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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/perl5/
H A Dtest-RNA.pl10 use RNA;
82 $RNA::cut_point=-1;
100 is(RNA::intP_getitem($RNA::iindx,3),108);
104 RNA::ushortP_setitem($RNA::xsubi, 0, 171);
105 RNA::ushortP_setitem($RNA::xsubi, 1, 42);
106 RNA::ushortP_setitem($RNA::xsubi, 2, 93);
107 is(RNA::cdata($RNA::xsubi, 6),pack('S3', 171,42,93));
114 my $ii = RNA::intP_getitem($RNA::iindx, 2);
115 my $p2 = (RNA::pf_float_precision() != 0) ? RNA::floatP_getitem($RNA::pr, $ii-15) : RNA::doubleP_ge…
129 is($RNA::loops,2);
[all …]
H A Dtest-RNA-file-formats.pl10 use RNA;
30 is($msa_format, RNA::FILE_FORMAT_MSA_STOCKHOLM);
34 is($msa_format, RNA::FILE_FORMAT_MSA_CLUSTAL);
38 is($msa_format, RNA::FILE_FORMAT_MSA_FASTA);
41 $msa_format = RNA::file_msa_detect_format($datadir . "/test.maf");
42 is($msa_format, RNA::FILE_FORMAT_MSA_MAF);
46 is($msa_format, RNA::FILE_FORMAT_MSA_UNKNOWN);
53 … RNA::FILE_FORMAT_MSA_STOCKHOLM | RNA::FILE_FORMAT_MSA_SILENT);
85 … RNA::FILE_FORMAT_MSA_CLUSTAL | RNA::FILE_FORMAT_MSA_SILENT);
98 … RNA::FILE_FORMAT_MSA_FASTA | RNA::FILE_FORMAT_MSA_SILENT);
[all …]
H A Dtest-RNA-pf_window.pl12 use RNA;
184 $md = new RNA::md();
187 $fc = new RNA::fold_compound($longseq, $md, RNA::OPTION_WINDOW);
242 $fc = new RNA::fold_compound($seq, $md, RNA::OPTION_WINDOW);
277 $fc = new RNA::fold_compound($shortseq, $md, RNA::OPTION_WINDOW);
304 $fc = new RNA::fold_compound($longseq, undef, RNA::OPTION_WINDOW);
346 $fc = new RNA::fold_compound($longseq, $md, RNA::OPTION_WINDOW);
390 $fc = new RNA::fold_compound($longseq, $md, RNA::OPTION_WINDOW);
418 $fc = new RNA::fold_compound($shortseq, $md, RNA::OPTION_WINDOW);
445 RNA::init_rand();
[all …]
H A Dtest-RNA-constraints.pl8 use RNA;
44 $fc = new RNA::fold_compound($seq_con);
70 $fc = new RNA::fold_compound($seq_con);
92 $fc= new RNA::fold_compound($seq_con);
93 $fc->hc_add_bp(1,20,RNA::CONSTRAINT_CONTEXT_ENFORCE | RNA::CONSTRAINT_CONTEXT_ALL_LOOPS);
103 $fc = new RNA::fold_compound($seq_con);
114 $fc = new RNA::fold_compound($seq_long, undef, RNA::OPTION_WINDOW);
115 $fc->hc_add_bp(1, 10, RNA::CONSTRAINT_CONTEXT_ALL_LOOPS | RNA::CONSTRAINT_CONTEXT_ENFORCE);
116 $fc->hc_add_bp(101, 110, RNA::CONSTRAINT_CONTEXT_ALL_LOOPS | RNA::CONSTRAINT_CONTEXT_ENFORCE);
124 my $pt = RNA::ptable($hit->{'structure'});
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python/
H A Dtest-RNA.py6 import RNA
98 ret = RNA.intP_getitem(RNA.cvar.iindx,3)
100 RNA.ushortP_setitem(RNA.cvar.xsubi, 0, 171)
101 RNA.ushortP_setitem(RNA.cvar.xsubi, 1, 42)
102 RNA.ushortP_setitem(RNA.cvar.xsubi, 2, 93)
103 self.assertEqual(RNA.cdata(RNA.cvar.xsubi, 6),pack('HHH',171,42,93))
108 ii = RNA.intP_getitem(RNA.cvar.iindx, 2)
111 p2 = RNA.floatP_getitem(RNA.cvar.pr, ii-15)
113 p2 = RNA.doubleP_getitem(RNA.cvar.pr, ii-15)
123 self.assertEqual(RNA.intP_getitem(RNA.cvar.loop_degree,1),2)
[all …]
H A Dtest-RNA-file-formats.py6 import RNA
34 self.assertTrue(msa_format == RNA.FILE_FORMAT_MSA_MAF)
48 RNA.FILE_FORMAT_MSA_SILENT)
67 RNA.FILE_FORMAT_MSA_SILENT)
82 RNA.FILE_FORMAT_MSA_FASTA | \
83 RNA.FILE_FORMAT_MSA_SILENT)
97 RNA.file_msa_read(datadir + "/test.maf",
98 RNA.FILE_FORMAT_MSA_MAF | \
99 RNA.FILE_FORMAT_MSA_SILENT)
116 RNA.file_msa_read_record(f)
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H A Dtest-RNA-sc-callbacks.py5 import RNA
14 RNA.cvar.dangles=0
21 if d == RNA.DECOMP_PAIR_HP:
25 elif d == RNA.DECOMP_PAIR_IL:
29 elif d == RNA.DECOMP_PAIR_ML:
42 elif d == RNA.DECOMP_ML_STEM:
47 elif d == RNA.DECOMP_ML_ML:
51 elif d == RNA.DECOMP_ML_UP:
71 if d == RNA.DECOMP_PAIR_HP:
91 if d == RNA.DECOMP_PAIR_HP:
[all …]
H A Dtest-RNA-pf_window.py7 import RNA
114 md = RNA.md()
117 fc = RNA.fold_compound(longseq, md, RNA.OPTION_WINDOW)
148 fc = RNA.fold_compound(seq, md, RNA.OPTION_WINDOW)
178 md = RNA.md()
184 fc = RNA.fold_compound(shortseq, md, RNA.OPTION_WINDOW)
212 fc = RNA.fold_compound(longseq, None, RNA.OPTION_WINDOW)
253 fc = RNA.fold_compound(longseq, md, RNA.OPTION_WINDOW)
289 fc = RNA.fold_compound(longseq, md, RNA.OPTION_WINDOW)
328 fc = RNA.fold_compound(shortseq, md, RNA.OPTION_WINDOW)
[all …]
H A Dtest-RNA-constraints.py5 import RNA
29 fc = RNA.fold_compound(seq_con)
54 fc = RNA.fold_compound(seq_con)
76 fc=RNA.fold_compound(seq_con)
77 fc.hc_add_bp(1,20,RNA.CONSTRAINT_CONTEXT_ENFORCE | RNA.CONSTRAINT_CONTEXT_ALL_LOOPS)
89 fc = RNA.fold_compound(seq_con)
98 fc = RNA.fold_compound(seq_long, None, RNA.OPTION_WINDOW)
99 fc.hc_add_bp(1, 10, RNA.CONSTRAINT_CONTEXT_ALL_LOOPS | RNA.CONSTRAINT_CONTEXT_ENFORCE);
100 fc.hc_add_bp(101, 110, RNA.CONSTRAINT_CONTEXT_ALL_LOOPS | RNA.CONSTRAINT_CONTEXT_ENFORCE);
106 pt = RNA.ptable(hit['structure'])
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/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/data/
H A Decoli-trna-qrna.out26 RNA ends = 0 12
57 winner = RNA
74 winner = RNA
91 winner = RNA
108 winner = RNA
125 winner = RNA
142 winner = RNA
159 winner = RNA
176 winner = RNA
193 winner = RNA
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H A Dsprintf.rnamotif4 >gi|173609|gb|M28984|ACARRDX A.castellani 5S ribosomal RNA
6 >gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
8 >gi|1236163|gb|L41047|ANNRRO Actinoplanes sp. ribosomal RNA (rRNA)
76 >gi|174363|gb|K01260|ECOPRM1 Escherichia coli 10sb (M1) RNA; the RNA component of RNase P
126 >gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
128 >gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
246 >gi|176199|gb|M21529|THCRRD T.celer 16S ribosomal RNA
357 >gi|174363|gb|K01260|ECOPRM1 Escherichia coli 10sb (M1) RNA; the RNA component of RNase P
407 >gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
409 >gi|174913|gb|M23820|HUMRRAUA Human U5-A ribosomal RNA
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/python3/
H A Dtest-RNA.py36 import RNA
22 (struct, mfe) = RNA.fold(seq1)
64 RNA.edit_backtrack = 1
66 # print RNA::get_aligned_line(0), RNA::get_aligned_line(1),"\n"
93 RNA.cvar.cut_point=-1
102 ii = RNA.intP_getitem(RNA.cvar.iindx, 2)
105 p2 = RNA.floatP_getitem(RNA.cvar.pr, ii-15)
107 p2 = RNA.doubleP_getitem(RNA.cvar.pr, ii-15)
117 self.assertEqual(RNA.intP_getitem(RNA.cvar.loop_degree,1),2)
192 md = RNA.md();
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/tests/
H A DMakefile.am51 BUILT_SOURCES = perl5/test-RNA-Design.t
65 PERL_TESTS = perl5/test-RNA.pl \
66 perl5/test-RNA-callbacks.pl \
68 perl5/test-RNA-Design.t \
71 perl5/test-RNA-mfe_eval.pl \
73 perl5/test-RNA-pf_window.pl \
90 perl5/test-RNA-Design.t: $(top_srcdir)/interfaces/Perl/RNA/t/Design.t
91 cp $(top_srcdir)/interfaces/Perl/RNA/t/Design.t $(builddir)/perl5/test-RNA-Design.t
117 python/test-RNA-utils.py \
118 python/test-RNA.py
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/doc/latex/
H A Dfiles.tex6 …sline{section}{Vienna\+RNA/\mbox{\hyperlink{alifold_8h}{alifold.\+h}} \\*Functions for comparative…
12 …item\contentsline{section}{Vienna\+RNA/\mbox{\hyperlink{cofold_8h}{cofold.\+h}} \\*MFE implementat…
15 …sline{section}{Vienna\+RNA/\mbox{\hyperlink{concentrations_8h}{concentrations.\+h}} \\*Concentrati…
25 \item\contentsline{section}{Vienna\+RNA/\mbox{\hyperlink{duplex_8h}{duplex.\+h}} \\*Functions for s…
36 \item\contentsline{section}{Vienna\+RNA/\mbox{\hyperlink{fold_8h}{fold.\+h}} \\*MFE calculations fo…
40 \item\contentsline{section}{Vienna\+RNA/\mbox{\hyperlink{grammar_8h}{grammar.\+h}} \\*Implementatio…
42 …entsline{section}{Vienna\+RNA/\mbox{\hyperlink{heat__capacity_8h}{heat\+\_\+capacity.\+h}} \\*Comp…
60 …ntsline{section}{Vienna\+RNA/\mbox{\hyperlink{part__func__co_8h}{part\+\_\+func\+\_\+co.\+h}} \\*P…
61 …ection}{Vienna\+RNA/\mbox{\hyperlink{part__func__up_8h}{part\+\_\+func\+\_\+up.\+h}} \\*Implementa…
90 …ontentsline{section}{Vienna\+RNA/\mbox{\hyperlink{units_8h}{units.\+h}} \\*Use \mbox{\hyperlink{ut…
[all …]
H A Dgroup__cofold.tex1 \hypertarget{group__cofold}{}\doxysection{RNA-\/\+RNA Interaction}
2 \label{group__cofold}\index{RNA-\/RNA Interaction@{RNA-\/RNA Interaction}}
6 Collaboration diagram for RNA-\/\+RNA Interaction\+:
20 \begin{DoxyCompactList}\small\item\em RNA-\/\+RNA interaction as a stepwise process. \end{DoxyCompa…
25 \begin{DoxyCompactList}\small\item\em Concentration computations for RNA-\/\+RNA interactions. \end…
27 \begin{DoxyCompactList}\small\item\em Functions for simple RNA-\/\+RNA duplex interactions. \end{Do…
29 \begin{DoxyCompactList}\small\item\em Implementations for accessibility and RNA-\/\+RNA interaction…
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python3/
H A DMakefile.am20 pkgpyexecdir = $(py3execdir)/RNA
24 pkgpyexec_DATA = RNA/__init__.py
88 $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
89 cp `test -f RNA.py || echo '$(srcdir)/'`RNA.py RNA/__init__.py
93 RNA/__pycache__/__init__.@PYTHON3_CACHE_TAG@.pyc: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
97 RNA/__pycache__/__init__.@PYTHON3_CACHE_OPT1_EXT@: RNA/__init__.py RNA/_RNA$(PYTHON3_SO)
101 RNA/_RNA$(PYTHON3_SO): _RNA.la
102 $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
108 RNA/_RNA$(PYTHON3_SO) \
109 RNA/__init__.py \
[all …]
/dports/biology/py-multiqc/multiqc-1.10/multiqc/utils/
H A Dconfig_defaults.yaml292 - RNA
312 - RNA
320 - RNA
327 - RNA
331 - RNA
339 - RNA
342 - RNA
345 - RNA
348 - RNA
351 - RNA
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/genefinding/rnaz/herpes/x/
H A Drnaz.out17 Prediction: RNA
49 Prediction: RNA
79 Prediction: RNA
108 Prediction: RNA
137 Prediction: RNA
166 Prediction: RNA
195 Prediction: RNA
224 Prediction: RNA
253 Prediction: RNA
282 Prediction: RNA
[all …]
H A Drnaz_random.out17 Prediction: RNA
46 Prediction: RNA
75 Prediction: RNA
104 Prediction: RNA
133 Prediction: RNA
162 Prediction: RNA
191 Prediction: RNA
220 Prediction: RNA
249 Prediction: RNA
307 Prediction: RNA
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/RNA-Tutorial/Data/rnaz/herpes/x/
H A Drnaz.out17 Prediction: RNA
49 Prediction: RNA
79 Prediction: RNA
108 Prediction: RNA
137 Prediction: RNA
166 Prediction: RNA
195 Prediction: RNA
224 Prediction: RNA
253 Prediction: RNA
282 Prediction: RNA
[all …]
H A Drnaz_random.out17 Prediction: RNA
46 Prediction: RNA
75 Prediction: RNA
104 Prediction: RNA
133 Prediction: RNA
162 Prediction: RNA
191 Prediction: RNA
220 Prediction: RNA
249 Prediction: RNA
307 Prediction: RNA
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Perl/
H A DMakefile.am7 perlext_LTLIBRARIES = RNA.la
31 RNA/Benchmark.pm \
32 RNA/Design.pm \
33 RNA/Files.pm \
34 RNA/Reliability.pm \
35 RNA/Utils.pm \
36 RNA/Params.pm
71 RNA.pod \
73 RNA/t/Design.t \
103 auto/RNA/RNA$(PERL_SO): RNA.la
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/interfaces/Python/
H A DMakefile.am19 pkgpy2execdir = $(py2execdir)/RNA
22 pkgpy2exec_DATA = RNA/__init__.py
86 $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
87 cp `test -f RNA.py || echo '$(srcdir)/'`RNA.py RNA/__init__.py
89 RNA/_RNA$(PYTHON2_SO): _RNA.la
90 $(AM_V_GEN)( test -d RNA || $(MKDIR_P) RNA ) && \
96 RNA/_RNA$(PYTHON2_SO) \
97 RNA/__init__.py \
98 RNA/__init__.pyc
103 -rm -rf RNA
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/examples/Python/
H A Dmaximum_matching.py1 import RNA
6 RNA.cvar.dangles = 0
10 mm_data = { 'dummy': RNA.fold_compound(seq1), 'params': RNA.param() }
20 RNA.DECOMP_ML_ML_ML: lambda i, j, k, l, f, p: 0,
21 RNA.DECOMP_ML_UP: lambda i, j, k, l, f, p: - (j - i + 1) * p.MLbase,
22 RNA.DECOMP_EXT_STEM: lambda i, j, k, l, f, p: - f.E_ext_loop(k, l),
23 RNA.DECOMP_EXT_EXT: lambda i, j, k, l, f, p: 0,
24 RNA.DECOMP_EXT_STEM_EXT: lambda i, j, k, l, f, p: - f.E_ext_loop(i, k),
25 RNA.DECOMP_EXT_EXT_STEM: lambda i, j, k, l, f, p: - f.E_ext_loop(l, j),
26 RNA.DECOMP_EXT_EXT_STEM1: lambda i, j, k, l, f, p: - f.E_ext_loop(l, j-1),
[all …]
/dports/biology/viennarna/ViennaRNA-2.4.18/examples/Perl5/
H A Dmaximum_matching.pl4 use RNA;
9 $RNA::dangles = 0;
13 my %mm_data = ( 'dummy' => new RNA::fold_compound($seq1), 'params' => new RNA::param() );
17 …RNA::DECOMP_PAIR_HP => sub { my ($i, $j, $k, $l, $f, $p) = @_; return - $f->eval_hp_loop($i, $j) -…
21 RNA::DECOMP_ML_ML_ML => sub { my ($i, $j, $k, $l, $f, $p) = @_; return 0},
24 …RNA::DECOMP_ML_UP => sub { my ($i, $j, $k, $l, $f, $p) = @_; return - ($j - $i + 1) * $p->{MLbase…
25 … RNA::DECOMP_EXT_STEM => sub { my ($i, $j, $k, $l, $f, $p) = @_; return - $f->E_ext_loop($k, $l)},
26 RNA::DECOMP_EXT_EXT => sub { my ($i, $j, $k, $l, $f, $p) = @_; return 0},
27 …RNA::DECOMP_EXT_STEM_EXT => sub { my ($i, $j, $k, $l, $f, $p) = @_; return - $f->E_ext_loop($i, $…
28 …RNA::DECOMP_EXT_EXT_STEM => sub { my ($i, $j, $k, $l, $f, $p) = @_; return : - $f->E_ext_loop($l, …
[all …]

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