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/dports/biology/fluctuate/fluctuate1.4/
H A Dgetdata.c324 dna->freqr = dna->freqa + dna->freqg; in getbasefreqs()
325 dna->freqy = dna->freqc + dna->freqt; in getbasefreqs()
326 dna->freqar = dna->freqa / dna->freqr; in getbasefreqs()
327 dna->freqcy = dna->freqc / dna->freqy; in getbasefreqs()
328 dna->freqgr = dna->freqg / dna->freqr; in getbasefreqs()
329 dna->freqty = dna->freqt / dna->freqy; in getbasefreqs()
332 dna->freqa * dna->freqg - dna->freqc * dna->freqt; in getbasefreqs()
333 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasefreqs()
336 dna->ttratio = dna->xi / dna->xv; in getbasefreqs()
346 dna->fracchange = dna->xi * (2 * dna->freqa * dna->freqgr + in getbasefreqs()
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/test/data/
H A DMakefile.am3 dna.acedb dna.aln dna.asn1 dna.codata dna.embl dna.fasta \
4 dna.fitch dna.gcg dna.gcg8 dna.genbank dna.ig dna.m-acedb \
5 dna.m-codata dna.m-embl dna.m-fasta dna.m-fasta-long \
6 dna.m-ncbi dna.m-strider dna.msf dna.msf8 dna.ncbi \
7 dna.phylip dna.phylip3 dna.staden dna.strider dna.text \
15 aligna.dna alignapart.dna alignb.dna \
/dports/biology/recombine/recombine1.41/
H A Dgetdata.c1195 dna->freqr = dna->freqa + dna->freqg; in getbasednafreqs()
1196 dna->freqy = dna->freqc + dna->freqt; in getbasednafreqs()
1197 dna->freqar = dna->freqa / dna->freqr; in getbasednafreqs()
1198 dna->freqcy = dna->freqc / dna->freqy; in getbasednafreqs()
1199 dna->freqgr = dna->freqg / dna->freqr; in getbasednafreqs()
1200 dna->freqty = dna->freqt / dna->freqy; in getbasednafreqs()
1203 dna->freqa * dna->freqg - dna->freqc * dna->freqt; in getbasednafreqs()
1204 bb = dna->freqa * dna->freqgr + dna->freqc * dna->freqty; in getbasednafreqs()
1207 dna->ttratio = dna->xi / dna->xv; in getbasednafreqs()
1217 dna->fracchange = dna->xi * (2 * dna->freqa * dna->freqgr + in getbasednafreqs()
[all …]
/dports/biology/wise/wise2.4.1/wisecfg/
H A Dwise.211 !rrmDNA rrmdna.in dna
12 embl em.in dna
13 EMBL_Est est.in dna
15 EMBL_fun fun.in dna
16 EMBL_inv inv.in dna
17 EMBL_mam mam.in dna
18 EMBL_org org.in dna
20 EMBL_phg phg.in dna
21 EMBL_pln pln.in dna
22 EMBL_pri pri.in dna
[all …]
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_translate.py17 dna = Seq.Seq(s)
21 dna = Seq.Seq(s)
31 dna,
37 dna = Seq.Seq(s)
41 dna = Seq.Seq(s)
45 dna = Seq.Seq(s)
49 dna = Seq.Seq(s)
53 dna = Seq.Seq(s)
57 dna = Seq.Seq(s)
63 dna = Seq.Seq(s)
[all …]
/dports/biology/p5-Bio-Graphics/Bio-Graphics-2.40/lib/Bio/Graphics/Glyph/
H A Ddna.pm1 package Bio::Graphics::Glyph::dna;
90 $dna = $dna->seq if ref($dna) and $dna->can('seq'); # to catch Bio::PrimarySeqI objects
91 $dna or return;
94 $dna = $dna->seq if ref($dna) && $dna->can('seq');
113 my @bases = split '',$strand >= 0 ? $dna : $self->reversec($dna);
149 $dna = $self->reversec($dna) if $self->{flip};
175 my @dna = split '', $dna;
177 if ($dna[$i] eq 'G' or $dna[$i] eq 'C' or $dna[$i] eq 'g' or $dna[$i] eq 'c') {
178 $dna[$i] = 1;
180 $dna[$i] = 0;
[all …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/app/asnval/TestRes.asnval/tests/test1/test-cases/
H A DSQD-1475-sqn.golden1464 …lid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig732: delta, dna len= 1882
1930 …alid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig964: delta, dna len= 713
2078 …lid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig1037: delta, dna len= 757
2948 …lid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig1470: delta, dna len= 693
2986 …lid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig1487: delta, dna len= 866
3336 …lid [SEQ_INST.TerminalGap] Gap at beginning of sequence BIOSEQ: lcl|contig1661: delta, dna len= 811
5601 WARNING: valid [SEQ_INST.TerminalNs] N at beginning of sequence BIOSEQ: lcl|contig2791: raw, dna le…
8106 WARNING: valid [SEQ_INST.TerminalNs] N at beginning of sequence BIOSEQ: lcl|contig4037: delta, dna …
8693 WARNING: valid [SEQ_INST.TerminalNs] N at beginning of sequence BIOSEQ: lcl|contig4330: raw, dna le…
8940 WARNING: valid [SEQ_INST.TerminalNs] N at beginning of sequence BIOSEQ: lcl|contig4453: delta, dna …
[all …]
H A DALACA30300-sqn.golden1 …s, but labels differ FEATURE: Gene: ND4 [lcl|ALACA30300:<1-672] [lcl|ALACA30300: raw, dna len= 672]
4 … but labels differ FEATURE: Gene: ND4 [lcl|ALLEW121106:<1-672] [lcl|ALLEW121106: raw, dna len= 672]
7 …s, but labels differ FEATURE: Gene: ND4 [lcl|ALLOA59698:<1-672] [lcl|ALLOA59698: raw, dna len= 672]
10 … but labels differ FEATURE: Gene: ND4 [lcl|ANGUW104349:<1-672] [lcl|ANGUW104349: raw, dna len= 672]
13 …als, but labels differ FEATURE: Gene: ND4 [lcl|ANIASP040:<1-672] [lcl|ANIASP040: raw, dna len= 672]
16 …als, but labels differ FEATURE: Gene: ND4 [lcl|ARANSP006:<1-672] [lcl|ARANSP006: raw, dna len= 672]
19 …als, but labels differ FEATURE: Gene: ND4 [lcl|ARCASP007:<1-658] [lcl|ARCASP007: raw, dna len= 658]
23 …s, but labels differ FEATURE: Gene: ND4 [lcl|ARNHA29158:<1-672] [lcl|ARNHA29158: raw, dna len= 672]
26 …s, but labels differ FEATURE: Gene: ND4 [lcl|ASTAA09043:<1-672] [lcl|ASTAA09043: raw, dna len= 672]
41 …als, but labels differ FEATURE: Gene: ND4 [lcl|COGGSP075:<1-602] [lcl|COGGSP075: raw, dna len= 602]
[all …]
H A Dasnfail_all-sqn.golden1 …licate feature FEATURE: Gene: rbcL [lcl|accJF701686:<1->1282] [lcl|accJF701686: raw, dna len= 1282]
18 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|AL_2:<1->1282] [lcl|AL_2: raw, dna len= 1282]
50 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|IT_2:<1->1282] [lcl|IT_2: raw, dna len= 1282]
54 …tentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|FR-R1:<1->1279] [lcl|FR-R1: raw, dna len= 1279]
94 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|TN-H:<1->1282] [lcl|TN-H: raw, dna len= 1282]
106 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|MI_2:<1->1282] [lcl|MI_2: raw, dna len= 1282]
110 …eatContentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|MN:<1->1282] [lcl|MN: raw, dna len= 1282]
122 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|NC-5:<1->1282] [lcl|NC-5: raw, dna len= 1282]
130 …ontentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|IN-2:<1->1282] [lcl|IN-2: raw, dna len= 1282]
240 …tContentDup] Duplicate feature FEATURE: Gene: rbcL [lcl|EST:<1->1282] [lcl|EST: raw, dna len= 1282]
[all …]
/dports/textproc/weka/weka-3-8-5/data/
H A Dsoybean.arff69 % 14. leafspots-marg: w-s-marg,no-w-s-marg,dna,?.
70 % 15. leafspot-size: lt-1/8,gt-1/8,dna,?.
77 % 22. canker-lesion: dna,brown,dk-brown-blk,tan,?.
83 % 28. fruit-pods: norm,diseased,few-present,dna,?.
108 @ATTRIBUTE leafspot-size {lt-1/8,gt-1/8,dna}
135 …abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, above-sec-nde, dna, present, firm-a…
136 …abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, above-sec-nde, dna, present, firm-a…
154 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
161 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
169 … abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, dk-brown-blk, absent, …
[all …]
/dports/math/p5-AI-DecisionTree/AI-DecisionTree-0.11/t/
H A D02-noisy.t104 … abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, dk-brown-blk, absent, …
117 …scattered, ?, ?, ?, abnorm, abnorm, absent, dna, dna, absent, present, ?, abnorm, ?, ?, ?, ?, ?, ?…
126 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
145 … abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, dk-brown-blk, absent, …
165 …scattered, ?, ?, ?, abnorm, abnorm, absent, dna, dna, absent, present, ?, abnorm, ?, ?, ?, ?, ?, ?…
200 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
277 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
306 …m, norm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, brown, absent, firm-an…
351 … abnorm, absent, dna, dna, absent, absent, absent, abnorm, yes, below-soil, dk-brown-blk, absent, …
371 …ole-field, ?, ?, ?, abnorm, abnorm, absent, dna, dna, absent, present, ?, abnorm, ?, ?, ?, ?, ?, ?…
[all …]
/dports/biology/wise/wise2.4.1/src/models/
H A Dgenedisplay.c138 if( strlen(dna->name) > name ) { in protdna_btc_display()
140 strncpy(dnaname,dna->name,name); in protdna_btc_display()
143 strcpy(dnaname,dna->name); in protdna_btc_display()
146 if( dna->offset > dna->end ) { in protdna_btc_display()
225 …tch(btp,'-',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq… in protdna_btc_display()
228 …tch(btp,'~',' ',alc->alu[1]->start+1,aminoacid_from_seq(ct,dna->seq+alc->alu[1]->start+1),dna->seq… in protdna_btc_display()
327 dnatemp[0] = tolower((int)dna->seq[alc->alu[1]->start+1]); in protdna_btc_display()
346 …write_intron_desc(btp,alc->alu[1]->start+1+d_phase+dna->offset,alc_temp->alu[1]->start+3+dna->offs… in protdna_btc_display()
477 if( dna->offset < dna->end ) in write_name_start_stuff()
478 sprintf(buffer,"%d",alc->alu[1]->start+1+dna->offset); in write_name_start_stuff()
[all …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/
H A DTrack.java312 writer.write("# line attributes: start="+dna.getStart()+ in writeHeader()
313 " end="+dna.getEnd()+" " + in writeHeader()
314 "line_size="+dna.getLineSize()+ in writeHeader()
315 " circular="+dna.isCircular()); in writeHeader()
317 if(!dna.isCircular()) in writeHeader()
318 writer.write(" line_height="+dna.getLineHeight()+ in writeHeader()
319 " bases_per_line="+dna.getBasesPerLine()); in writeHeader()
325 Vector<Graph> userGraphs = dna.getUserGraphs(); in writeHeader()
329 if(dna.containsGraph(userGraph)) in writeHeader()
337 if(dna.getGcGraph() != null && dna.containsGraph(dna.getGcGraph())) in writeHeader()
[all …]
H A DWizard.java198 dna.setStart(s); in Wizard()
201 dna.setEnd(s); in Wizard()
224 if(dna == null) in loadTemplate()
241 if(dna == null) in loadTemplate()
449 dna.add(gcGraph); in loadGraphs()
450 dna.repaint(); in loadGraphs()
451 dna.revalidate(); in loadGraphs()
465 dna.repaint(); in loadGraphs()
466 dna.revalidate(); in loadGraphs()
490 dna.repaint(); in loadGraphs()
[all …]
/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/seq/
H A D_twobit.pyx29 cdef char * dna
38 dna = PyBytes_AsString( dna_py )
58 dna = dna + 1
70 dna = dna + partCount
78 dna[3] = valToNt[partial&3];
80 dna[2] = valToNt[partial&3];
82 dna[1] = valToNt[partial&3];
84 dna[0] = valToNt[partial&3];
85 dna = dna + 4;
97 dna = PyBytes_AsString( dna_py )
[all …]
/dports/biology/ugene/ugene-40.1/data/cmdline/
H A Dgenerate-dna.uwl8 generate-dna {
9 type:generate-dna;
26 generate-dna.algorithm {
30 generate-dna.content {
34 generate-dna.count {
38 generate-dna.length {
42 generate-dna.percent-a {
46 generate-dna.percent-c {
50 generate-dna.percent-g {
62 generate-dna.seed {
[all …]
/dports/biology/emboss/EMBOSS-6.6.0/jemboss/org/emboss/jemboss/draw/
H A DWizard.java41 private DNADraw dna = null; field in Wizard
59 dna = new DNADraw(dnaRead.getBlock(), in Wizard()
70 dna = new DNADraw(); in Wizard()
73 dna = dna_current; in Wizard()
84 gm = new GeneticMarker(dna,block); in Wizard()
143 dna.setGeneticMarker(block); in Wizard()
145 dna.setLineAttributes(la.getLineAttr()); in Wizard()
146 dna.setStartTick(tk.getStartTick()); in Wizard()
151 dna.setStart(s); in Wizard()
154 dna.setEnd(s); in Wizard()
[all …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/circular/digest/
H A DUtils.java92 DNADraw dna = new DNADraw(); in createDNADrawFromReportDetails() local
93 dna.setArtemisEntryGroup(entryGroup); in createDNADrawFromReportDetails()
101 dna.setLineAttributes(lineAttr); in createDNADrawFromReportDetails()
123 dna.setMinorTickInterval(tick); in createDNADrawFromReportDetails()
124 dna.setTickInterval(tick); in createDNADrawFromReportDetails()
125 dna.setOpaque(true); in createDNADrawFromReportDetails()
194 dna.setGeneticMarker(new Vector()); in createDNADrawFromReportDetails()
198 trackManager = new TrackManager(dna); in createDNADrawFromReportDetails()
199 dna.setTrackManager(trackManager); in createDNADrawFromReportDetails()
203 return dna; in createDNADrawFromReportDetails()
[all …]
/dports/graphics/blender/blender-2.91.0/doc/blender_file_format/
H A DREADME8 This creates a temporary dna.blend to be inspected and it produces two new files:
10 * dna.html: the list of all the structures saved in a blend file with the blender2.5
12 the dna.html file will also show which svn revision the html refers to.
13 * dna.css: the css for the html above
21 --dna-keep-blend: doesn't delete the produced blend file DNA export to html
22 --dna-debug: sets the logging level to DEBUG (lots of additional info)
23 --dna-versioned saves version information in the html and blend filenames
24 --dna-overwrite-css overwrite dna.css, useful when modifying css in the script
27 …lender2.5 --background -noaudio --python BlendFileDnaExporter_25.py -- --dna-keep-blend --dna-debug
/dports/devel/p5-B-C/B-C-1.57/ramblings/
H A Dblogs-optimizing-1.md1 regex-dna - regex matching fast enough
40 $ perlcc -O3 -o regex-dna-c -S t/regex-dna.pl
64 $ perlcc -O -o regex-dna-cc t/regex-dna.pl
73 $ perlcc -O3 -v5 -S -oregex-dna-c -v5 t/regex-dna.pl
128 $ perlcc -O3 -Uwarnings -Uwarnings::register -S -oregex-dna-c1 t/regex-dna.pl
129 $ wc regex-dna-c.c
131 $ wc regex-dna-c1.c
132 1201 7488 57236 regex-dna-c1.c
136 $ perlcc -O -O2 -Uwarnings -Uwarnings::register -S -oregex-dna-cc1 t/regex-dna.pl
158 $ perl -S perlcc -O3 -Uwarnings -Uwarnings::register -S -oregex-dna-c1 t/regex-dna.pl
[all …]
/dports/biology/seaview/seaview/
H A Dviewasprots.cxx179 while(memcmp(dna, "---", 3) == 0) dna += 3; in back_translate_with_gaps()
185 if(*dna == '@') *dna = '-'; in back_translate_with_gaps()
186 if(*(dna + 1) == '@') *(dna + 1) = '-'; in back_translate_with_gaps()
187 if(*(dna + 2) == '@') *(dna + 2) = '-'; in back_translate_with_gaps()
188 memcpy(pd, dna, 3); in back_translate_with_gaps()
190 dna += 3; in back_translate_with_gaps()
194 while(memcmp(dna, "---", 3) == 0) dna += 3; in back_translate_with_gaps()
195 if (*dna != 0 && *dna != '-') {//if a partial codon remains at end in back_translate_with_gaps()
198 q = dna + strlen(dna); in back_translate_with_gaps()
201 l = ld+(q-dna)+5; in back_translate_with_gaps()
[all …]
/dports/biology/p5-BioPerl/BioPerl-1.7.7/examples/
H A Dlongorf.pl40 my $dna=Bio::Seq->new(-seq => $_[0]);
41 my %strand=('+'=>$dna->seq,
42 '-'=>$dna->revcom->seq);
61 push @ends,($dna->length-2,$dna->length-1,$dna->length);
90 while (my $dna = $seqio->next_seq) {
92 ($length,$start,$end,$direction,$sequence)=longestORF($dna->seq,$notstrict);
94 print $dna->display_id," ",$dna->desc,": ";
/dports/biology/p5-Bio-Das-Lite/Bio-Das-Lite-2.11/t/
H A D40-dna.t4 # Id: $Id: 40-dna.t 53 2011-05-06 10:18:40Z zerojinx $
5 # Source: $Source: /var/lib/cvsd/cvsroot/Bio-DasLite/Bio-DasLite/t/40-dna.t,v $
6 # $HeadURL: https://bio-das-lite.svn.sourceforge.net/svnroot/bio-das-lite/trunk/t/40-dna.t $
8 package dna;
18 'filedata' => 't/data/dna.xml',
21 my $result = $das->dna();
23 'foo/dna' => [
27 …'dna' => 'atttcttggcgtaaataagagtctcaatgagactctcagaagaaaattgataaatattattaatgatataataataatcttgttgatc…
/dports/biology/p5-AcePerl/AcePerl-1.92/t/
H A Dsequence.t46 test(11,length($zk154s->dna)==100,"dna() failure");
54 test(16,length($zk154r->dna) == 100,"dna() failure");
83 test(28,length($features[0]->dna) == 99,'dna() error');
94 test(35,length($features[0]->dna) == 57,'dna() error');
99 test(36,substr($zk154->dna,1,10) eq $zk154_3->dna,'offset error');
126 test(49,$exons1[0]->dna eq $exons2[0]->dna,"absolute and relative exons don't match");
134 test(53,$exons1[-1]->dna eq $exons2[0]->dna,"absolute and relative exons don't match (1)");
135 test(54,$exons1[0]->dna eq $exons2[-1]->dna,"absolute and relative exons don't match (2)");
/dports/biology/stringtie/stringtie-2.1.1/gclib/
H A Dcodons.cpp92 char translateCodon(const char* dna) { //returns the aminoacid code for the 1st codon at dna in translateCodon() argument
93 if (dna==NULL) return 0; in translateCodon()
94 if (dna[0]==0 || dna[1]==0 || dna[2]==0) return 0; in translateCodon()
95 return codonTable[packCodon(toupper(dna[0]),toupper(dna[1]),toupper(dna[2]))]; in translateCodon()

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