In my case i have a data frame contaning some biological data which are: protein name, ecnumber (which could be more than one) and protein domains (which could be also more than one domain). The data frame is a one column containing all those data which i would like to split it into three columns, but the problem is that if a line (containing more than one ECnumber) is splitted, the second ECnumber goes to the third column and the domains will be then disappeared.
here is my code:
val df = rdd.toDF()
val mydf = df.withColumn("_tmp", split($"value", ";")).select(
$"_tmp".getItem(0).as("Entry"),
$"_tmp".getItem(1).as("ECnumber"),
$"_tmp".getItem(2).as("Domains")
And here is the result
enter image description here
Based on the provided reference data, I see you can use the following regular expression to retrieve your data into independent columns (by extracting using regular expression):
val dataFrameValueRegex = "(\\w++);(([0-9.-]*+;)++)((\\w++;?)++)".r
For example if data frame value has got the following:
val dataFrameValue = "A6MML6;2.1.-.-;2.1.3.16;IPR037431;IPR037432;IPR037433"
Now using regular expression, you can extract independent values from data frame value:
val dataFrameValueRegex(entry, ecNumbers, _, domains, _) = dataFrameValue
Above: All values will be retrieved in corresponding variables:
1.) entry: Entry string
2.) ecNumbers: Complete string of ecnumbers separated by semicolon's. There would be a semicolon present at the end of the string.
3.) domains: Complete string of domains separated by semicolon's.
Note: If for any reason the data frame value was not as expected you would get a MatchError exception been thrown.
In the below code just printing variables information.
println(s"Data value: Entry = [$entry], ECnumbers = [${ecNumbers.init}], Domains = [$domains]")
val ecNumber = ecNumbers.init.split(";")
ecNumber.foreach(e => println(s"ecNumber = [$e]"))
val domain = domains.split(";")
domain.foreach(d => println(s"Domain = [$d]"))
I have UDF output as :-
Sample records:-
({(Todd,1),(Todd,1),(Todd,1),(Todd,1),(Todd,1),(Todd,5),(Todd,10),(Todd,20),(Todd,10),(Todd,10),(Todd,10),(Todd,10),(Todd,10),(Todd,10)})
({(Jon,1),(Jon,1),(Jon,1),(Jon,1),(Jon,1),(Jon,5),(Jon,10),(Jon,20),(Jon,10),(Jon,10),(Jon,10),(Jon,10),(Jon,5),(Jon,20),(Jon,1)})
Schema for UDF:- name:chararray(1 single column)
Now i want to read this bag of tuples and generate output as :-
Todd,240
Jon,422
The output of the UDF i stored in a temp file and read it back using different schema as:-
D = LOAD '/home/training/pig/pig/UDFdata.txt' AS (B: bag {T: tuple(name:chararray, denom:int)});
After that i am trying to use foreach loop and reference dot notation to find the sum.
X = foreach D generate B.T.name,SUM(B.T.denom);
2017-03-04 13:52:59,507 ERROR org.apache.pig.tools.grunt.Grunt: ERROR
1128: Cannot find field T in name:chararray,denom:int Details at
logfile: /home/training/pig_1488648405070.log
Can you please let me know how to find it? I am new to Apache Pig so not sure how it traverse in Bag of Tuples and find sum.
GROUP the dataset on name before performing SUM.
FLATTEN the bag to perform GROUP.
flattened = FOREACH D GENERATE FLATTEN(B);
dump flattened;
...
(Todd,10)
(Todd,10)
(Jon,1)
(Jon,1)
....
Then, GROUP them on name
grouped = GROUP flattened by name;
dump grouped;
(Jon,{(Jon,1),(Jon,20),(Jon,5),(Jon,10),(Jon,10),(Jon,10),(Jon,10),(Jon,20),(Jon,10),(Jon,5),(Jon,1),(Jon,1),(Jon,1),(Jon,1),(Jon,1)})
(Todd,{(Todd,10),(Todd,10),(Todd,10),(Todd,10),(Todd,10),(Todd,10),(Todd,20),(Todd,10),(Todd,5),(Todd,1),(Todd,1),(Todd,1),(Todd,1),(Todd,1)})
And apply SUM() over the result
final_sum = FOREACH grouped GENERATE group, SUM(flattened.denom);
dump final_sum;
(Jon,106)
(Todd,100)
I have been trying to search for an item which is there in a text file.
The text file is like
Eg: `
>HEADING
00345
XYZ
MethodName : fdsafk
Date: 23-4-2012
More text and some part containing instances of XYZ`
So I did a dictionary search for XYZ initially and found the positions, but I want only the 1st XYZ and not the rest. There is a property of XYZ that , it will always be between the 5 digit code and the text MethondName .
I am unable to do that.
WORDLIST ZipList = 'Zipcode.txt';
DECLARE Zip;
Document
Document{-> MARKFAST(Zip, ZipList)};
DECLARE Method;
"MethodName" -> Method;
WORDLIST typelist = 'typelist.txt';
DECLARE type;
Document{-> MARKFAST(type, typelist)};
Also how do we use REGEX in UIMA RUTA?
There are many ways to specify this. Here are some examples (not tested):
// just remove the other annotations (assuming type is the one you want)
type{-> UNMARK(type)} ANY{-STARTSWITH(Method)};
// only keep the first one: remove any annotation if there is one somewhere in front of it
// you can also specify this with POSISTION or CURRENTCOUNT, but both are slow
type # #type{-> UNMARK(type)}
// just create a new annotation in between
NUM{REGEXP(".....")} #{-> type} #Method;
There are two options to use regex in UIMA Ruta:
(find) simple regex rules like "[A-Za-z]+" -> Type;
(matches) REGEXP conditions for validating the match of a rule element like
ANY{REGEXP("[A-Za-z]+")-> Type};
Let me know if something is not clear. I will extend the description then.
DISCLAIMER: I am a developer of UIMA Ruta
I'm learning Pig Latin and am using regular expressions. Not sure if the regex is language agnostic or not but here is what I'm trying to do.
If I have a table with two fields: tweet id and tweet, I'd like to go through each tweet and pull out all mentions up to 3.
So if a tweet goes something like "#tim bla #sam #joe something bla bla" then the line item for that tweet will have tweet id, tim, sam, joe.
The raw data has twitter ids not the actual handles so this regex seems to return a mention (.*)#user_(\\S{8})([:| ])(.*)
Here is what I have tried:
a = load 'data.txt' AS (id:chararray, tweet:chararray);
b = foreach a generate id, LOWER(tweet) as tweet;
// filter data so only tweets with mentions
c = FILTER b BY tweet MATCHES '(.*)#user_(\\S{8})([:| ])(.*)';
// try to pull out the mentions.
d = foreach c generate id,
REGEX_EXTRACT(tweet, '((.*)#user_(\\S{8})([:| ])(.*)){1}',3) as mention1,
REGEX_EXTRACT(tweet, '((.*)#user_(\\S{8})([:| ])(.*)){1,2}',3) as mention2,
REGEX_EXTRACT(tweet, '((.*)#user_(\\S{8})([:| ])(.*)){2,3}',3) as mention3;
e = limit d 20;
dump e;
So in that try I was playing with quantifiers, trying to return the first, second and 3rd instance of a match in a tweet {1}, {1,2}, {2,3}.
That did not work, mention 1-3 are just empty.
So I tried changing d:
d = foreach c generate id,
REGEX_EXTRACT(tweet, '(.*)#user_(\\S{8})([:| ])(.*)',2) as mention1,
REGEX_EXTRACT(tweet, '(.*)#user_(\\S{8})([:| ])(.*)#user_(\\S{8})([:| ])(.*)',5) as mention2,
REGEX_EXTRACT(tweet, '(.*)#user_(\\S{8})([:| ])(.*)#user_(\\S{8})([:| ])(.*)#user_(\\S{8})([:| ])(.*)',8) as mention3,
But, instead of returning each user mentioned, this returned the same mention 3 times. I had expected that by cutting n pasting the expression again I'd get the second match, and pasting it a 3rd time would get the 3rd match.
I'm not sure how well I've managed to word this question but to put it another way, imagine that the function regex_extract() returned an array of matched terms. I would like to get mention[0], mention[1], mention[2] on a single line item.
Whenever you use PATTERN_EXTRACT or PATTERN_EXTRACT_ALL udf, keep in mind that it is just pure regex handled by Java.
It is easier to test the regex through a local Java test. Here is the regex I found to be acceptable :
Pattern p = Pattern.compile("#(\\S+).*?(?:#(\\S+)(?:.*?#(\\S+))?)?");
String input = "So if a tweet goes something like #tim bla #sam #joe #bill something bla bla";
Matcher m = p.matcher(input);
if(m.find()){
for(int i=0; i<=m.groupCount(); i++){
System.out.println(i + " -> " + m.group(i));
}
}
With this regex, if there is at least a mention, it will returns three fields, the seconds and/or third being null if a second/third mention is not found.
Therefore, you may use the following PIG code :
d = foreach c generate id, REGEX_EXTRACT_ALL(
tweet, '#(\\S+).*?(?:#(\\S+)(?:.*?#(\\S+))?)?');
You do not even need to filter the data first.
I have my input string as
{(100),(200),(300)}
and I want to split them into different columns using regex_extract_all.
I have used REGEX_EXTRACT_ALL(data,'[^{(,)}]+') and I am getting an error saying:
Could not infer the matching function for org.apache.pig.builtin.REGEX_EXTRACT_ALL as multiple or none of them fit. Please use an explicit cast.
What am I missing ?
If it's a tuple of bags, you can't use it as a chararray field - thus you can't use REGEX_EXTRACT_ALL with it. If you want to split it into multiple tuples, use the function BagToTuple and FLATTEN.
e.g.:
...
a = load '/tmp/1.txt';
b = group a by $0;
c = foreach b generate group, FLATTEN(BagToTuple(a.$1));
...