[Biopython-dev] [Bug 3043] New: test_NCBI_BLAST_tools fails

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=3043

           Summary: test_NCBI_BLAST_tools fails
           Product: Biopython
           Version: 1.54b
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Unit Tests
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: mdehoon at ims.u-tokyo.ac.jp


This is the error I get:

======================================================================
FAIL: Check all blastn arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 121, in test_blastn
    self.check("blastn", Applications.NcbiblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all blastp arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 117, in test_blastp
    self.check("blastp", Applications.NcbiblastpCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all blastx arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 113, in test_blastx
    self.check("blastx", Applications.NcbiblastxCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all psiblast arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 133, in test_psiblast
    self.check("psiblast", Applications.NcbipsiblastCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all rpsblast arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 137, in test_rpsblast
    self.check("rpsblast", Applications.NcbirpsblastCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all rpstblastn arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 141, in test_rpstblastn
    self.check("rpstblastn", Applications.NcbirpstblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all tblastn arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 129, in test_tblastn
    self.check("tblastn", Applications.NcbitblastnCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

======================================================================
FAIL: Check all tblastx arguments are supported
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test_NCBI_BLAST_tools.py", line 125, in test_tblastx
    self.check("tblastx", Applications.NcbitblastxCommandline)
  File "test_NCBI_BLAST_tools.py", line 109, in check
    "Wrapper is missing: " + ", ".join(sorted(missing)))
AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
-
verbose

but actually these seem to be extra options rather than missing options:

$ blastn -h
USAGE
  blastn [-h] [-help] [-import_search_strategy filename]
    [-export_search_strategy filename] [-task task_name] [-db database_name]
    [-dbsize num_letters] [-gilist filename] [-negative_gilist filename]
    [-entrez_query entrez_query] [-db_soft_mask filtering_algorithm]
    [-subject subject_input_file] [-subject_loc range] [-query input_file]
    [-out output_file] [-evalue evalue] [-word_size int_value]
    [-gapopen open_penalty] [-gapextend extend_penalty]
    [-perc_identity float_value] [-xdrop_ungap float_value]
    [-xdrop_gap float_value] [-xdrop_gap_final float_value]
    [-searchsp int_value] [-penalty penalty] [-reward reward] [-no_greedy]
    [-min_raw_gapped_score int_value] [-template_type type]
    [-template_length int_value] [-dust DUST_options]
    [-filtering_db filtering_database]
    [-window_masker_taxid window_masker_taxid]
    [-window_masker_db window_masker_db] [-soft_masking soft_masking]
    [-ungapped] [-culling_limit int_value] [-best_hit_overhang float_value]
    [-best_hit_score_edge float_value] [-window_size int_value]
    [-use_index boolean] [-index_name string] [-lcase_masking]
    [-query_loc range] [-strand strand] [-parse_deflines] [-outfmt format]
    [-show_gis] [-num_descriptions int_value] [-num_alignments int_value]
    [-html] [-max_target_seqs num_sequences] [-num_threads int_value]
    [-remote] [-verbose] [-remote_verbose] [-use_test_remote_service]
    [-version]

DESCRIPTION
   Nucleotide-Nucleotide BLAST 2.2.22+

Use '-help' to print detailed descriptions of command line arguments


In any case, probably there will be slight differences in the options used by
different versions of Blast, and this shouldn't cause tests to fail.


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