Module Expr Str Import alias Import alias Import alias Import alias Import alias Import alias Import alias Import alias Import alias Expr Str Import alias identifier ImportFrom alias Import alias identifier Import alias identifier ImportFrom alias Assign NameStore Call AttributeLoad NameLoad attr keyword Str If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr Str Str keyword Str keyword Str keyword Str keyword Str Expr Call AttributeLoad NameLoad attr keyword ListLoad Assign TupleStore NameStore NameStore Call AttributeLoad NameLoad attr NameLoad Assign NameStore Call AttributeLoad NameLoad attr Assign TupleStore NameStore NameStore NameStore TupleLoad Num Num Num For NameStore AttributeLoad NameLoad attr body If CompareEq SubscriptLoad NameLoad Index Num Str body Continue Assign NameStore SubscriptLoad Call AttributeLoad SubscriptLoad NameLoad Slice Num attr Str Index Num AugAssignAdd NameStore Num TryExcept body Assign NameStore Call AttributeLoad Call AttributeLoad NameLoad attr NameLoad attr handlers ExceptHandler type NameLoad body Expr Call AttributeLoad AttributeLoad NameLoad attr attr BinOpMod Str NameLoad AugAssignAdd NameStore Num Continue Assign NameStore Call AttributeLoad NameLoad attr Call AttributeLoad NameLoad attr NameLoad NameLoad TryExcept body Assign NameStore Call AttributeLoad NameLoad attr handlers ExceptHandler type NameLoad body Print BinOpMod Str NameLoad Continue Assign NameStore ListLoad NameLoad For NameStore AttributeLoad NameLoad attr body If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body For NameStore AttributeLoad NameLoad attr body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr orelse If CompareEq NameLoad Str body Expr Call AttributeLoad NameLoad attr AttributeLoad NameLoad attr Print Call AttributeLoad Str attr NameLoad AugAssignAdd NameStore Num Print BinOpMod Str TupleLoad NameLoad NameLoad NameLoad Expr Call AttributeLoad NameLoad attr
N/A N/A 
get_sequences_from_www.py - retrieve sequences from Expasy
==========================================================

:Author: Andreas Heger
:Release: $Id$
:Date: |today|
:Tags: Python

Purpose
-------

.. todo::
   
   describe purpose of the script.

Usage
-----

Example::

   python get_sequences_from_www.py --help

Type::

   python get_sequences_from_www.py --help

for command line help.

Documentation
-------------

Code
----

 N/A os N/A sys N/A string N/A re N/A tempfile N/A subprocess N/A optparse N/A time N/A math N/A Convert EMBL formatted file into a tab-separated table.
 N/A CGAT.Experiment E Bio SeqRecord N/A Bio.ExPASy ExPASy N/A Bio.SwissProt SProt Bio File N/A parser N/A N/A E OptionParser version %prog version: $Id: get_sequences_from_www.py 2782 2009-09-10 11:40:29Z andreas $ N/A N/A __name__ __main__ N/A N/A N/A N/A parser add_option -f --field dest fields type string help field to write to table. action append N/A N/A N/A parser set_defaults fields N/A N/A N/A options args N/A N/A E Start parser N/A s_parser N/A N/A SProt RecordParser N/A N/A ninput nfound nmissed N/A 0 0 0 N/A line N/A sys stdin N/A N/A N/A N/A line N/A 0 # N/A N/A N/A id N/A N/A N/A N/A line N/A -1 split N/A 0 N/A ninput 1 N/A N/A N/A result N/A N/A N/A N/A ExPASy get_sprot_raw id read N/A N/A N/A IOError N/A N/A N/A N/A N/A options stdlog write N/A # warning: sequence for id %s not found. id N/A nmissed 1 N/A N/A s_iterator N/A N/A SProt Iterator N/A N/A File StringHandle result s_parser N/A N/A N/A cur_record N/A N/A s_iterator next N/A N/A N/A SyntaxError N/A N/A N/A # Sequence not found: %s id N/A N/A columns N/A id N/A f N/A options fields N/A N/A N/A f description N/A N/A N/A N/A columns append N/A cur_record description N/A N/A N/A f references N/A N/A ref N/A cur_record references N/A N/A N/A N/A columns append N/A ref authors N/A ref title N/A N/A N/A f organism_classification N/A N/A N/A N/A columns append N/A cur_record organism_classification N/A N/A N/A f organism N/A N/A N/A N/A columns append N/A cur_record organism N/A N/A N/A f sequence N/A N/A N/A N/A columns append N/A cur_record sequence N/A N/A N/A join columns N/A nfound 1 N/A N/A # input=%i, found=%i, missed=%i N/A ninput nfound nmissed N/A N/A N/A E Stop