Created on 18 Feb 2013
@author: jmht
Query the octopus server http://octopus.cbr.su.se to get transmembrane predictions
OctopusPredict
[source]¶Bases: object
Query the octopus server http://octopus.cbr.su.se to get transmembrane predictions
Methods
getFasta (fastafile) |
Given a fastafile, extract the first sequence |
getPredict (name, fasta[, directory]) |
Get the octopus prediction for the given fasta sequence string |
octopusFileUrls (fasta) |
Query the server for a prediction for the given fasta sequence. |
writeFiles (name, directory) |
Write the files on the server to disk |
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
ParseFileUrl
[source]¶Bases: HTMLParser.HTMLParser
Parse the page returned by an octopus search to get the links to the files
Attributes: |
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Methods
check_for_whole_start_tag (i) |
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close () |
Handle any buffered data. |
feed (data) |
Feed data to the parser. |
get_starttag_text () |
Return full source of start tag: ‘<…>’. |
getpos () |
Return current line number and offset. |
goahead (end) |
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handle_charref (name) |
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handle_comment (data) |
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handle_data (data) |
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handle_decl (decl) |
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handle_endtag (tag) |
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handle_entityref (name) |
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handle_pi (data) |
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handle_startendtag (tag, attrs) |
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handle_starttag (tag, attrs) |
Set recording whenever we encounter a tag so handle_data can process it |
parse_bogus_comment (i[, report]) |
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parse_comment (i[, report]) |
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parse_declaration (i) |
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parse_endtag (i) |
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parse_html_declaration (i) |
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parse_marked_section (i[, report]) |
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parse_pi (i) |
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parse_starttag (i) |
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reset () |
Reset this instance. |
updatepos (i, j) |
clear_cdata_mode | |
error | |
set_cdata_mode | |
unescape | |
unknown_decl |