Welcome

Setup guide

• Setup Guide

Visually explore the data

Web Artemis is a very cool genome browser. It talks to Crawl services, so can be used to explore the data they hold.

REST Services

Metadata about each service can be accessed at :

• Organisms
• Regions
• Features
• SAM/BAM files
• VCF/BCF files

Organisms

• Listing all organisms
• Getting Pfalciparum

Regions

• Getting regions in an oranism.
• Getting the sequence of a region
• Getting features on a sequence.

Features

• Getting the gene hiearchy of a feature
• Getting synonyms
• Getting properties
• Getting pubs
• Getting dbxrefs
• Getting cv terms
• Getting orthologues

Sequence Alignment/Map files (SAM/BAM)

• Listing alignment files that match a sequence
• Querying an alignment
• Getting the coverage for an alignment

Variation files (VCF/BCF)

• Listing all variant files
• Listing all variant files that match an organism
• Listing all variant files that match a region in an organism
• Listing all regions in a variant file
• Querying a variant file
• Querying a variant file, using an integer filter.
• Querying a variant file, using string filters.

SOAP Services

As an alternative to the RESTful approach, Crawl also publishes SOAP services too.

These services, and their WSDLS, are described here in more detail.

All the same Crawl RESTful resources are available as SOAP endpoints too. What follows is a simple python program illustrating how to use them.

# first you must "easy_install suds"

import suds
from suds.client import Client

wsdl = "http://localhost:8080/services/soap/%s?wsdl"

organisms = Client(wsdl % "organisms")
regions = Client(wsdl % "regions")
features = Client(wsdl % "features")

print organisms
print regions
print features


first_organism = organisms.service.listOrganisms()[0]
print first_organism

# get the Pfalciparum organism
pfalciparum = organisms.service.getByString('Pfalciparum')[0]
print pfalciparum

# get the first region in Pfalciparum
first_pfalciparum_region = regions.service.inorganism(pfalciparum._commonName)[0]
print first_pfalciparum_region

# extract the first gene from all the regions in Pfalciparum
for region in regions.service.inorganism(pfalciparum._commonName):
    genes = regions.service.locations(region._uniqueName, 1, 1000)
    if len(genes) > 0 :
        gene = genes[0]
        print gene
        print features.service.hierarchy(genes[0]._uniqueName )