NAME
MRS::Client - A SOAP-based client of the MRS Retrieval server
VERSION
version 0.600100
SYNOPSIS
# 1. create a client that does all the work:
use MRS::Client;
# ...by default it connects to the MRS service at http://mrs.cmbi.ru.nl
my $client = MRS::Client->new();
# ...or let the client talk to your own MRS servers
my $client = MRS::Client->new ( search_url => 'http://localhost:18081/',
blast_url => 'http://localhost:18082/',;
clustal_url => 'http://localhost:18083/');
# ...or specify only a host, assuming the default ports are used
my $client = MRS::Client->new ( host => 'localhost');
# 2a. make various queries to a selected database:
print $client->db ('uniprot')->find ('sapiens')->count;
175642
print $client->db ('uniprot')->find ('sapiens')->next;
ID Q14547_HUMAN Unreviewed; 60 AA.
AC Q14547;
DT 01-NOV-1996, integrated into UniProtKB/TrEMBL.
DT 01-NOV-1996, sequence version 1.
DT 19-JAN-2010, entry version 51.
DE SubName: Full=Homeobox-like;
DE Flags: Fragment;
OS Homo sapiens (Human).
...
# show id, relevance score and title of two terms connected by AND
my $query = $client->db ('enzyme')->find (and => ['snake', 'human'],
'format' => MRS::EntryFormat->HEADER);
while (my $record = $query->next) {
print $record . "\n";
}
enzyme 3.4.21.95 17.6527424 Snake venom factor V activator.
# ...show only title, but now the same two terms are connected by OR
my $query = $client->db ('enzyme')->find (or => ['snake', 'human'],
'format' => MRS::EntryFormat->TITLE);
while (my $record = $query->next) {
print $record . "\n";
}
Snake venom factor V activator.
Jararhagin.
Bothropasin.
Trimerelysin I.
...
# combine term-based (ranked) query with additional boolean expression
my $query = $client->db ('uniprot')->find (and => ['snake', 'human'],
query => 'NOT (kinase OR reductase)',
'format' => MRS::EntryFormat->HEADER);
print "Count: " . $query->count . "\n";
while (my $record = $query->next) {
print $record . "\n";
}
Count: 75
nxs11_micsu 23.3861961 Short neurotoxin MS11;
nxl2_micsu 22.7922745 Long neurotoxin MS2;
nxl5_micsu 22.2648716 Long neurotoxin MS5;
...
# 2b. explore full information about a database
print $client->db ('enzyme');
# ...or extract only information parts you want
print $client->db ('enzyme')->version;
print $client->db ('enzyme')->count;
# 3. Or, almost all functionality is also available in a provided
# script I<mrsclient>:
[scripts/]mrsclient -h
[scripts/]mrsclient -C
[scripts/]mrsclient -c -n insulin
[scripts/]mrsclient -c -p -d enzyme -a 'endothelin tyrosine'
# 4. Run blastp on protein sequences:
my @run_args = (fasta_file => 'protein.fasta', db => 'uniprot');
my $job = $client->blast->run (@run_args);
print STDERR 'JOB ID: ' . $job->id . ' [' . $job->status . "]\n";
print $job;
while (not $job->completed) {
print STDERR 'Waiting for 10 seconds... [status: ' . $job->status . "]\n";
sleep 10;
}
print $job->error if $job->failed;
print $job->results;
# Or, use for it the provide script I<mrsblast>:
[scripts/]mrsblast -h
[scripts/]mrsblst -i /tmp/snake.protein.fasta -d uniprot -x result.xml
# 5. Run clustalw multiple alignment:
my $result = $client->clustal->run (fasta_file => 'multiple.fasta' );
print "ERROR: " . $result->failed if $result->failed;
print $result->diagnostics;
print $result;
# Or, use for it the provide script I<mrsclustal>:
[scripts/]mrsclustal -h
[scripts/]mrsclustal -i multiple.fasta
DESCRIPTION
This module is a SOAP-based (Web Services) client that can talk, and get
data from an MRS server, a search engine for biological and medical
databanks that searches well over a terabyte of indexed text. See
details about MRS and its author Maarten Hekkelman in "ACKNOWLEDGMENTS".
Because this module is only a client, you need an MRS server running.
You can install your own (see details in the MRS distribution), or you
need to know a site that runs it. By default, this module contacts the
MRS server at CMBI (http://mrs.cmbi.ru.nl/).
The usual scenario is the following:
* Create a new instance of a client by calling:
my $client = MRS::Client->new (%args);
* Optionally, find out what databanks are available by calling:
my @ids = map { $_->id } $client->db;
print "Names:\n" . join ("\n", @ids) . "\n";
* Make one or more queries on a selected databanks and iterate over
the result:
my $query = $client->db ('enzyme')->find (['cone', 'snail']);
while (my $record = $query->next) {
print $record . "\n";
}
Or, make the same query on all available databanks:
my $query = $client->find (['cone', 'snail']);
while (my $record = $query->next) {
print $record . "\n";
}
The format of returned records is specified by a parameter of the
*find* method (see more in "METHODS").
* Additionally, this module provides access to *blastp* program, using
MRS indexed databases. And it can invoke multiple alignment program
*clustalw*.
METHODS
MRS::Client
The main module is "MRS::Client". It lets the user specify which MRS
server to use, and few other global options. It also has a factory
method for creating individual databanks objects. Additionally, it
allows making query over all databanks. Finally, it covers all the SOAP
communication with the server.
new
use MRS::Client;
my $client = MRS::Client->new (@parameters);
The parameters are name-value pairs. The following names are recognized:
search_url, blast_url, clustal_url
The URLs of the individual MRS servers, one providing searches (the
main one), one running blast and one running clustal. Default values
lead your searches to CMBI. If you have installed MRS servers on
your own site, and you are using the default values coming with the
MRS distribution, you create a client by (but see below parameter
*host* for a shortcut):
my $client = MRS::Client->new ( search_url => 'http://localhost:18081/',
blast_url => 'http://localhost:18082/',
clustal_url => 'http://localhost:18083/',
);
Technical detail: These URLs will be used in the location field of
the WSDL description.
Alternatively, you can specify these parameters by environment
variables (because they will be probably same for most users from
the same site). The parameters, however, still have precedence over
the values of environment variables (even if they exist). The
variables are: *MRS_SEARCH_URL*, *MRS_BLAST_URL* and
*MRS_CLUSTAL_URL*.
NOTE: Some sites may not have all MRS servers running.
host
A shortcut for specifying a host name in all URLs. The same as in
the above example can be accomplished by:
my $client = MRS::Client->new (host => 'localhost');
Again, you can specify this parameter by an environment variables
MRS_HOST.
search_service, blast_service, clustal_service
The MRS servers are SOAP-based Web Services. Every Web Service has
its own *service name* (the name used in the WSDL). You can change
this service name if you are accessing site where they use
non-default names. The default names - I guess almost always used -
are: mrsws_search, mrsws_blast, mrsws_clustal.
search_wsdl, blast_wsdl, clustal_wsdl
You can also specify your own WSDL file, each one for each set of
operations. It is meant more for debugging purposes because this
"MRS::Client" module understands only current operations and adding
new ones to a new WSDL does not magically start using them. These
parameters may be useful when extending the "MRS::Client".
setters/getters
The same names as the argument names described above can be used as
method names to get or set the parameter value. A method without an
argument gets the current value, a method with an argument sets the new
value. For example:
print $client->search_url;
$client->search_url ('http://my.own.server/mrs/search');
db
This is a factory method creating one or more databanks instances. It
accepts a single argument, a databank ID:
print $client->db ('enzyme');
Id: enzyme
Version: Tue Jun 13 21:29:00 2006
Count: 4645
URL: http://ca.expasy.org/enzyme/
Parser: enzyme
Files:
Version: Tue Jun 13 21:29:00 2006
Modified: 2010-01-31 22:39:37
Entries count: 4645
Raw data size: 3235666
File size: 10857715
Unique Id: fe2a908e-5ecd-4f72-9d27-e1ef7bccc3af
Indices:
__ALL_TEXT__ 164412 FullText __ALL_TEXT__
an 4534 FullText Alternate Name
ca 4594 FullText Catalytic Activity
cc 8184 FullText Comments
cf 66 FullText CoFactor
de 3341 FullText Description
di 574 FullText Disease
dr 145912 FullText Database Reference
id 4645 Unique Identification
pr 418 FullText Prosite Reference
You can find out what databanks IDs are available by:
print join ("\n", map { $_->id } $client->db);
Which brings us to the usage of the *db* method without any parameter,
or with an empty parameter. In such cases, it creates an array of
"MRS::Client::Databank" instances.
find
Make the same query to all databanks. The parameters are the same as for
the *find* method called for an individual databank (see below).
print "Databank\tID\tScore\tTitle\n";
my $query = $client->find (and => ['cone', 'snail'],
'format' => MRS::EntryFormat->HEADER);
while (my
$record = $query->next) {
print $record . "\n";
}
print $query->count . "\n";
Databank ID Score Title
interpro ipr020242 29.7122746 Conotoxin I2-superfamily
interpro ipr012322 27.8191032 Conotoxin, delta-type, conserved site
...
omim 114020 3.40963793 cadherin 2
omim 192090 3.40769672 cadherin 1
sprot cxd6d_concn 19.4017849 Delta-conotoxin CnVID;
sprot cxd6c_concn 19.3984871 Delta-conotoxin CnVIC;
...
taxonomy 6495 53.980381 Conus tulipa fish-hunting cone snail
trembl q71ks8_contu 22.1446457 Four-loop conotoxin preproprotein;
trembl q9u7q6_contu 20.6787205 Calmodulin;
...
149
The query (method *next*) returns entries sequentially, one databank
after another. As with individual databanks, even here you can select
maximum number of entries to deliver - the number is applied for each
databank separately:
my $query = $client->find (and => ['cone', 'snail'],
max_entries => 2,
'format' => MRS::EntryFormat->HEADER);
while (my
$record = $query->next) {
print $record . "\n";
}
interpro ipr020242 29.7122746 Conotoxin I2-superfamily
interpro ipr012322 27.8191032 Conotoxin, delta-type, conserved site
omim 114020 3.40963793 cadherin 2
omim 192090 3.40769672 cadherin 1
sprot cxd6d_concn 19.4017849 Delta-conotoxin CnVID;
sprot cxd6c_concn 19.3984871 Delta-conotoxin CnVIC;
taxonomy 6495 53.980381 Conus tulipa fish-hunting cone snail
trembl q71ks8_contu 22.1446457 Four-loop conotoxin preproprotein;
trembl q9u7q6_contu 20.6787205 Calmodulin;
blast
$client->blast
A factory method for creating a singleton instance of
MRS::Client::Blast.
clustal
$client->clustal
A factory method for creating instances of MRS::Client::Clustal.
MRS::Client::Databank
This package represents an MRS databank and allows to query it. Each
databank consists of one or more files (represented by
"MRS::Client::Databank::File") and of indices
("MRS::Client::Databank::Index").
A databank instance can be created by a *new* method but usually it is
created by a factory method available in the "MRS::Client":
my $db = $client->db ('enzyme');
The factory method, as well as the *new* method, creates only a "shell"
databank instance - that is good enough for making queries but which
does not contain any databank properties (name, indices, etc.). The
properties will be fetched from the MRS server only when you ask for
them (using the "getters" method described below).
new
The only, and mandatory, parameter is *id*:
$db = MRS::Client::Databank->new (id => 'interpro');
The arguments syntax (the hash) is prepared for more arguments later
(perhaps). But it should not bother you because you would rarely use
this method - having the factory method *db* in the client.
find
This is the crucial method of the whole "MRS::Client" module. It queries
a databank and returns an "MRS::Client::Find" instance that can be used
to iterate over found entries.
It takes many arguments. At least one of the "query" arguments (which
are *query*, *and* and *or*) must be supplied; other arguments are
optional.
The arguments can always be specified as a hash, but for usual cases
there are few shortcuts. Let's look at the arguments as used in the
hash:
"and"
The value is an array reference where elements are terms that will
be combined by the AND boolean operator in a ranked query. For
example:
$find = $db->find (and => ['human', 'snake']);
This argument can also be used directly, not as a hash, assuming
that you do not need to use any other arguments:
$find = $db->find (['human', 'snake']);
"or"
The value is an array reference where elements are terms that will
be combined by the OR boolean operator in a ranked query. For
example:
$find = $db->find (or => ['human', 'snake']);
There can be either an *and* or an *or* argument, but not both. If
there are used both, a warning is issued and the *and* one will take
precedence.
"query"
The value is an expression, usually using some boolean operators (in
upper cases!):
$find = $db->find (query => 'hemoglobinase AND NOT human');
If there are no boolean operators, it is used as a single term. For
example, these are equivalent:
$find = $db->find (query => 'hemoglobinase activity');
$find = $db->find (and => ['hemoglobinase activity']);
You can also use both, *and* or *or*, and *query*. The query then is
an additional filter applied to the results found by the *and* or
*or* terms. For example:
$find = $db->find (and => ['human', 'snake'],
query => 'NOT neurotoxin');
As a shortcut, the query parameter can also be used without a hash,
assuming again that you do not need to use any other arguments:
$find = $db->find ('hemoglobinase AND NOT human');
"algorithm"
The ranked queries (the ones achieved by *and* or *or* arguments)
have assigned relevance score to their hits. The relevance score
depends on the used algorithm. The available values for this
arguments are defined in "MRS::Algorithm":
package MRS::Algorithm;
use constant {
VECTOR => 'Vector',
DICE => 'Dice',
JACCARD => 'Jaccard',
};
The default algorithm is "Vector". For example (using the format
"header" - which is the only one that shows relevance scores):
$client->$db('enzyme')->find (and => 'venom',
algorithm => MRS::Algorithm->Dice,
max_entries => 3,
'format' => MRS::EntryFormat->HEADER);
enzyme 3.4.24.43 14.9607477 Atroxase.
enzyme 3.4.24.49 13.6817474 Bothropasin.
enzyme 3.4.24.73 13.2007284 Jararhagin.
$client->$db('enzyme')->find (and => 'venom',
algorithm => MRS::Algorithm->Vector,
max_entries => 3,
'format' => MRS::EntryFormat->HEADER);
enzyme 3.1.15.1 21.6520195 Venom exonuclease.
enzyme 3.4.21.60 19.3931656 Scutelarin.
enzyme 5.1.1.16 16.7410889 Protein-serine epimerase.
"start", "offset", "max_entries"
These arguments do not affect the query itself but it tells which
entries from the found ones to retrieve (by the *next* method - see
below).
All these three arguments have an integer value.
"start" tells to skip entries at the beginning of the whole result
and start returning only with the entry with this order number. The
counting start from 1.
"offset" is the same as the "start", except the counting starts from
zero.
"max_entries" is the maximum entries to retrieve.
"format"
This argument also does not affect the query itself but it defines
the format of the returned entries. The available values for this
arguments are defined in "MRS::EntryFormat":
package MRS::EntryFormat;
use constant {
PLAIN => 'plain',
TITLE => 'title',
HTML => 'html',
FASTA => 'fasta',
SEQUENCE => 'sequence',
HEADER => 'header',
};
The default format is 'plain'. The 'fasta' and 'sequence' formats
are available only for databanks that have sequence data. For all
formats, except for the 'header', the entries are returned as
strings. For 'header', the entries are instances of
"MRS::Client::Hit".
Be aware that "format" is also a built-in Perl function, so better
quote it when used as a hash key (it seems to work also without
quotes except the emacs TAB key is confused if there are no
surrounding quotes; just a minor annoyance).
"xformat"
This argument ("eXtended format") enhances the "format" argument. It
is used (at least at the moment) only for HTML format; for other
formats, it is ignored.
Be aware, however, that the "xformat" depends on the structure of
the HTML provided by the MRS. This structure is not defined in the
MRS server API, so it can change easily. It even depends on the way
how the authors write their parsing scripts. When the HTML output
changes this module must be changed, as well. Caveat emptor.
The "xformat" is a hashref with keys that change (slightly or
significantly) the returned HTML. Here are all possible keys (with a
randomly picked up values):
xformat => { MRS::XFormat::CSS_CLASS() => 'mrslink',
MRS::XFormat::URL_PREFIX() => 'http://cbrcgit:8080/mrs-web/'
MRS::XFormat::REMOVE_DEAD() => 1, # or => ['...']
MRS::XFormat::ONLY_LINKS() => 1 }
"MRS::XFormat::CSS_CLASS" specifies a CSS-class name that will be
added to all "a" tags in the returned HTML. It allows, for example,
an easy post-processing by various JavaScript libraries. For
example, if the original HTML contains:
<a href="entry.do?db=go&id=0005576"></a>
it will become (using the value shown above):
<a class="mrslinks" href="entry.do?db=go&id=0005576"></a>
"MRS::XFormat::URL_PREFIX" helps to keep the returned HTML
independent on the machine where it was created. This option
pre-pends the given prefix to the relative URLs in the hyperlinks
that point to the data in an MRS web application. For example, if
the original HTML contains:
<a href="entry.do?db=go&id=0005576"></a>
it will become:
<a href="http://cbrcgit:8080/mrs-web/entry.do?db=go&id=0005576"></a>
Other hyperlinks - those not starting with "query" or "entry" - are
not affected.
"XFormat::REMOVE_DEAD" deals with the fact that the MRS server
creates hyperlinks pointing to other MRS databanks without checking
that they actually exists in the local MRS installation. This may be
fixed later (quoting Maarten) but before it happens this option (if
with a true value) removes (from the returned HTML) all hyperlinks
that point to the not-installed MRS databanks. For example, if the
original HTML has these hyperlinks:
<a href="query.do?db=embl&query=ac:AF536179">AF536179</a>
<a href="query.do?db=embl&query=ac:D00735">D00735</a>
<a href="entry.do?db=pdb&id=1VZN">1VZN</a>
<a href="entry.do?db=pdb&id=2FK4">2FK4</a>
and the "pdb" database is not locally installed, the returned HTML
will change to:
<a href="query.do?db=embl&query=ac:AF536179">AF536179</a>
<a href="query.do?db=embl&query=ac:D00735">D00735</a>
1VZN
2FK4
There is a small caveat, however. The MRS::Client needs to know what
databanks are installed. It finds out by asking the MRS server by
using the method "db()" (explained elsewhere in this document). This
method returns much more than is needed, so it can be slightly
expensive. Therefore, if your concern is the highest speed, you can
help the MRS::Client by providing a list of databanks that you know
you have installed. Actually, in most cases, you can create such
list also by calling the "db()" method but depending on your code
you can call it just ones an reuse it. For example, if you wish to
keep hyperlinks only for 'uniprot' and 'embl', you specify;
xformat => { MRS::XFormat::REMOVE_DEAD() => ['uniprot', 'embl'] }
Finally, there is an option "MRS::XFormat::ONLY_LINKS". It has a
very specific function: to extract and return "only" the hyperlinks,
not the whole HTML. It is, therefore, predestined for further
post-processing. Note that all changes in the hyperlinks described
earlier are also applied here (e.g. adding an absolute URL or a CSS
class).
When this option is used, the whole method "$find->next" (or
"db->entry") returns a reference to an array of extracted
hyperlinks:
my $find = $client->db('sprot')->find
(and => ['DNP_DENAN'],
'format' => MRS::EntryFormat->HTML,
xformat => {
MRS::XFormat::ONLY_LINKS() => 1,
MRS::XFormat::CSS_CLASS() => 'mrslink',
},
);
while (my $record = $find->next) {
print join ("\n", @$record) . "\n";
Which prints something like:
<a class="mrslink" href="entry.do?db=taxonomy&id=8618">8618</a>
<a class="mrslink" href="query.do?db=taxonomy&query=Eukaryota">Eukaryota</a>
...
<a class="mrslink" href="query.do?db=uniprot&query=kw:Disulfide kw:bond ">Disulfide bond</a>
...
<a class="mrslink" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=...">92332489</a>
...
<a class="mrslink" href="entry.do?db=go&id=0009405"></a>
count
It returns a number of entries in the whole databank.
print $client->db ('enzyme')->count;
4645
Do not confuse it with the method of the same name but called on the
object returned by the *find* method - that one returns a number of hits
of that particular query.
entry
It takes an entry ID (mandatory), and optionally its format and extended
format, and it returns the given entry:
print $client->db ('enzyme')->entry ('3.4.21.60');
ID 3.4.21.60
DE Scutelarin.
AN Taipan activator.
CA Selective cleavage of Arg-|-Thr and Arg-|-Ile in prothrombin to form
CA thrombin and two inactive fragments.
CC -!- From the venom of Taipan snake (Oxyuranus scutellatus).
CC -!- Converts prothrombin to thrombin in the absence of coagulation factor
CC Va, and is potentiated by phospholipid and calcium.
CC -!- Specificity is similar to that of factor Xa.
CC -!- Binds calcium via gamma-carboxyglutamic acid residues.
CC -!- Similar enzymes are known from the venom of other Australian elapid
CC snakes Pseudonaja textilis, Oxyuranus microlepidotus and Demansia
CC nuchalis affinis.
CC -!- Formerly EC 3.4.99.28.
//
print $client->db ('enzyme')->entry ('3.4.21.60',
MRS::EntryFormat->TITLE);
Scutelarin.
The optional "extended format" is a hashref and it was explained earlier
in the section about the "find()" method.
id, name, version, blastable, url, script, files, indices
There are several methods delivering databank properties. They have no
arguments:
my $db = $client->db('omim');
print $db->id . "\n";
print $db->name . "\n";
print $db->version . "\n";
print $db->blastable . "\n";
print $db->url . "\n";
print $db->script . "\n";
files
Each databank consists of one or more files. This method returns a
reference to an array of "MRS::Client::Databank::File" instances. Each
such instance has properties reachable by the following "getters"
methods:
sub say { print @_, "\n"; }
my $db_files = $client->db('uniprot')->files;
foreach my $file (@{ $db_files }) {
say $file->id;
say $file->version;
say $file->last_modified;
say $file->entries_count;
say $file->raw_data_size;
say $file->file_size;
say '';
}
indices
Each databank is indexed by (usually several) indices. This method
returns a reference to an array of "MRS::Client::Databank::Index"
instances. Each such instance has properties reachable by the "getters"
method:
my $db_indices = $client->db('uniprot')->indices;
foreach my $idx (@{ $db_indices }) {
printf ("%-15s%9d %-9s %s\n",
$idx->id,
$idx->count,
$idx->type,
$idx->description);
}
The index *id* is important because it can be used in the queries. For
example, assuming that the database has an index *os* (organism
species):
$db->find (query => 'rds AND os:human');
MRS::Client::Find
This object carries results of a query; it is returned by the *find*
method, called either on a databank instance or on the whole client.
Actually, in case of the whole client, the returned type is of type
"MRS::Client::MultiFind" which is a subclass "MRS::Client::Find".
db, terms, query, all_terms_required, max_entries
The getter methods just reflect query arguments (the ones given to the
"find" method):
sub say { print @_, "\n"; }
my $find = $client->db('uniprot')->find('sapiens');
say $find->db;
say join (", ", @ {$find->terms });
say $find->query;
say $find->max_entries;
say $find->all_terms_required;
The *terms* (a ref array) are either from the *and* or *or* argument,
and the *all_terms_required* is 1 (when terms are coming from the *and*)
or zero.
count
Finally, you can get the number of hits of this query. Be aware (as
mentioned elsewhere in this document) that boolean queries return only
an estimate, usually much higher than is the reality.
MRS::Client::MultiFind
This object is returned from the "find" method made to all databanks. It
is a subclass of the "MRS::Client::Find" with one additional method:
db_counts
It returns databank names and their total counts in a hash (not a
reference) where keys are the databank names and values the entry
counts:
my %counts = $find->db_counts;
foreach my $db (sort keys %counts) {
printf ("%-15s %9d\n", $db, $counts{$db});
}
MRS::Client::Hit
Finally, a tiny object representing a hit, a result of a query before
going to a databank for the full contents of a found entry. It contains
the databank's ID (where the hit was found), the score that this hit
achieved (for boolean queries, the score is always 1) and the ID and
title of the entry represented by this hit.
The corresponding getters methods are *db*, *score*, *id* and *title*.
The *next* method (as shown above) returns just hits (instead of the
full entries) when the format *MRS::EntryFormat-*HEADER> is specified.
MRS::Client::Blast
The MRS servers provide sequence homology searches, the famous Blast
program (namely the *blastp* program for protein sequences). An input
sequence (in FASTA format) is searched against one of the MRS databanks.
It can be any MRS databank whose method "blastable" returns true (e.g.
uniprot). An input sequence and a databank are the only mandatory input
parameters. Other common Blast parameters are also supported.
The invocation is asynchronous. It means that the *run* method returns
immediately, without waiting for the Blast program to finish, giving
back a *job id*, a handler that can be used later for polling for
status, and, once status indicates the Blast finishes, for getting
results (or an error message). This is the typical usage:
my @run_args = (fasta_file => '...', db => '...', ...);
my $job = $client->blast->run (@run_args);
sleep 10 while (not $job->completed);
print $job->error if $job->failed;
print $job->results;
529.0 1.346582e-149 [vsph_trije ] 1 Snake venom serine protease homolog;
509.0 1.411994e-143 [vspa_triga ] 1 Venom serine proteinase 2A;
508.0 2.823987e-143 [vsp1m_trist ] 1 Venom serine protease 1 homolog;
506.0 1.129595e-142 [vsp07_trist ] 1 Venom serine protease KN7 homolog;
488.0 2.961165e-137 [vsp2_trifl ] 1 Venom serine proteinase 2;
487.0 5.922331e-137 [vsp1_trije ] 1 Venom serine proteinase-like protein;
456.0 1.271811e-127 [vsp04_trist ] 1 Venom serine protease KN4 homolog;
...
You can also use provided script "mrsblast" that polls for you (if you
wish so).
In order to create an "MRS::Client::Blast" instance, use the factory
method:
my $blast = $client->blast;
run
The main method that starts Blast with the given parameters and
immediately returns an object "MRS::Client::Blast::Job" that can be used
for all other important methods. If you plan to stop your Perl program
and start it again later, you need to remember the job ID:
my $job = $blast->run (...);
print $job->id;
The job ID can be later used to re-create the same (well, similar) Job
object (see method *job* below) that again provides all important
methods (such as getting results).
The method *run* has following arguments (the Job object has the same
"getter" methods), all given as a hash:
db An MRS databank to search against. Mandatory parameter.
fasta
A protein sequence in a FASTA format. Mandatory parameter unless
"fasta_file" is given.
fasta_file
A name of a file containing a protein sequence in a FASTA format.
Mandatory parameter unless "fasta" is given.
filter
Low complexity filter. Boolean parameter. Default is 1.
expect
E-value cutoff. A float value. Default is 10.0.
word_size
An integer. Default is 3.
matrix
Scoring matrix. Default BLOSUM62.
open_cost
Gap opening penalty. An integer. Default is 11.
extend_cost
Gap extension penalty. Default is 1.
query
An MRS boolean query to limit the search space.
gapped
A boolean parameter. Its true value performs gapped alignment.
Default is true.
max_hits
Limit reported hits. An integer. Default is 250.
job
The method finds or re-creates a Job object of the given ID:
my $job = $client->blast->job ('0f37a544-a7a2-4239-b950-65a6aa07d1ef');
print $job->id;
print $job->status;
It dies with an error if such Job is not known to the MRS server.
The returned Job object can be used to ask for the Job status, or for
getting the Job results. There is one caveat, however. The re-created
Job object is not that "rich" as was its original version: it does not
know, for example, what parameters were used to start this blast job.
Unfortunately, the MRS server keeps only the Job ID and nothing else.
Fortunately, the parameters are needed only for the results in the XML
format (see more about available formats below, in the method
*$job->results*) - and you can add them (if you still have them), as a
hash, to the "job" method when re-creating a new Job instance:
my $job - $client->blast->job ('0f37a544-a7a2-4239-b950-65a6aa07d1ef',
fasta => '...',
db => 'iniprot', ...);
MRS::Client::Blast::Job
The Job object represents a single Blast invocation with a set of input
parameters and, later, with results. It is also used to poll for the
status of the running job. Instances of this objects are created by the
*run* or *job* methods of the "blast" object. The Job's methods are:
id Job ID, an important handler if you have to re-create an
"MRS::Client::Blast::Job" object.
"getter" methods
All these methods are equivalent to (and named the same as) the
parameters given to the "run" method (described above):
db
fasta
fasta_file
filter
expect
word_size
matrix
open_cost
extend_cost
query
max_hits
gapped
status, completed, failed
The *status* returns one of the "MRS::JobStatus":
use constant {
UNKNOWN => 'unknown',
QUEUED => 'queued',
RUNNING => 'running',
ERROR => 'error',
FINISHED => 'finished',
};
The *completed* returns true if the status is either "ERROR" or
"FINISHED". The *failed* returns true if the status is "ERROR".
Typical usage for polling a running job is:
sleep 10 while (not $job->completed);
error
It returns an error message, or undef if the status is not "ERROR".
Typical usage is:
print $job->error if $job->failed;
results
Finally, the more interesting method. It returns an object of type
"MRS::Client::Blast::Result" that can be either used on its own (see
its "getter" method below), or converted to strings of one of the
format predefined in "MRS::BlastOutputFormat":
use constant {
XML => 'xml',
HITS => 'hits',
FULL => 'full',
STATS => 'stats',
};
The format is the only parameter of this method. Default format is
"HITS". The conversion to the given format is done by overloading
the double quotes operator, calling internally the method
"as_string". You just print the object:
print $job->results;
447.0 6.511672e-125 [vspgl_glosh ] 1 Thrombin-like enzyme gloshedobin;
429.0 1.706996e-119 [vsp2_viple ] 1 Venom serine proteinase-like protein 2;
421.0 4.369909e-117 [vsp12_trist ] 1 Venom serine protease KN12;
419.0 1.747964e-116 [vsps1_trist ] 1 Thrombin-like enzyme stejnefibrase-1;
...
Where lines are individual hits and columns are: *bit_score*,
*expect*, sequence ID, number of HSPs for this hit, sequence
description.
Or, giving just the Blast run statistics:
print $job->results (MRS::BlastOutputFormat->STATS);
DB count: 514212
DB length: 180900945
Search space: 23664675636
Kappa: 0.041
Lambda: 0.267
Entropy: 0.140
Or, showing everything (in a rather un-parsable form, useful more
for testing than anything else):
print $job->results (MRS::BlastOutputFormat->FULL);
Or, in an XML format:
print $job->results (MRS::BlastOutputFormat->XML);
MRS::Client::Blast::Result
You can explore the returned Blast results by the following "getter"
methods - going from the whole result to the individual hits and inside
hits to the individual HSPs (High-scoring pairs):
db_count
db_length
db_space
Effective search space.
kappa
lambda
entropy
hits
It returns a reference to an array of "MRS::Client::Blast::Hit"s
where each hit has methods:
id
title
sequences
It is a reference to an array of sequence IDs.
hsps
It is a reference to an array of "MRS::Client::Blast::HSP"s
where each HSP has methods:
score
bit_score
expect
query_start
subject_start
identity
positive
gaps
subject_length
query_align
subject_align
midline
Try to explore various result formats by using the provided script
"mrsblast". This waits for a job to be completed and then prints its
hits:
mrsblast -d sprot -i 'your.fasta'
This shows Blast statistics:
mrsblast -d sprot -i 'your.fasta' -N
This produces an XML output to a given file:
mrsblast -d sprot -i 'your.fasta' -x results.xml
Finally, this gives a long listing with all details:
mrsblast -d sprot -i 'your.fasta' -f
MRS::Client::Clustal
The module wrapping the multiple alignment program *clustalw*. The
program is optional and, therefore, not all MRS servers may have it. Use
the factory method for creating instances of MRS::Client::Clustal:
$client->clustal
run
The main method, invoking *clustalw* with mandatory input sequences and
optionally a couple of other parameters:
my $result = $client->clustal->run (fasta_file => 'my.proteins.fasta');
fasta_file
A file with multiple sequences in FASTA format.
open_cost
A gap opening penalty (an integer).
extend_cost
A gap extension penalty (a float).
It returns result in an instance of MRS::Client::Clustal::Result.
open_cost
It returns what gap opening penalty has been set in the *run* method.
extend_cost
It returns what gap extension penalty has been set in the *run* method.
MRS::Client::Clustal::Result
It is created by running:
$client->clustal->run (...);
alignment
It returns a reference to an array of MRS::Client::Clustal::Sequence
instances. Each of them has methods *id* and *sequence*. You can also
just print the formatted alignment (it uses its own *as_string* method
that overloads double quotes operator):
print $client->clustal->run (fasta_file => 'several.proteins.fasta');
vsph_trije : -VMGWGTISATKETHPDVPYCANINILDYSVCRAAYARLPATSRTLCAGILE-----GGKDSCLTD----SGGPLICNGQFQGIVSWGGHPCGQP-RKPGLYTKVFDHLDWIKSIIAGNKDATCPP
nxsa_latse : ----MKTLLLTLVVVTIV--CLDLGYTR--ICFNHQSSQPQTTKT-CS---------PGESSCYNK----QWS------DFRGTIIERG--CGCPTVKPGI------KLSCCESEVCNN-------
pa21b_pseau: NLIQFGNMIQCANKGSRP--SLDYADYG-CYCGWGGSGTPVDELDRCCQVHDNCYEQAGKKGCFPKLTLYSWKCTGNVPTCNSKPGCKSFVCACDAAAAKC----FAKAPYKKENYNIDTKKRCK-
diagnostics
It shows the standard output of the underlying clustalw program:
my $result = $client->clustal->run (fasta_file => 'several.proteins.fasta');
print $result->diagnostics;
CLUSTAL 2.0.10 Multiple Sequence Alignments
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: vsph_trije 115 aa
Sequence 2: nxsa_latse 83 aa
Sequence 3: pa21b_pseau 118 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 13
Sequences (1:3) Aligned. Score: 5
Sequences (2:3) Aligned. Score: 8
Guide tree file created: ...
There are 2 groups
Start of Multiple Alignment
Aligning...
Group 1: Delayed
Group 2: Delayed
Alignment Score -93
GDE-Alignment file created ...
failed
It returns standard error output of the underlying clustalw program. It
the program finished without problems, it returns undef.
MISSING FEATURES, CAVEATS, BUGS
* The MRS distinguishes between so-called *ranked queries* and
*boolean queries*, and it recognizes also *boolean filters*. I
probably need to learn more about their differences. That's why you
may see some differences in query results shown by this module and
the mrsweb web application (an application distributed together with
the implementation of the MRS servers).
The contents of the search field in the *mrsweb* is first parsed in
order to find out if it is a boolean expression, or not. Depending
on the result it uses either a ranked or boolean query. It also
splits the terms and combine them (by default) with the logical AND.
For example, in *mrsweb* if you type (using the uniprot):
cone snail
you get 134 entries. You get the same number of hits by the
"MRS::Client" module when using an *and* argument:
print $client->db('uniprot')->find (and => ['cone','snail'])->count;
134
But you cannot just pass the whole expression as a query string (as
you do in *mrsweb*):
print $client->db('uniprot')->find ('cone snail')->count;
0
You get zero entries because the "MRS::Client" considers the above
as one term. And if you add a boolean operator:
print $client->db('uniprot')->find ('cone AND snail')->count;
4609
then the boolean query was used and, as explained by the MRS, the
"query did not return an exact result, displaying the closest
matches". But, fortunately, when you iterate over this result, you
will get, correctly, just the 134 entries.
* The MRS servers provide few more operations that are not-yet covered
by this module. It would be useful to discuss which of those are
worth to implement. They are:
GetMetaData
FindSimilar
GetLinked
Cooccurrence
SpellCheck
SuggestSearchTerms
CompareDocuments
ClusterDocuments
There is also a potentially useful attribute *links* in the
databank's info which has not been yet explored by this module.
ADDITIONAL FILES
Almost all functionality of the "MRS::Client" module is also available
from a command-line controlled scripts mrsclient, mrsblast and
mrsclustal. Try , for example:
mrsclient -h
mrsclient -C
mrsclient -c -n insulin
mrsclient -c -p -d enzyme -a 'endothelin tyrosine'
mrsblast -h
mrsclustal -h
DEPENDENCIES
The "MRS::Client" module uses the following modules:
XML::Compile::SOAP11
XML::Compile::WSDL11
XML::Compile::Transport::SOAPHTTP
File::Basename
File::Path
Math::BigInt
FindBin
Getopt::Std
AUTHORS
Martin Senger <martin.senger@gmail.com>
BUGS
Please report any bugs or feature requests to "bug-mrs-client at
rt.cpan.org", or through the web interface at
<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=MRS-Client>. I will be
notified, and then you'll automatically be notified of progress on your
bug as I make changes.
SUPPORT
You can find documentation for this module with the perldoc command.
perldoc MRS::Client
You can also look for information at:
* RT: CPAN's request tracker
<http://rt.cpan.org/NoAuth/Bugs.html?Dist=MRS-Client>
* AnnoCPAN: Annotated CPAN documentation
<http://annocpan.org/dist/MRS-Client>
* CPAN Ratings
<http://cpanratings.perl.org/d/MRS-Client>
* Search CPAN
<http://search.cpan.org/dist/MRS-Client>
ACKNOWLEDGMENTS
This client module would be useless without having an MRS server (e.g.
at http://mrs.cmbi.ru.nl/mrs-web/). The MRS stands for Maarten's
Retrieval System and was developed (and is maintained) by *Maarten
Hekkelman* at the CMBI (http://www.cmbi.ru.nl/), with the help and
contributions from many others.
The MRS itself has also its own Perl module MRS.pm, called plugin and
distributed together with the MRS, that accesses MRS server(s) directly,
without using the SOAP Web Services protocol. The plugin was helpful to
find out what the server might expect.
Additionally, the MRS distribution has few testing scripts that use SOAP
protocol to access data in the same way as this "MRS::Client" module
does. Therefore, this module can be seen as an extension of these
testing scripts into a slightly more comprehensive and perhaps more
documented package.
The MRS server provides Blast results that are not in XML. In order to
make an XML output, this module uses, hopefully, the same format and
conversion as found in the MRS web application *mrsweb*.
AUTHOR
Martin Senger <martin.senger@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2012 by Martin Senger, CBRC - KAUST
(Computational Biology Research Center - King Abdullah University of
Science and Technology) All Rights Reserved..
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.