BLAST 2.2.28+ added -comp_based_stats and -use_sw_tback to rpsblast

biopython · Jul 30, 2013 · 6e45a34 · 6e45a34
1 parent d833495
commit 6e45a34
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Showing 2 changed files with 30 additions and 10 deletions.
diff --git a/Bio/Blast/Applications.py b/Bio/Blast/Applications.py
@@ -980,14 +980,15 @@ def __init__(self, cmd="blastx", **kwargs):
                     equate=False),
             _Option(["-comp_based_stats", "comp_based_stats"],
                     """Use composition-based statistics for blastp, blastx, or tblastn:
-                        D or d: default (equivalent to 2 )
-                        0 or F or f: no composition-based statistics
-                        1: Composition-based statistics as in NAR 29:2994-3005, 2001
-                        2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
-                        3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
-
-                        For programs other than tblastn, must either be absent or be D, F or 0
-                        Default = `2'
+
+                    D or d: default (equivalent to 2 )
+                    0 or F or f: no composition-based statistics
+                    1: Composition-based statistics as in NAR 29:2994-3005, 2001
+                    2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties
+                    3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally
+
+                    For programs other than tblastn, must either be absent or be D, F or 0
+                    Default = `2'
                     """,
                     equate=False),
             #Query filtering options:
@@ -1325,6 +1326,22 @@ def __init__(self, cmd="rpsblast", **kwargs):
 
                     Incompatible with: culling_limit.""",
                     equate=False),
+            #General search options:
+            _Option(["-comp_based_stats", "comp_based_stats"],
+                    """Use composition-based statistics.
+
+                    D or d: default (equivalent to 0 )
+                    0 or F or f: Simplified Composition-based statistics as in
+                                 Bioinformatics 15:1000-1011, 1999
+                    1 or T or t: Composition-based statistics as in NAR 29:2994-3005, 2001
+
+                    Default = `0'
+                    """,
+                    checker_function=lambda value : value in "Dd0Ff1Tt",
+                    equate=False),
+            #Misc options:
+            _Switch(["-use_sw_tback", "use_sw_tback"],
+                    "Compute locally optimal Smith-Waterman alignments?"),
             ]
         _NcbiblastCommandline.__init__(self, cmd, **kwargs)
 

diff --git a/Tests/test_NCBI_BLAST_tools.py b/Tests/test_NCBI_BLAST_tools.py
@@ -220,21 +220,24 @@ def check(self, exe_name, wrapper) :
         if "-msa_master_idx" in extra and exe_name=="psiblast":
             #New in BLAST 2.2.25+ so will look like an extra arg on old BLAST
             extra.remove("-msa_master_idx")
-        if exe_name=="rpsblast":
+        if exe_name == "rpsblast":
             #New in BLAST 2.2.25+ so will look like an extra arg on old BLAST
             extra = extra.difference(["-best_hit_overhang",
                                       "-best_hit_score_edge",
                                       "-culling_limit"])
         if "-max_hsps_per_subject" in extra:
             #New in BLAST 2.2.26+ so will look like an extra arg on old BLAST
             extra.remove("-max_hsps_per_subject")
-        if exe_name=="blastx":
+        if exe_name == "blastx":
             #New in BLAST 2.2.27+ so will look like an extra arg on old BLAST
             extra = extra.difference(["-comp_based_stats",
                                       "-use_sw_tback"])
         if exe_name in ["blastx", "tblastn"]:
             #Removed in BLAST 2.2.27+ so will look like extra arg on new BLAST
             extra = extra.difference(["-frame_shift_penalty"])
+        if exe_name == "rpsblast":
+            #New in BLAST 2.2.28+ so will look like extra args on old BLAST:
+            extra = extra.difference(["-comp_based_stats", "-use_sw_tback"])
 
         if extra or missing:
             import warnings