-
Notifications
You must be signed in to change notification settings - Fork 5
/
Copy path_blastn
executable file
·103 lines (100 loc) · 6.31 KB
/
_blastn
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
#compdef blastn
# Descriptions are mostly taken from https://www.ncbi.nlm.nih.gov/books/NBK279675/
# More descriptions from http://computing.bio.cam.ac.uk/local/doc/blast+_user_manual.pdf
_blastn() {
local ret=1
local args
args+=(
'(-culling_limit)-best_hit_overhang[Best Hit algorithm overhang value]:float_value: '
'(-culling_limit)-best_hit_score_edge[Best Hit algorithm score edge value]:float_value: '
'(-best_hit_overhang -best_hit_score_edge)-culling_limit[Delete a hit that is enveloped by at least this many higher-scoring hits]:int_value: '
'(-subject -subject_loc)-db[BLAST data base]:db_file:_files'
'(-db_soft_mask -subject -subject_loc)-db_hard_mask[Filtering algorithm ID to apply to the BLAST database as hard mask]:filtering_algorithm: '
'(-db_hard_mask -subject -subject_loc)-db_soft_mask[Filtering algorithm ID to apply to the BLAST database as soft mask]:filtering_algorithm: '
'-dbsize[Effective size of the database]:num_letters: '
'-dust[Filter query sequence with dust]:DUST_options: '
'-entrez_query[Restrict search with the given Entrez query]:entrez_query: '
'-evalue[Expected Value (E) for saving hits]:evalue: '
'(-import_search_strategy)-export_search_strategy[Record search strategy to this file]:filename:_files'
'-filtering_db[Mask query using the sequences in this database]:filtering_database:_files'
'-gapextend[Cost to extend a gap]:extend_penalty: '
'-gapopen[Cost to open a gap]:open_penalty: '
'(-negative_gilist -seqidlist -negative_seqidlist -remote -subject -subject_loc)-gilist[Restrict search of database to GI’s listed in this file]:filename:_files'
'(-h -help)'{-h,--help}'[Show help]'
'-html[Produce HTML output]'
'(-export_search_strategy)-import_search_strategy[Search strategy file to read]:filename:_files'
'-index_name[MegaBLAST database index name]:string: '
'-lcase_masking[Use lower case filtering in query and subject sequences]'
'-line_length[Line length for output]:line_length: '
'-max_hsps[Maximum number of HSPs to keep]:int_value: '
'(-num_alignments -num_descriptions)-max_target_seqs[Number of aligned sequences to keep]:num_sequences: '
'-min_raw_gapped_score[Minimum raw gapped score to keep an alignment in the preliminary gapped and trace-back stages]:int_value: '
'(-gilist -seqidlist -remote -subject -subject_loc)-negative_gilist[Restrict search of database to everything except the listed GIs]:filename:_files'
'(-gilist -seqidlist -remote -subject -subject_loc)-negative_seqidlist[Restrict search of database to everything except the listed SeqIDs]:filename:_files'
'-no_greedy[Use non-greedy dynamic programming extension]'
'(-max_target_seqs)-num_alignments[Show alignments for this number of database sequences]:int_value: '
'(-max_target_seqs)-num_descriptions[Show one-line descriptions for this number of database sequences]:int_value: '
'(-remote)-num_threads[Number of threads (CPUs) to use in blast search]:int_value: '
'-off_diagonal_range[Maximum number of diagonals separating two hits used to initiate an extension]:int_value: '
'-out[Output file name]:output_file:_files'
'-outfmt[Output format]:format:((
0\:pairwise
1\:query-anchored\ showing\ identities
2\:query-anchored\ no\ identities
3\:flat\ query-anchored,\ show\ identities
4\:flat\ query-anchored,\ no\ identities
5\:XML\ Blast\ output
6\:tabular
7\:tabular\ with\ comment\ lines
8\:Text\ ASN.1
9\:Binary\ ASN
10\:Comma-separated\ value
11\:BLAST\ archive\ format\ \(ASN.1\)
12\:Seqalign\ \(JSON\)
13\:Multiple\-file\ BLAST\ JSON
14\:Multiple\-file\ BLAST\ XML2
15\:Single\-file\ BLAST\ JSON
16\:Single\-file\ BLAST\ XML2
17\:Sequence\ Alignment\/Map\ \(SAM\)
18\:Organism\ Report
))'
'-parse_deflines[Parse query and subject bar delimited sequence identifiers]'
'-penalty[Penalty for a nucleotide mismatch]:penalty: '
'-perc_identity[Percent identity cutoff]:float_value: '
'-qcov_hsp_perc[Percent query coverage per hsp]:float_value: '
'-query[Query file name]:input_file:_files'
'-query_loc[Location on the query sequence]:range: '
'(-gilist -seqidlist -negative_gilist -negative_seqidlist -subject_loc -num_threads)-remote[Execute search on NCBI servers]'
'-reward[Reward for a nucleotide match]:reward: '
'-searchsp[Effective length of the search space]:int_value: '
'(-gilist -negative_gilist -negative_seqidlist -remote -subject -subject_loc)-seqidlist[Restrict search of database to list of SeqIds]:filename:_files'
'-show_gis[Show NCBI GIs in report]'
'-soft_masking[Apply filtering locations as soft masks]:soft_masking: '
'-strand[Query strands to search against database/subject]:strand:(both minus plus)'
'(-db -gilist -seqidlist -negative_gilist -negative_seqidlist -db_soft_mask -db_hard_mask)-subject[File with subject sequence(s) to search]:subject_input_file:_files'
'(-db -gilist -seqidlist -negative_gilist -negative_seqidlist -db_soft_mask -db_hard_mask)-subject_loc[Location on the subject sequence]:range: '
'-sum_stats[Use sum statistics]:bool_value: '
'-task[Commonly performed tasks]:task_name:((
blastn\:Traditional\ BLASTN\ requiring\ an\ exact\ match\ of\ 11
blastn-short\:BLASTN\ program\ optimized\ for\ sequences\ shorter\ than\ 50\ bases
megablast\:Traditional\ megablast\ used\ to\ find\ very\ similar\ sequences
dc-megablast\:Discontiguous\ megablast\ used\ to\ find\ more\ distant\ sequences
rmblastn\:RepeatMasker\ compatible\ version
))'
'-template_length[Discontiguous MegaBLAST template length]:int_value: '
'-template_type[Discontiguous MegaBLAST template type]:type:(coding optimal coding_and_optimal)'
'-ungapped[Perform ungapped alignment]'
'-use_index[Use MegaBLAST database index]:boolean:(true false)'
'-version[Print version information]'
'-window_masker_db[Enable WindowMasker filtering using this file]:window_masker_db:_files'
'-window_masker_taxid[Enable WindowMasker filtering using a Taxonomic ID]:window_masker_taxid: '
'-window_size[Multiple hits window size, use 0 to specify 1-hit algorithm]:int_value: '
'-word_size[Length of initial exact match]:int_value: '
'-xdrop_gap[Heuristic value for preliminary gapped extensions]:float_value: '
'-xdrop_gap_final[Heuristic value for final gapped alignment]:float_value: '
'-xdrop_ungap[Heuristic value for ungapped extensions]:float_value: '
)
_arguments $args[@] && ret=0
return ret
}
_blastn