From b308b4cb1a6c6f0dedd5a2adfefbe2a81ede4b54 Mon Sep 17 00:00:00 2001 From: Peter Date: Wed, 3 Mar 2010 13:12:39 +0000 Subject: [PATCH] Declare Bio.Blast.NCBIStandalone obsolete (as discussed on the mailing list) --- Bio/Blast/NCBIStandalone.py | 19 +++++++++++++++---- DEPRECATED | 11 ++++++++--- 2 files changed, 23 insertions(+), 7 deletions(-) diff --git a/Bio/Blast/NCBIStandalone.py b/Bio/Blast/NCBIStandalone.py index 42dbea589d3..c45d3f28bc6 100644 --- a/Bio/Blast/NCBIStandalone.py +++ b/Bio/Blast/NCBIStandalone.py @@ -5,10 +5,21 @@ # Patches by Mike Poidinger to support multiple databases. # Updated by Peter Cock in 2007 to do a better job on BLAST 2.2.15 -""" -This module provides code to work with the standalone version of -BLAST, either blastall, rpsblast or blastpgp, provided by the NCBI. -http://www.ncbi.nlm.nih.gov/BLAST/ +"""Code for calling standalone BLAST and parsing plain text output (OBSOLETE). + +Rather than parsing the human readable plain text BLAST output (which seems to +change with every update to BLAST), we and the NBCI recommend you parse the +XML output instead. The plain text parser in this module still works at the +time of writing, but is considered obsolete and updating it to cope with the +latest versions of BLAST is not a priority for us. + +This module also provides code to work with the "legacy" standalone version of +NCBI BLAST, tools blastall, rpsblast and blastpgp via three helper functions of +the same name. These functions are very limited for dealing with the output as +files rather than handles, for which the wrappers in Bio.Blast.Applications are +prefered. Furthermore, the NCBI themselves regard these command line tools as +"legacy", and encourage using the new BLAST+ tools instead. Biopython has +wrappers for these under Bio.Blast.Applications (see the tutorial). Classes: LowQualityBlastError Except that indicates low quality query sequences. diff --git a/DEPRECATED b/DEPRECATED index 50a886693c5..27633ed47f6 100644 --- a/DEPRECATED +++ b/DEPRECATED @@ -22,12 +22,17 @@ This module (originally in C) offered complement and antiparallel functions check_bases (also available as Bio.Restriction.Restriction.check_bases). Deprecated in Release 1.53. -Bio.Blast.NCBIStandalone.blastall, blastpgp and rpsblast -======================================================== -These command line tools calling functions were declared obsolete in Release +Bio.Blast.NCBIStandalone +======================== +The three functions for calling the "legacy" NCBI BLAST command line tools +blastall, blastpgp and rpsblast were declared obsolete in Biopython Release 1.53, please use the BLAST+ wrappers in Bio.Blast.Applications and the Python subprocess module instead. +The remainder of this module is a parser for the plain text BLAST output, +which was delclared obsolete in Release 1.54. For some time now, both the NCBI +and Biopython have encouraged people to parse the XML output instead. + Bio.Blast.Applications ====================== NCBI "legacy" BLAST tool wrappers FastacmdCommandline, BlastallCommandline,