[Biopython-dev] [Bug 3043] test_NCBI_BLAST_tools fails

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





------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2010-04-06 02:22 EST -------
(In reply to comment #0)
> This is the error I get:
> 
> ...
> AssertionError: Wrapper is missing: -remote_verbose, -use_test_remote_service,
> ...
> 
> 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.

I thought I was using 2.2.22+ on my dev machine - I'll check.

Assuming you have installed the latest BLAST+ and our wrappers are missing some
recently added switches, the test is functioning as designed. I really did
WANT it to fail in this situation, to alert us to the fact the wrappers need
updating. By design the test should pass fine on older BLAST+ releases with
less options.

OK, maybe it could be a warning, but if we let this pass silently we risk the
wrappers getting out of date without anyone noticing, and then missing options
being added ad-hoc as an when people need them. i.e. What seemed to have
happens with other wrappers in the past.

Peter


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