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Re: Consolidating biological data into occurance of each biological unit per sample in table

by CountZero (Chancellor)
on Jan 13, 2013 at 09:39 UTC ( #1013094=note: print w/ replies, xml ) Need Help??


in reply to Consolidating biological data into occurance of each biological unit per sample in table

One split can get you your data:

use Modern::Perl; while (<DATA>) { chomp; my ($id, $sample_id, undef, $animal, undef, $color) = split /[\t_; +]+/; say "$id ($sample_id) is a $animal colored $color"; } __DATA__ occurence1 A a__bear;c__black occurence2 B a__wolf;c__grey occurence3 A a__wolf;c__white occurence4 A a__bear;c__ occurence5 C a__wolf;c__grey occurence6 C a__bear;c__brown
Output:
occurence1 (A) is a bear colored black occurence2 (B) is a wolf colored grey occurence3 (A) is a wolf colored white occurence4 (A) is a bear colored occurence5 (C) is a wolf colored grey occurence6 (C) is a bear colored brown
Now that we have the data, why not putting it into a database such as SQLite?
use Modern::Perl; use DBI; my $dbh = DBI->connect( "dbi:SQLite:dbname=c:/data/strawberry-perl/perl/script-chrome/animals. +sqlite", "", "" ) or die "Could not open database"; my $statement = q{CREATE TABLE IF NOT EXISTS "main"."sightings" ("id" TEXT PRIMARY KEY + NOT NULL, "sampleid" TEXT, "animal" TEXT, "color" TEXT)}; my $rows = $dbh->do($statement) or die $dbh->errstr; $dbh->{AutoCommit} = 0; $dbh->do('BEGIN TRANSACTION'); my $sth = $dbh->prepare( q{INSERT INTO sightings (id, sampleid, animal, color) VALUES (?, ? +, ?, ?)}) or die "Could not prepare INSERT statement"; while (<DATA>) { chomp; my ( $id, $sample_id, undef, $animal, undef, $color ) = split /[\t +_;]+/; $color ||= 'unknown'; $sth->execute( $id, $sample_id, $animal, $color ); } $dbh->commit;
Now we can interrogate the database and use aggregate functions to get your answers:
SELECT sampleid, animal, count(*) FROM sightings GROUP BY sampleid, an +imal
will return
"A","bear","6" "A","wolf","4" "B","bear","2" "B","wolf","7" "C","bear","6" "C","wolf","5"
And
SELECT sampleid, color, count(*) FROM sightings GROUP BY sampleid, col +or
will give you
"A","black","1" "A","brown","3" "A","grey","1" "A","red","1" "A","unknown","3" "A","white","1" "B","brown","1" "B","grey","5" "B","red","1" "B","unknown","2" "C","black","1" "C","brown","4" "C","grey","3" "C","unknown","2" "C","white","1"

CountZero

A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James

My blog: Imperial Deltronics


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