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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.
"""Hold GEO data in a straightforward format.
classes:
o Record - All of the information in an GEO record.
See http://www.ncbi.nlm.nih.gov/geo/
"""
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):
"""Initialize the class."""
self.entity_type = ""
self.entity_id = ""
self.entity_attributes = {}
self.col_defs = {}
self.table_rows = []
def __str__(self):
"""Return the GEO record as a string."""
output = ""
output += "GEO Type: %s\n" % self.entity_type
output += "GEO Id: %s\n" % self.entity_id
att_keys = sorted(self.entity_attributes)
for key in att_keys:
contents = self.entity_attributes[key]
if isinstance(contents, list):
for item in contents:
try:
output += "%s: %s\n" % (key, item[:40])
output += out_block(item[40:])
except Exception: # TODO: IndexError?
pass
elif isinstance(contents, str):
output += "%s: %s\n" % (key, contents[:40])
output += out_block(contents[40:])
else:
print(contents)
output += "%s: %s\n" % (key, contents[:40])
output += out_block(contents[40:])
col_keys = sorted(self.col_defs)
output += "Column Header Definitions\n"
for key in col_keys:
val = self.col_defs[key]
output += " %s: %s\n" % (key, val[:40])
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 += "%s: " % self.table_rows.index(row)
for col in row:
output += "%s\t" % col
output += "\n"
if len(self.table_rows) > MAX_ROWS:
output += "...\n"
row = self.table_rows[-1]
output += "%s: " % self.table_rows.index(row)
for col in row:
output += "%s\t" % col
output += "\n"
return output
def out_block(text, prefix=""):
"""Format text in blocks of 80 chars with an additional optional prefix."""
output = ""
for j in range(0, len(text), 80):
output += "%s%s\n" % (prefix, text[j : j + 80])
output += "\n"
return output
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