ample.modelling.octopus_predict module
Created on 18 Feb 2013
@author: jmht
Query the octopus server http://octopus.cbr.su.se to get transmembrane predictions
-
class
OctopusPredict
[source]
Bases: object
Query the octopus server http://octopus.cbr.su.se to get transmembrane predictions
-
getFasta
(fastafile)[source]
Given a fastafile, extract the first sequence and return it as
separated string
-
getPredict
(name, fasta, directory=None)[source]
Get the octopus prediction for the given fasta sequence string
Args:
fasta – fasta sequence string
name – name for the files
directory – directory to write files to
Sets the topo and nnprf attributes
-
octopusFileUrls
(fasta)[source]
Query the server for a prediction for the given fasta sequence.
Args:
fasta – a single fasta sequence as a string
Sets the urls of the topo and nnprf files
-
writeFiles
(name, directory)[source]
Write the files on the server to disk
Args:
directory: where to write files
name: name for files (with suffix .topo and .nnprf)
-
class
ParseFileUrl
[source]
Bases: HTMLParser.HTMLParser
Parse the page returned by an octopus search to get the links to the files
-
handle_starttag
(tag, attrs)[source]
Set recording whenever we encounter a tag so handle_data can process it