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Removed internal references to RecordFile, which are really not needed.

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1 parent 2b2cb31 commit 23b046bd90d429e55bbe0b6585049772bc0f1c45 chapmanb committed May 4, 2004
Showing with 9 additions and 7 deletions.
  1. +0 −1 Bio/Ais/__init__.py
  2. +0 −1 Bio/CDD/__init__.py
  3. +8 −0 DEPRECATED
  4. +0 −1 Tests/test_cdd.py
  5. +1 −4 Tests/test_nbrf.py
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@@ -27,7 +27,6 @@
from urllib import FancyURLopener
from urllib import urlencode
-from Bio.RecordFile import RecordFile
from Bio.SGMLExtractor import SGMLExtractorHandle
from Bio.NetCatch import NetCatch
from Bio.NetCatch import ExtractUrls
View
@@ -19,7 +19,6 @@
import Martel
from Martel import RecordReader
-from Bio.RecordFile import RecordFile
from Bio.FilteredReader import FilteredReader
from Bio.FilteredReader import remove_empty_line
from Bio.FilteredReader import remove_leading_whitespace
View
@@ -16,6 +16,14 @@ interface. We recommend using LIBSVM:
http://www.csie.ntu.edu.tw/~cjlin/libsvm/
+Bio.RecordFile
+==============
+Deprecated as of Release 1.30.
+RecordFile wasn't completely implemented and duplicates the work
+of most standard parsers. We recommend using a specific iterator
+(Bio.Fasta.Iterator for example) without a parser to get back
+text records.
+
Bio.kMeans and Bio.xkMeans
==========================
Deprecated as of Release 1.30.
View
@@ -5,7 +5,6 @@
import sys
import Bio.CDD
-from Bio.RecordFile import RecordFile
from Bio.FilteredReader import FilteredReader
from Bio.FilteredReader import remove_empty_line
from Bio.FilteredReader import remove_leading_whitespace
View
@@ -4,18 +4,15 @@
import os
import Bio.NBRF
-from Bio.RecordFile import RecordFile
from Bio.File import SGMLHandle
testfiles = [ 'B_nuc.pir', 'Cw_prot.pir', 'DMA_nuc.pir', 'DMB_prot.pir',
'clustalw.pir']
for file in testfiles:
fh = open(os.path.join("NBRF", file))
- record_file = RecordFile( fh, '>', chr( 0x2a ) )
print "Testing Bio.NBRF on " + file + "\n\n"
- records = Bio.NBRF.Iterator(record_file, Bio.NBRF.RecordParser(debug_level=0))
-# records = Bio.NBRF.Iterator(record_file, None)
+ records = Bio.NBRF.Iterator(fh, Bio.NBRF.RecordParser(debug_level=0))
while 1:
# for j in range( 0, 1 ):
record = records.next()

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