Data Laundry, Revisited
March 22, 2019
Awk is my normal detergent for data laundry:
{ second[$1] = second[$1] "," $2; third[$1] = third[$1] "," $3 }
END { for (i in second) print i, substr(second[i],2), substr(third[i],2) }
The first line stores the second and third fields in associative arrays indexed by the first field, accumulating fields with identical indices with leading commas before each field, and the second line iterates over the two arrays, deleting the leading comma on output. Here is the output:
AAKRLN ACAT1,SUCLG2 LMTADAAKRLNVTPL,NEALEAAKRLNAKEI AAKRMA VCL NDIIAAAKRMALLMA AAKRQK MTA2 SSSQPAAKRQKLNPA AAKRPL WIZ YLGSVAAKRPLQEDR AAKRLR GTF2F1 VSEMPAAKRLRLDTG AAKRKA HIST1H1B,HIST1H1E AAGAGAAKRKATGPP,RKSAGAAKRKASGPP
I made no assumptions about the order of the input or the output. If you want sorted output, pipe the output through sort. You can run the program at https://ideone.com/sbgLNk.
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awk version
$ cat data-laundry-revisited.awk # Data Laundry, Revisited # function createname(str) { buffer = ""; name = $1; n = split($0,arr); for (i = 2; i <= n; i++) { buffer = buffer arr[i] " "; } return substr(buffer,1,length(buffer)-1); } function addname(str,buffer,name) { n1 = split(buffer,arr1); n2 = split(str,arr2); for (i = 2; i <= n2; i++) { arr2[i] = arr2[i] "," arr1[i-1] } buffer2 = ""; for (i = 2; i <= n2; i++) { buffer2 = buffer2 arr2[i] " "; } return substr(buffer2,1,length(buffer2)-1); } BEGIN { buffer = ""; name = "" } { if ($1 != name) { if (buffer == "") { buffer = createname($0); } else { print name " " buffer; buffer = createname($0); } } else { buffer = addname($0,buffer,name); } } END { if (buffer != "") { print name " " buffer; } } $ cat data-laundry.txt AAKRKA HIST1H1B AAGAGAAKRKATGPP AAKRKA HIST1H1E RKSAGAAKRKASGPP AAKRLN ACAT1 LMTADAAKRLNVTPL AAKRLN SUCLG2 NEALEAAKRLNAKEI AAKRLR GTF2F1 VSEMPAAKRLRLDTG AAKRMA VCL NDIIAAAKRMALLMA AAKRPL WIZ YLGSVAAKRPLQEDR AAKRQK MTA2 SSSQPAAKRQKLNPA $ awk -f data-laundry-revisited.awk data-laundry.txt AAKRKA HIST1H1E,HIST1H1B RKSAGAAKRKASGPP,AAGAGAAKRKATGPP AAKRLN SUCLG2,ACAT1 NEALEAAKRLNAKEI,LMTADAAKRLNVTPL AAKRLR GTF2F1 VSEMPAAKRLRLDTG AAKRMA VCL NDIIAAAKRMALLMA AAKRPL WIZ YLGSVAAKRPLQEDR AAKRQK MTA2 SSSQPAAKRQKLNPAScheme (Chicken):
(import (srfi-1) (srfi-13) (chicken io)) (define (words line) (string-tokenize line)) (define (lines-mergeable? line1 line2) (equal? (car (words line1)) (car (words line2)))) (define (merge-lines line1 line2) (let ((line1-words (words line1)) (line2-words (words line2))) (string-join (cons (car line1-words) (map (lambda (l) (string-join l ",")) (zip (cdr line1-words) (cdr line2-words))))))) (define (do-merge input-lines) (let loop ((remaining (cdr input-lines)) (current (car input-lines)) (output '())) (if (null? remaining) (reverse (cons current output)) (let ((next (car remaining))) (if (lines-mergeable? next current) (loop (cdr remaining) (merge-lines current next) output) (loop (cdr remaining) next (cons current output))))))) (with-input-from-file "laundry-input-file.txt" (lambda () (for-each print (do-merge (read-lines)))))For something a bit different, here’s a solution using SQLite.
Here’s a solution in Python.
from collections import OrderedDict import sys d = OrderedDict() with open(sys.argv[1]) as f: for line in f: key, val1, val2 = line.strip().split() if key not in d: d[key] = [] d[key].extend((val1, val2)) for key, vals in d.items(): vals1 = ','.join(vals[0::2]) vals2 = ','.join(vals[1::2]) print('{} {} {}'.format(key, vals1, vals2))Example Usage:
In SWI-Prolog 7 and up:
collapse([], []).
collapse([X], [X]).
collapse([[A,B1,C1],[A,B2,C2]|Rest], CollapsedRest) :-
atomics_to_string([B1,B2], ",", B3),
atomics_to_string([C1,C2], ",", C3),
collapse([[A,B3,C3]|Rest], CollapsedRest).
collapse([X|Rest], [X|CollapsedRest]) :-
collapse(Rest, CollapsedRest).
read_file_to_lines(Filename, Lines) :-
read_file_to_string(Filename, String, []),
split_string(String, "\n", "\n", Lines).
process(Lines, CollapsedLines) :-
maplist(split_line, Lines, SplitLines),
collapse(SplitLines, CollapsedLines).
split_line(Line, Parts) :-
split_string(Line, " ", " ", Parts).
go :-
read_file_to_lines("data-laundry-input.txt", Lines),
process(Lines, CollapsedLines),
maplist(format("~w ~w ~w~n"), CollapsedLines).
Another AWK solution. (Well, GNU AWK…) It makes various assumptions, such as fields not being printf format strings, etc.
#!/usr/local/bin/gawk -f { for (i = 2; i <= NF; i++) { field[$1][i-2][NR] = $i } } END { PROCINFO["sorted_in"] = "@ind_num_asc" for (key in field) { printf key for (i = 0; i < length(field[key]); i++) { s = "" for (j in field[key][i]) { s = s "," field[key][i][j] } printf " " gensub(/^,/, "", "1", s) } print "" } }