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# Copyright 2001 by Katharine Lindner. All rights reserved.
# Copyright 2006 by PeterC. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Martel based parser to read GEO formatted files.
This is a huge regular regular expression for GEO, built using
the 'regular expressiona on steroids' capabilities of Martel.
#http://www.ncbi.nlm.nih.gov/geo/
Notes:
Just so I remember -- the new end of line syntax is:
New regexp syntax - \R
\R means "\n|\r\n?"
[\R] means "[\n\r]"
This helps us have endlines be consistent across platforms.
"""
# standard library
import string
from Bio.Seq import Seq
from Bio.Align.Generic import Alignment
import Bio.Alphabet
"""Hold GEO data in a straightforward format.
classes:
o Record - All of the information in an GEO record.
"""
class Record:
"""Hold GEO information in a format similar to the original record.
The Record class is meant to make data easy to get to when you are
just interested in looking at GEO data.
Attributes:
entity_type
entity_id
entity_attributes
col_defs
table_rows
"""
def __init__(self):
self.entity_type = ''
self.entity_id = ''
self.entity_attributes = {}
self.col_defs = {}
self.table_rows = []
def __str__( self ):
output = ''
output = output + 'GEO Type: %s\n' % self.entity_type
output = output + 'GEO Id: %s\n' % self.entity_id
att_keys = self.entity_attributes.keys()
att_keys.sort()
for key in att_keys:
contents = self.entity_attributes[ key ]
if( type( contents ) == type( [] ) ):
for item in contents:
try:
output = output + '%s: %s\n' % ( key, item[ :40 ] )
output = output + out_block( item[ 40: ] )
except:
pass
elif( type( contents ) == type( '' ) ):
output = output + '%s: %s\n' % ( key, contents[ :40 ] )
output = output + out_block( contents[ 40: ] )
else:
print contents
output = output + '%s: %s\n' % ( key, val[ :40 ] )
output = output + out_block( val[ 40: ] )
col_keys = self.col_defs.keys()
col_keys.sort()
output = output + 'Column Header Definitions\n'
for key in col_keys:
val = self.col_defs[ key ]
output = output + ' %s: %s\n' % ( key, val[ :40 ] )
output = output + out_block( val[ 40: ], ' ' )
#May have to display VERY large tables,
#so only show the first 20 lines of data
MAX_ROWS = 20+1 # include header in count
for row in self.table_rows[0:MAX_ROWS]:
output = output + '%s: ' % self.table_rows.index( row )
for col in row:
output = output + '%s\t' % col
output = output + '\n'
if len(self.table_rows) > MAX_ROWS :
output = output + '...\n'
row = self.table_rows[-1]
output = output + '%s: ' % self.table_rows.index( row )
for col in row:
output = output + '%s\t' % col
output = output + '\n'
return output
def out_block( text, prefix = '' ):
output = ''
for j in range( 0, len( text ), 80 ):
output = output + '%s%s\n' % ( prefix, text[ j: j + 80 ] )
output = output + '\n'
return output
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