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Marking Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast as o…

…bsolete. Need to update the tutorial still...
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1 parent cc63d03 commit 2ed247ad71a8a163f8c724a6b09e8d13db7689e5 @peterjc peterjc committed Oct 19, 2009
Showing with 26 additions and 9 deletions.
  1. +21 −9 Bio/Blast/NCBIStandalone.py
  2. +5 −0 DEPRECATED
@@ -7,7 +7,7 @@
"""
This module provides code to work with the standalone version of
-BLAST, either blastall or blastpgp, provided by the NCBI.
+BLAST, either blastall, rpsblast or blastpgp, provided by the NCBI.
http://www.ncbi.nlm.nih.gov/BLAST/
Classes:
@@ -28,10 +28,14 @@
_ParametersConsumer Consumes parameters information.
Functions:
-blastall Execute blastall.
-blastpgp Execute blastpgp.
-rpsblast Execute rpsblast.
-
+blastall Execute blastall (OBSOLETE).
+blastpgp Execute blastpgp (OBSOLETE).
+rpsblast Execute rpsblast (OBSOLETE).
+
+For calling the BLAST command line tools, we encourage you to use the
+command line wrappers in Bio.Blast.Applications - the three functions
+blastall, blastpgp and rpsblast are considered to be obsolete now, and
+are likely to be deprecated and then removed in future releases.
"""
import os
@@ -1576,8 +1580,11 @@ def __iter__(self):
return iter(self.next, None)
def blastall(blastcmd, program, database, infile, align_view='7', **keywds):
- """Execute and retrieve data from standalone BLASTPALL as handles.
+ """Execute and retrieve data from standalone BLASTPALL as handles (OBSOLETE).
+ NOTE - This function is obsolete, you are encouraged to the command
+ line wrapper Bio.Blast.Applications.BlastallCommandline instead.
+
Execute and retrieve data from blastall. blastcmd is the command
used to launch the 'blastall' executable. program is the blast program
to use, e.g. 'blastp', 'blastn', etc. database is the path to the database
@@ -1683,7 +1690,10 @@ def blastall(blastcmd, program, database, infile, align_view='7', **keywds):
def blastpgp(blastcmd, database, infile, align_view='7', **keywds):
- """Execute and retrieve data from standalone BLASTPGP as handles.
+ """Execute and retrieve data from standalone BLASTPGP as handles (OBSOLETE).
+
+ NOTE - This function is obsolete, you are encouraged to the command
+ line wrapper Bio.Blast.Applications.BlastpgpCommandline instead.
Execute and retrieve data from blastpgp. blastcmd is the command
used to launch the 'blastpgp' executable. database is the path to the
@@ -1809,8 +1819,11 @@ def blastpgp(blastcmd, database, infile, align_view='7', **keywds):
def rpsblast(blastcmd, database, infile, align_view="7", **keywds):
- """Execute and retrieve data from standalone RPS-BLAST as handles.
+ """Execute and retrieve data from standalone RPS-BLAST as handles (OBSOLETE).
+ NOTE - This function is obsolete, you are encouraged to the command
+ line wrapper Bio.Blast.Applications.RpsBlastCommandline instead.
+
Execute and retrieve data from standalone RPS-BLAST. blastcmd is the
command used to launch the 'rpsblast' executable. database is the path
to the database to search against. infile is the path to the file
@@ -2086,4 +2099,3 @@ def _diagnose_error(self, handle, data_record):
raise LowQualityBlastError("Blast failure occured on query: ",
data_record.query)
line = handle.readline()
-
View
@@ -7,6 +7,11 @@ Python 2.3
No longer supported as of Release 1.51, having triggered a warning with
Release 1.50, with a mention in the release notes for Release 1.49.
+Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast
+========================================================
+These command line tools were declared obsolete in Release 1.53, please use
+the wrappers in Bio.Blast.Applications and the subprocess module instead.
+
Bio.Clustalw
============
Declared obsolete in Release 1.52, having been replaced with Bio.AlignIO for

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