API documentation

cpg_islands Package

cpg_islands – Finding CpG islands in genetic sequences.

metadata Module

cpg_islands.metadata — Project metadata

Information describing the project.

models Module

presenters Module

utils Module

cpg_islands.utils — Miscellaneous utilities

class cpg_islands.utils.Event

Bases: list

Event subscription.

A list of callable objects. Calling an instance of this will cause a call to each item in the list in ascending order by index.

Example Usage: >>> def f(x): ... print ‘f({0})’.format(x) >>> def g(x): ... print ‘g({0})’.format(x) >>> e = Event() >>> e() >>> e.append(f) >>> e(123) f(123) >>> e.remove(f) >>> e() >>> e += (f, g) >>> e(10) f(10) g(10) >>> del e[0] >>> e(2) g(2)

views Module

cpg_islands.views — View interfaces

class cpg_islands.views.BaseAppView

Bases: object

file_load_requested = Event([])

Called when the user requests to load a file. Callbacks should look like:

callback(file_path)

Parameters:file_path (str) – path the the file to load

show_results()

Show the results view.

show_seq_input()

Show the sequence input view.

start()

Start the view.

class cpg_islands.views.BaseEntrezView

Bases: object

load_requested = Event([])

query_changed = Event([])

result_selected = Event([])

search_requested = Event([])

set_query_translation(query_translation)

Set the query text which has been translated to Entrez search terms.

Parameters:query_translation (str) – the translated query

set_result(results)

Set the list of sequence ids.

Parameters:result (list) – list of sequence ids

set_selected_seq(seq_str)

Set the selected sequence.

Parameters:seq_str (str) – the sequence data

set_seq_desc(desc)

Set the selected sequence’s description.

Parameters:desc (str) – sequence’s description

set_seq_len(len_str)

Set the length of the sequence.

Parameters:len (str) – sequence length as a string

set_seq_locus(locus, ncbi_url)

Set the selected sequence’s locus and URL to access on NCBI. Basically, identify the sequence on NCBI.

Parameters:

• locus (str) – sequence’s locus
• ncbi_url (str) – URL to sequence on NCBI

set_suggestion(suggestion)

Set the suggestions based on spelling.

Parameters:result (str) – the encoded text

class cpg_islands.views.BaseResultsView

Bases: object

clear_subseq()

Clear subsequence field.

highlight_global_seq(start, end)

Highlight the subsequence within the global sequence.

Parameters:

• start (str) – start index of the currently selected island
• end (str) – end index of the currently selected island

island_selected = Event([])

set_algo_name(algo_name)

Set the name of the algorithm used.

Parameters:algo_name (str) – the algorithm name

set_end(end_str)

Set end index of the island

Parameters:end_str (str) – end index of island

set_exec_time(exec_time_str)

Set the execution time of the algorithm.

Parameters:exec_time_str – execution time as a string

set_gc_ratio(gc_ratio_str)

Set GC ratio of the island.

Parameters:gc_ratio_str – GC ratio of island

set_global_seq(seq_str)

Set the global sequence string.

Parameters:seq_str (str) – DNA sequence of feature

set_islands(islands)

Set the CpG island locations.

Parameters:islands (list of tuple) – CpG island locations

set_length(length_str)

Set length of the island.

Parameters:length (str) – length of island

set_obs_exp_cpg_ratio(obs_exp_cpg_ratio_str)

Set observed/expected CpG ratio of the island.

Parameters:obs_exp_cpg_ratio_str (str) – observed/expected ratio

set_start(start_str)

Set start index of the island.

Parameters:start_str (str) – start index of island

set_subseq(seq_str)

Set the subsequence.

Parameters:seq_str (str) – DNA sequence of island

class cpg_islands.views.BaseSeqInputView

Bases: object

set_algorithms(algorithm_names)

Set the list of algorithm names.

Parameters:algorithm_names (list of str) – list of algorithm names

set_island_size(island_size_str)

Set the size of the CpG island.

Parameters:island_size (str) – number of bases in the island as a string

set_min_gc_ratio(min_gc_ratio)

Set minimum GC ratio.

Parameters:min_gc_ratio (str) – the ratio of Guanine/Cytosine as a string

set_min_obs_exp_cpg_ratio(min_obs_exp_cpg_ratio)

Set the minimum observed/expected CpG ratio.

Parameters:min_gc_ratio (str) – the ratio of Guanine/Cytosine as a string

set_seq(seq_str)

Set the sequence text.

Parameters:seq_str (str) – the sequence in string form

show_error(message)

Show the user an error dialog.

Parameters:message (str) – error message

submitted = Event([])

Called when the form is submitted, i.e., submit is clicked by the user. Callbacks should look like:

callback(seq_str, island_size_str, min_gc_ratio_str)

Parameters:

• seq_str (str) – the sequence as a string
• island_size_str (str) – number of bases which an island may contain
• min_gc_ratio_str (str) – the ratio of GC to other bases

Subpackages

• qt Package
  • qt Package
  • composers Module
  • main Module
  • views Module