File Coverage

blib/lib/Bio/Tools/Run/BlastPlus/Config.pm

Criterion	Covered	Total	%
statement	18	18	100.0
branch			n/a
condition			n/a
subroutine	6	6	100.0
pod			n/a
total	24	24	100.0

line	stmt	sub	time	code
1				#$Id$
2				package Bio::Tools::Run::BlastPlus::Config;
3	1	1	3	use strict;
	1		1
	1		21
4	1	1	3	use warnings;
	1		1
	1		19
5	1	1	3	no warnings qw(qw);
	1		1
	1		34
6	1	1	3	use Bio::Root::Root;
	1		2
	1		14
7	1	1	2	use Exporter;
	1		1
	1		76
8	1	1	16	use base qw(Bio::Root::Root);
	1		1
	1		468
9
10				our (@ISA, @EXPORT, @EXPORT_OK);
11				push @ISA, 'Exporter';
12				@EXPORT = qw(
13				@program_commands
14				%command_prefixes
15				%composite_commands
16				@program_params
17				@program_switches
18				%param_translation
19				%command_files
20				$program_name
21				$program_dir
22				$use_dash
23				$join
24				);
25
26				@EXPORT_OK = qw();
27
28				# getting the parms and switches from the usage string:
29
30				#$ blastp -h \| perl -ne '@a = m/\[(.*?)\]/g; for $a (@a) { @b = split(/\s+/,$a); $b[0]=~s/-//; $ptr = (@b==1 ? \@s : \@p ); push @$ptr, $b[0]; } END { print "p arms\n", join("\n",@p), "\n\n", "switches\n", join("\n",@s); }'
31
32				# '*' indicates a 'pseudo'-program : i.e. each
33				# command has its own executable...
34
35				our $program_name = '*blast+';
36				our $use_dash = 'single';
37				our $join = ' ';
38
39				our @program_commands = qw(
40				run
41				blastn
42				blastx
43				tblastx
44				tblastn
45				blastp
46				psiblast
47				rpsblast
48				rpstblastn
49				makeblastdb
50				blastdb_aliastool
51				blastdbcmd
52				blastdbcheck
53				convert2blastmask
54				dustmasker
55				segmasker
56				windowmasker
57				);
58
59				# full command => prefix
60				our %command_prefixes = (
61				run => 'run',
62				blastn => 'bln',
63				blastx => 'blx',
64				tblastx => 'tbx',
65				tblastn => 'tbn',
66				blastp => 'blp',
67				psiblast => 'psi',
68				rpsblast => 'rps',
69				rpstblastn => 'rpst',
70				makeblastdb => 'mak',
71				blastdb_aliastool => 'dba',
72				blastdbcmd => 'dbc',
73				blastdbcheck => 'dbk',
74				convert2blastmask => 'c2m',
75				dustmasker => 'dms',
76				segmasker => 'sms',
77				windowmasker => 'wms'
78				);
79
80				# each elt : pfx\|wrapper_parm_name
81
82				our @program_params = qw(
83				command
84				tbn\|import_search_strategy
85				tbn\|export_search_strategy
86				tbn\|db
87				tbn\|dbsize
88				tbn\|gilist
89				tbn\|negative_gilist
90				tbn\|entrez_query
91				tbn\|subject
92				tbn\|subject_loc
93				tbn\|query
94				tbn\|out
95				tbn\|evalue
96				tbn\|word_size
97				tbn\|gapopen
98				tbn\|gapextend
99				tbn\|xdrop_ungap
100				tbn\|xdrop_gap
101				tbn\|xdrop_gap_final
102				tbn\|searchsp
103				tbn\|db_gencode
104				tbn\|frame_shift_penalty
105				tbn\|max_intron_length
106				tbn\|seg
107				tbn\|soft_masking
108				tbn\|matrix
109				tbn\|threshold
110				tbn\|culling_limit
111				tbn\|best_hit_overhang
112				tbn\|best_hit_score_edge
113				tbn\|window_size
114				tbn\|query_loc
115				tbn\|outfmt
116				tbn\|num_descriptions
117				tbn\|num_alignments
118				tbn\|max_target_seqs
119				tbn\|num_threads
120				tbn\|comp_based_stats
121				tbn\|in_pssm
122				blx\|import_search_strategy
123				blx\|export_search_strategy
124				blx\|db
125				blx\|dbsize
126				blx\|gilist
127				blx\|negative_gilist
128				blx\|entrez_query
129				blx\|db_soft_mask
130				blx\|subject
131				blx\|subject_loc
132				blx\|query
133				blx\|out
134				blx\|evalue
135				blx\|word_size
136				blx\|gapopen
137				blx\|gapextend
138				blx\|xdrop_ungap
139				blx\|xdrop_gap
140				blx\|xdrop_gap_final
141				blx\|searchsp
142				blx\|frame_shift_penalty
143				blx\|max_intron_length
144				blx\|seg
145				blx\|soft_masking
146				blx\|matrix
147				blx\|threshold
148				blx\|culling_limit
149				blx\|best_hit_overhang
150				blx\|best_hit_score_edge
151				blx\|window_size
152				blx\|query_loc
153				blx\|strand
154				blx\|query_gencode
155				blx\|outfmt
156				blx\|num_descriptions
157				blx\|num_alignments
158				blx\|max_target_seqs
159				blx\|num_threads
160				bln\|import_search_strategy
161				bln\|export_search_strategy
162				bln\|task
163				bln\|db
164				bln\|dbsize
165				bln\|gilist
166				bln\|negative_gilist
167				bln\|entrez_query
168				bln\|db_soft_mask
169				bln\|subject
170				bln\|subject_loc
171				bln\|query
172				bln\|out
173				bln\|evalue
174				bln\|word_size
175				bln\|gapopen
176				bln\|gapextend
177				bln\|perc_identity
178				bln\|xdrop_ungap
179				bln\|xdrop_gap
180				bln\|xdrop_gap_final
181				bln\|searchsp
182				bln\|penalty
183				bln\|reward
184				bln\|min_raw_gapped_score
185				bln\|template_type
186				bln\|template_length
187				bln\|dust
188				bln\|filtering_db
189				bln\|window_masker_taxid
190				bln\|window_masker_db
191				bln\|soft_masking
192				bln\|culling_limit
193				bln\|best_hit_overhang
194				bln\|best_hit_score_edge
195				bln\|window_size
196				bln\|use_index
197				bln\|index_name
198				bln\|query_loc
199				bln\|strand
200				bln\|outfmt
201				bln\|num_descriptions
202				bln\|num_alignments
203				bln\|max_target_seqs
204				bln\|num_threads
205				blp\|import_search_strategy
206				blp\|export_search_strategy
207				blp\|task
208				blp\|db
209				blp\|dbsize
210				blp\|gilist
211				blp\|negative_gilist
212				blp\|entrez_query
213				blp\|db_soft_mask
214				blp\|subject
215				blp\|subject_loc
216				blp\|query
217				blp\|out
218				blp\|evalue
219				blp\|word_size
220				blp\|gapopen
221				blp\|gapextend
222				blp\|xdrop_ungap
223				blp\|xdrop_gap
224				blp\|xdrop_gap_final
225				blp\|searchsp
226				blp\|seg
227				blp\|soft_masking
228				blp\|matrix
229				blp\|threshold
230				blp\|culling_limit
231				blp\|best_hit_overhang
232				blp\|best_hit_score_edge
233				blp\|window_size
234				blp\|query_loc
235				blp\|outfmt
236				blp\|num_descriptions
237				blp\|num_alignments
238				blp\|max_target_seqs
239				blp\|num_threads
240				blp\|comp_based_stats
241				psi\|import_search_strategy
242				psi\|export_search_strategy
243				psi\|db
244				psi\|dbsize
245				psi\|gilist
246				psi\|negative_gilist
247				psi\|entrez_query
248				psi\|subject
249				psi\|subject_loc
250				psi\|query
251				psi\|out
252				psi\|evalue
253				psi\|word_size
254				psi\|gapopen
255				psi\|gapextend
256				psi\|xdrop_ungap
257				psi\|xdrop_gap
258				psi\|xdrop_gap_final
259				psi\|searchsp
260				psi\|seg
261				psi\|soft_masking
262				psi\|matrix
263				psi\|threshold
264				psi\|culling_limit
265				psi\|best_hit_overhang
266				psi\|best_hit_score_edge
267				psi\|window_size
268				psi\|query_loc
269				psi\|outfmt
270				psi\|num_descriptions
271				psi\|num_alignments
272				psi\|max_target_seqs
273				psi\|num_threads
274				psi\|comp_based_stats
275				psi\|gap_trigger
276				psi\|num_iterations
277				psi\|out_pssm
278				psi\|out_ascii_pssm
279				psi\|in_msa
280				psi\|in_pssm
281				psi\|pseudocount
282				psi\|inclusion_ethresh
283				psi\|phi_pattern
284				rpst\|import_search_strategy
285				rpst\|export_search_strategy
286				rpst\|db
287				rpst\|dbsize
288				rpst\|gilist
289				rpst\|negative_gilist
290				rpst\|entrez_query
291				rpst\|query
292				rpst\|out
293				rpst\|evalue
294				rpst\|word_size
295				rpst\|xdrop_ungap
296				rpst\|xdrop_gap
297				rpst\|xdrop_gap_final
298				rpst\|searchsp
299				rpst\|query_gencode
300				rpst\|seg
301				rpst\|soft_masking
302				rpst\|window_size
303				rpst\|query_loc
304				rpst\|strand
305				rpst\|outfmt
306				rpst\|num_descriptions
307				rpst\|num_alignments
308				rpst\|max_target_seqs
309				rpst\|num_threads
310				mak\|in
311				mak\|dbtype
312				mak\|title
313				mak\|mask_data
314				mak\|out
315				mak\|max_file_sz
316				mak\|taxid
317				mak\|taxid_map
318				mak\|logfile
319				dba\|gi_file_in
320				dba\|gi_file_out
321				dba\|db
322				dba\|dbtype
323				dba\|title
324				dba\|gilist
325				dba\|out
326				dba\|dblist
327				dba\|num_volumes
328				dba\|logfile
329				tbx\|import_search_strategy
330				tbx\|export_search_strategy
331				tbx\|db
332				tbx\|dbsize
333				tbx\|gilist
334				tbx\|negative_gilist
335				tbx\|entrez_query
336				tbx\|subject
337				tbx\|subject_loc
338				tbx\|query
339				tbx\|out
340				tbx\|evalue
341				tbx\|word_size
342				tbx\|gapopen
343				tbx\|gapextend
344				tbx\|xdrop_ungap
345				tbx\|xdrop_gap
346				tbx\|xdrop_gap_final
347				tbx\|searchsp
348				tbx\|max_intron_length
349				tbx\|seg
350				tbx\|soft_masking
351				tbx\|matrix
352				tbx\|threshold
353				tbx\|culling_limit
354				tbx\|best_hit_overhang
355				tbx\|best_hit_score_edge
356				tbx\|window_size
357				tbx\|query_loc
358				tbx\|strand
359				tbx\|query_gencode
360				tbx\|db_gencode
361				tbx\|outfmt
362				tbx\|num_descriptions
363				tbx\|num_alignments
364				tbx\|max_target_seqs
365				tbx\|num_threads
366				dbc\|db
367				dbc\|dbtype
368				dbc\|entry
369				dbc\|entry_batch
370				dbc\|pig
371				dbc\|range
372				dbc\|strand
373				dbc\|mask_sequence_with
374				dbc\|out
375				dbc\|outfmt
376				dbc\|line_length
377				c2m\|in
378				c2m\|out
379				c2m\|outfmt
380				dms\|in
381				dms\|out
382				dms\|window
383				dms\|level
384				dms\|linker
385				dms\|outfmt
386				sms\|in
387				sms\|out
388				sms\|infmt
389				sms\|outfmt
390				sms\|window
391				sms\|locut
392				sms\|hicut
393				wms\|ustat
394				wms\|in
395				wms\|out
396				wms\|checkdup
397				wms\|window
398				wms\|t_extend
399				wms\|t_thres
400				wms\|t_high
401				wms\|t_low
402				wms\|set_t_high
403				wms\|set_t_low
404				wms\|infmt
405				wms\|outfmt
406				wms\|sformat
407				wms\|convert
408				wms\|fa_list
409				wms\|mem
410				wms\|smem
411				wms\|unit
412				wms\|genome_size
413				wms\|dust
414				wms\|dust_level
415				wms\|exclude_ids
416				wms\|ids
417				wms\|text_match
418				wms\|use_ba
419				);
420
421				# each elt : pfx\|wrapper_switch_name
422				our @program_switches = qw(
423				tbn\|h
424				tbn\|help
425				tbn\|ungapped
426				tbn\|lcase_masking
427				tbn\|parse_deflines
428				tbn\|show_gis
429				tbn\|html
430				tbn\|remote
431				tbn\|use_sw_tback
432				tbn\|version
433				blx\|h
434				blx\|help
435				blx\|ungapped
436				blx\|lcase_masking
437				blx\|parse_deflines
438				blx\|show_gis
439				blx\|html
440				blx\|remote
441				blx\|version
442				bln\|h
443				bln\|help
444				bln\|no_greedy
445				bln\|ungapped
446				bln\|lcase_masking
447				bln\|parse_deflines
448				bln\|show_gis
449				bln\|html
450				bln\|remote
451				bln\|version
452				blp\|h
453				blp\|help
454				blp\|lcase_masking
455				blp\|parse_deflines
456				blp\|show_gis
457				blp\|html
458				blp\|ungapped
459				blp\|remote
460				blp\|use_sw_tback
461				blp\|version
462				psi\|h
463				psi\|help
464				psi\|lcase_masking
465				psi\|parse_deflines
466				psi\|show_gis
467				psi\|html
468				psi\|remote
469				psi\|use_sw_tback
470				psi\|version
471				rpst\|h
472				rpst\|help
473				rpst\|ungapped
474				rpst\|lcase_masking
475				rpst\|parse_deflines
476				rpst\|show_gis
477				rpst\|html
478				rpst\|remote
479				rpst\|version
480				mak\|h
481				mak\|help
482				mak\|parse_seqids
483				mak\|hash_index
484				mak\|version
485				dba\|h
486				dba\|help
487				dba\|version
488				tbx\|h
489				tbx\|help
490				tbx\|lcase_masking
491				tbx\|parse_deflines
492				tbx\|show_gis
493				tbx\|html
494				tbx\|remote
495				tbx\|version
496				dbc\|h
497				dbc\|help
498				dbc\|info
499				dbc\|target_only
500				dbc\|get_dups
501				dbc\|ctrl_a
502				dbc\|version
503				c2m\|h
504				c2m\|help
505				c2m\|parse_seqids
506				c2m\|version
507				dms\|h
508				dms\|help
509				dms\|xmlhelp
510				dms\|parse_seqids
511				dms\|version-full
512				sms\|h
513				sms\|help
514				sms\|xmlhelp
515				sms\|parse_seqids
516				sms\|version-full
517				wms\|h
518				wms\|help
519				wms\|xmlhelp
520				wms\|parse_seqids
521				wms\|version-full
522				wms\|mk_counts
523				);
524
525				#each pair : pfx\|wrapper_opt_name => command_line_name (without dashes)
526				# for blast+, the options are all long and mnemonic, so a param translation
527				# isn't required. In CommandExts, a parameter name should be passed through
528				# as-is, if a translation is not found---.
529				our %param_translation = (
530				);
531
532				our %composite_commands = (
533				);
534
535				our %command_files = (
536				);
537
538				1;