NAME
Webservice::InterMine::Cookbook::List::Upload - Uploading Lists
SYNOPSIS
use Webservice::InterMine;
my $service = Webservice::InterMine->get_service('www.flymine.org/query', $TOKEN);
# From a file on disk containing gene symbols (one per line).
my $file = '/path/to/some/file/somewhere.tsv';
my $list = $service->new_list(content => $file, type => 'Gene', name => 'an uploaded list');
# From an array of strings
my @symbols = qw/eve zen rudimentary Mad/;
my $list = $service->new_list(content => \@symbols, type => 'Gene', name => 'an uploaded list');
# From a query
my $query = $service->new_query(class => 'Gene');
$query->add_constraint(
path => 'Gene',
op => 'IN',
value => 'my other list'
);
$query->add_constraint(
path => 'Gene.length',
op => '<',
value => 2000
);
# The type of this list can be inferred
my $list = $service->new_list(content => $query, name => 'an uploaded list');DESCRIPTION
You can create lists associated with your account in two main ways. Either you can provide a collection of identifiers (for example gene symbols) and get the InterMine server try and unambiguously resolve them into objects in the database, or you can provide a query that specifies exactly what you want.
If you don't specify a name, a default name will be assigned, and unless the query is renamed, the list will be deleted when the program terminates.
Notes:
- Uploading from files
-
All text in the files will be interpreted as identifiers, so you wouldn't want to, say, try to upload a gff3 file directly. Valid separators are spaces, tabs and new-lines, so you will want to quote (with either double or single quotes) and identifiers that have these characters.
- Uploading from an array of strings
-
These strings will be automatically quoted.
- Uploading from a query
-
If the query has no output columns (an empty view) the root of the query will be used to define what to save. If there are output columns, they should all be attached to the same object, and that will be used to identify the objects to save. ie:
# If used this query would save a list of one gene. my $query = $service->new_query(class => 'Gene'); $query->add_constraint(path => 'Gene.symbol', op => '=', value => 'eve'); # Adding this view would make this query save the list of proteins associated with eve. $query->add_view('Gene.proteins.name'); - Duplicates and Conversions
-
These will be ignored. See Webservice::InterMine::Cookbook::IdResolution for ways to deal with these issues.
CONCLUSION
Lists can be created from a variety of sources.