSMutableDictionary()
		// Implicit conversions turn String into NSString here…
		result["name"] = self.name
		result["abbreviation"] = self.abbreviation
		// …and Int into NSNumber here.
		result["population"] = self.population
		return result.copy()
	}
}
let california = State(name: "California",
					   abbreviation: "CA",
					   population: 39_000_000)
// NSDictionary then implicitly converts to [NSObject: AnyObject] here.
NSNotification(name: "foo", object: nil,
			   userInfo: california.asPropertyList)

// Swift 3
struct State {
	var name: String
	var abbreviation: String
	var population: Int
	// Change the dictionary type to [AnyHashable: Any] here...
	var asPropertyList: [AnyHashable: Any] {
		var result: [AnyHashable: Any] = [:]
		// No implicit conversions necessary, since String and Int are subtypes
		// of Any and AnyHashable
		result["name"] = self.name
		result["abbreviation"] = self.abbreviation
		result["population"] = self.population
		return result
	}
}
let california = State(name: "California",
					   abbreviation: "CA",
					   population: 39_000_000)
// ...and you can still use it with Cocoa API here
Notification(name: "foo", object: nil,
			 userInfo: california.asPropertyList)

// ObjC
@interface Foo
- (void)updateString:(NSString *)string;
- (void)updateObject:(id *)obj;
@end

// Swift
func interactWith(foo: Foo) -> (String, Any) {
	var string = "string" as NSString // explicit conversion
	foo.updateString(&string) // parameter imports as UnsafeMutablePointer<NSString>
	let finishedString = string as String
	var object = "string" as AnyObject
	foo.updateObject(&object) // parameter imports as UnsafeMutablePointer<AnyObject>
	let finishedObject = object as Any
	return (finishedString, finishedObject)
}

// Swift 2
func foo(x: NSArray) {
	// Invokes -description by magic AnyObject lookup
	print(x[0].description)
}

// Swift 3
func foo(x: NSArray) {
	// Result of subscript is now Any, needs to be coerced to get method lookup
	print((x[0] as AnyObject).description)
}

func foo(x: NSArray) {
	// Cast to the concrete object type you expect
	print((x[0] as! NSObject).description)
}

// Swift 2
struct CreditCard { number: UInt64, expiration: NSDate }
let PaymentMade = "PaymentMade"
// We can't attach CreditCard directly to the notification, since it
// isn't a class, and doesn't bridge.
// Wrap it in a Box class.
class Box<T> {
	let value: T
	init(value: T) { self.value = value }
}
let paymentNotification =
	NSNotification(name: PaymentMade,
				   object: Box(value: CreditCard(number: 1234_0000_0000_0000,
												 expiration: NSDate())))

// Swift 3
let PaymentMade = Notification.Name("PaymentMade")
// We can associate the CreditCard value directly with the Notification
let paymentNotification =
	Notification(name: PaymentMade,
				 object: CreditCard(number: 1234_0000_0000_0000,
									expiration: Date()))

// Swift 3
let paymentCard = paymentNotification.object as! CreditCard
print(paymentCard.number) // 1234000000000000

let oneMillion = 1000000
let startTimes = NSDate().timeIntervalSince1970 * 1000
func loop() {
	for _ in 1...oneMillion {
	
	}
}
loop()
let endTimes = NSDate().timeIntervalSince1970 * 1000
let usedTimes = endTimes - startTimes
print("loop a million times used \(usedTimes) ms")

int oneMillion = 1000000;
NSTimeInterval startTimes = [[NSDate date] timeIntervalSince1970] * 1000;
for (NSUInteger i = 0; i < oneMillion; i++){
}
NSTimeInterval endTimes = [[NSDate date] timeIntervalSince1970] * 1000;
NSTimeInterval usedTimes = endTimes - startTimes;
printf("used times %f ms", usedTimes);

let count = 10000
let arr = Array(1...count)
let startTimes = NSDate().timeIntervalSince1970 * 1000
// *** Simple but inefficient version of quicksort ***
func quicksort<T: Comparable>(_ a: [T]) -> [T] {
    guard a.count > 1 else { return a }
    
    let pivot = a[a.count/2]
    let less = a.filter { $0 < pivot }
    let equal = a.filter { $0 == pivot }
    let greater = a.filter { $0 > pivot }
    
    // Uncomment this following line to see in detail what the
    // pivot is in each step and how the subarrays are partitioned.
    //print(pivot, less, equal, greater)  return quicksort(less) + equal + quicksort(greater)
    
    return quicksort(less) + equal + quicksort(greater)
}
quicksort(arr)
let endTimes = NSDate().timeIntervalSince1970 * 1000
let usedTimes = endTimes - startTimes
print("times used \(usedTimes) ms")

NSUInteger cap = 10000;
NSMutableArray *arr = [NSMutableArray arrayWithCapacity:cap];
for (NSUInteger i = 0; i < cap; i++) {
    NSNumber *num = [NSNumber numberWithInteger:i];
    arr[i] =num;
}
NSTimeInterval startTimes = [[NSDate date] timeIntervalSince1970] * 1000;
[self QuickSorkOC:arr Count:[arr count]];
NSTimeInterval endTimes = [[NSDate date] timeIntervalSince1970] * 1000;
NSTimeInterval usedTimes = endTimes - startTimes;
printf("used times %f ms", usedTimes);

var arr = Array(1...count)
arr.sort(by: >)

arr = (NSMutableArray *)[[arr reverseObjectEnumerator] allObjects];

let count = 10000
var arr = Array(repeating: 0, count: count)

for (NSUInteger i = 0; i < cap; i++) {
    NSNumber *num = [NSNumber numberWithInteger:0];
    arr[i] = num;
}

pip3 install --upgrade pip

pip3 install django

Mac-mini:Django adu$ python3
Python 3.6.1 (v3.6.1:69c0db5050, Mar 21 2017, 01:21:04) 
[GCC 4.2.1 (Apple Inc. build 5666) (dot 3)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import django
>>> print(django.get_version())
2.0

django-admin.py startproject HelloDjango

python3 manage.py runserver

Performing system checks...
System check identified no issues (0 silenced).
You have 14 unapplied migration(s). Your project may not work properly until you apply the migrations for app(s): admin, auth, contenttypes, sessions.
Run 'python manage.py migrate' to apply them.
June 06, 2017 - 08:11:05
Django version 2.0, using settings 'Django.settings'
Starting development server at http://127.0.0.1:8000/
Quit the server with CONTROL-C.
[06/Jun/2017 08:11:22] "GET / HTTP/1.1" 200 1699
Not Found: /favicon.ico
[06/Jun/2017 08:11:22] "GET /favicon.ico HTTP/1.1" 404 1961

from django.http import HttpResponse
 
def hello(request):
    return HttpResponse("Hello django ! ")

from django.conf.urls import url
 
from . import view
 
urlpatterns = [
    url(r'^$', view.hello),
]

#ClassOne.py 
class Calculator(object):
    #define class to simulate a simple calculator
    def __init__ (self):
        #start with zero
        self.current = 0
    def add(self, amount):
        #add number to current
        self.current += amount
    def getCurrent(self):
        return self.current

from ClassOne import * #get classes from ClassOne file
myBuddy = Calculator() # make myBuddy into a Calculator object
myBuddy.add(2) #use myBuddy's new add method derived from the Calculator class
print(myBuddy.getCurrent()) #print myBuddy's current instance variable