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 |