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Deprecating Bio.IntelliGenetics in favour of the ig format in Bio.SeqIO

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commit 5be422121e2dd528e67659959ebbea916c99abea 1 parent 06f2bfb
@peterjc peterjc authored
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17 Bio/IntelliGenetics/Record.py
@@ -3,21 +3,10 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""Martel based parser to read IntelliGenetics formatted files.
-
-This is a huge regular regular expression for IntelliGenetics, built using
-the 'regular expressiona on steroids' capabilities of Martel.
-
-http://hiv-web.lanl.gov/ALIGN_97/HIV12SIV-index.html
-
-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.
+"""Martel based parser to read IntelliGenetics formatted files (DEPRECATED).
+This module defines a Record class to hold a sequence from the IntelliGenetics/
+MASE file format in a similar represenation to the original raw file.
"""
# standard library
import string
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14 Bio/IntelliGenetics/__init__.py
@@ -2,10 +2,18 @@
# 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.
-"""Parser for the MASE/Intelligenetics alignment file format.
+"""Parser for the MASE/IntelliGenetics alignment file format (DEPRECATED).
+
+Please use Bio.SeqIO with the "ig" format instead."""
+
+import warnings
+warnings.warn("Bio.IntelliGenetics is deprecated." \
+ + " We hope the new 'ig' format support in Bio.SeqIO will be" \
+ + " suitable for most users. Please get in touch on the " \
+ + " mailing lists if this (or its removal) causes any problems "\
+ + "for you.",
+ DeprecationWarning)
-http://pbil.univ-lyon1.fr/help/formats.html
-"""
# standard library
import string
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5 Bio/IntelliGenetics/intelligenetics_format.py
@@ -3,9 +3,10 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""Martel regular expression for Intelligenetic format.
+"""Martel regular expression for Intelligenetic format (DEPRECATED).
-http://hiv-web.lanl.gov/ALIGN_97/HIV12SIV-index.html
+This is a huge regular regular expression for the IntelliGenetics/MASE format,
+built using the 'regular expressions on steroids' capabilities of Martel.
"""
# standard library
#http://immuno.bme.nwu.edu/seqhunt.html
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3  DEPRECATED
@@ -2,6 +2,9 @@ This file provides documentation for modules in Biopython that have been moved
or deprecated in favor of other modules. This provides some quick and easy
to find documentation about how to update your code to work again.
+Bio.IntelliGenetics
+===================
+Deprecated in favor of the "ig" format in Bio.SeqIO
Bio.ECell
=========
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