/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_motifs.py | 613 motif = record[0] 669 motif = record[1] 765 motif = record[0] 1005 motif = record[1] 1197 motif = record[0] 1372 motif = record[1] 1536 motif = record[0] 1540 self.assertEqual(motif.length, 19) 2098 motif = record[0] 2151 motif = record[1] [all …]
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/dports/biology/viennarna/ViennaRNA-2.4.18/tests/RNAfold/results/ |
H A D | rnafold.small.cmds.gold | 4 ud motif 0 detected in MFE structure: [54:56] 5 ud motif 0 detected in MFE structure: [64:66] 8 ud motif 0 detected in centroid structure: [54:56] 10 ud motif 0 detected in MEA structure: [54:56] 11 ud motif 0 detected in MEA structure: [64:66] 16 ud motif 0 detected in MFE structure: [16:18] 21 ud motif 0 detected in MEA structure: [16:18] 33 ud motif 0 detected in MFE structure: [6:8] 34 ud motif 0 detected in MFE structure: [76:78] 40 ud motif 0 detected in MEA structure: [6:8] [all …]
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/dports/math/oleo/oleo-1.99.16/po/ |
H A D | oleo.pot | 96 #: src/io-motif.c:722 100 #: src/io-motif.c:791 105 #: src/io-motif.c:946 src/io-motif.c:1111 109 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031 110 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955 111 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694 112 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747 121 #: src/io-motif.c:1436 src/io-motif.c:2927 178 #: src/io-motif.c:3060 src/io-motif.c:5933 217 #: src/io-motif.c:3312 src/io-motif.c:3347 [all …]
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H A D | en.po | 100 #: src/io-motif.c:722 105 #: src/io-motif.c:791 110 #: src/io-motif.c:946 src/io-motif.c:1111 114 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031 115 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955 116 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694 117 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747 126 #: src/io-motif.c:1436 src/io-motif.c:2927 185 #: src/io-motif.c:3060 src/io-motif.c:5933 228 #: src/io-motif.c:3312 src/io-motif.c:3347 [all …]
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H A D | fr.po | 100 #: src/io-motif.c:722 105 #: src/io-motif.c:791 110 #: src/io-motif.c:946 src/io-motif.c:1111 114 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031 115 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955 116 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694 117 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747 126 #: src/io-motif.c:1436 src/io-motif.c:2927 186 #: src/io-motif.c:3060 src/io-motif.c:5933 231 #: src/io-motif.c:3312 src/io-motif.c:3347 [all …]
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H A D | nl.po | 100 #: src/io-motif.c:722 105 #: src/io-motif.c:791 110 #: src/io-motif.c:946 src/io-motif.c:1111 116 #: src/io-motif.c:985 src/io-motif.c:1008 src/io-motif.c:1031 117 #: src/io-motif.c:1053 src/io-motif.c:1070 src/io-motif.c:1955 118 #: src/io-motif.c:3647 src/io-motif.c:3656 src/io-motif.c:3694 119 #: src/io-motif.c:3703 src/io-motif.c:3738 src/io-motif.c:3747 128 #: src/io-motif.c:1436 src/io-motif.c:2927 189 #: src/io-motif.c:3060 src/io-motif.c:5933 234 #: src/io-motif.c:3312 src/io-motif.c:3347 [all …]
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/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/motif/io/ |
H A D | transfac.py | 5 from bx.motif.pwm import FrequencyMatrix 58 for motif in self: 59 rval[getattr(motif, key)] = motif 103 motif = TransfacMotif() 120 setattr(motif, key, rest) 125 if not getattr(motif, key): 126 setattr(motif, key, []) 135 getattr(motif, key)[k] = v 173 if motif.id or motif.accession or motif.name: 174 return motif [all …]
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/dports/biology/py-biopython/biopython-1.79/Bio/motifs/ |
H A D | pfm.py | 21 return "\n".join(str(motif) for motif in self) 181 motif.name = motif_name 182 record.append(motif) 194 record.append(motif) 206 record.append(motif) 258 motif.name = motif_name 259 record.append(motif) 269 motif.name = motif_name 270 record.append(motif) 370 record.append(motif) [all …]
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H A D | clusterbuster.py | 19 return "\n".join(str(motif) for motif in self) 38 motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts) 39 motif.name = motif_name 40 record.append(motif) 59 motif = motifs.Motif(alphabet="GATC", counts=nucleotide_counts) 60 motif.name = motif_name 61 record.append(motif)
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H A D | meme.py | 122 for motif in self: 123 if motif.name == key: 124 return motif 176 motif = Motif(record.alphabet, instances) 177 motif.id = motif_tree.get("id") 178 motif.name = motif_tree.get("name") 179 motif.alt_id = motif_tree.get("alt") 180 motif.length = int(motif_tree.get("width")) 181 motif.num_occurrences = int(motif_tree.get("sites")) 182 motif.evalue = float(motif_tree.get("e_value")) [all …]
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H A D | minimal.py | 61 motif = motifs.Motif(alphabet=record.alphabet, counts=counts) 62 motif.background = record.background 63 motif.length = length 64 motif.num_occurrences = num_occurrences 65 motif.evalue = evalue 66 motif.name = name 67 record.append(motif) 87 for motif in self: 88 if motif.name == key: 89 return motif
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/dports/biology/emboss/EMBOSS-6.6.0/emboss/data/ |
H A D | Ememe.dat | 1 For each motif that it discovers in the training set, MEME prints the 7 the training set (`sites') of the motif. MEME numbers the motifs 20 the motif, the simplified motif shows the letter probabilities multiplied 36 the motif for database searches. For a motif to be useful for database 43 more than one motif since they can be combined in multiple motif 57 motif 2 in the sample output is: 64 motif. First, the most likely form of the motif can be read from the top 79 motif in BLOCKS format. 87 the motif sites in FASTA format instead of BLOCKS format. 93 by converting the motif letter-probability matrix into a [all …]
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/dports/biology/vt/vt-0.57721/ |
H A D | vntr.cpp | 38 motif.clear(); in clear() 116 motif==vntr.motif); in equals() 142 std::string cmotif = motif; in canonicalize2() 145 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize2() 169 std::string cmotif = motif; in canonicalize() 171 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize() 196 if (smotif == motif) in is_periodic() 208 bool VNTR::is_aperiodic(std::string& motif) in is_aperiodic() argument 214 if (smotif == motif) in is_aperiodic() 228 return get_basis(const_cast<char*>(motif.c_str()), motif.size()); in get_basis() [all …]
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H A D | candidate_motif_picker.cpp | 160 char *motif = NULL; in set_motif_from_info_field() local 164 vntr.motif.assign(motif); in set_motif_from_info_field() 165 vntr.basis = vntr.get_basis(vntr.motif); in set_motif_from_info_field() 166 vntr.mlen = vntr.motif.size(); in set_motif_from_info_field() 168 free(motif); in set_motif_from_info_field() 172 vntr.motif = ""; in set_motif_from_info_field() 424 variant.vntr.motif = cm.motif; in next_motif() 454 for (uint32_t i=0; i<motif.size(); ++i) in is_in_indel_fragment() 456 std::string shifted_motif = motif.substr(i) + motif.substr(0,i); in is_in_indel_fragment() 477 for (uint32_t i=0; i<motif.size(); ++i) in choose_repeat_unit() [all …]
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H A D | flank_detector.cpp | 347 std::string best_motif = motif; in choose_5prime_repeat_unit() 350 int32_t mlen = motif.size(); in choose_5prime_repeat_unit() 375 return motif; in choose_5prime_repeat_unit() 385 std::string best_motif = motif; in choose_fuzzy_5prime_repeat_unit() 388 int32_t mlen = motif.size(); in choose_fuzzy_5prime_repeat_unit() 426 int32_t mlen = motif.size(); in choose_3prime_repeat_unit() 442 return motif; in choose_3prime_repeat_unit() 452 std::string best_motif = motif; in choose_fuzzy_3prime_repeat_unit() 455 int32_t mlen = motif.size(); in choose_fuzzy_3prime_repeat_unit() 538 int32_t mlen = motif.size(); in polish_repeat_tract_ends() [all …]
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H A D | compute_rl_dist.cpp | 95 std::string cmotif = motif; in canonicalize() 97 for (uint32_t i=0; i<motif.size(); ++i) in canonicalize() 99 std::string shifted_motif = motif.substr(i) + motif.substr(0,i); in canonicalize() 115 std::string motif = canonicalize(del); in update_stats() local 117 if (stats.find(motif)==stats.end()) in update_stats() 120 stats[motif] = v; in update_stats() 121 stats[motif].resize(rl, 0); in update_stats() 123 ++stats[motif][rl-1]; in update_stats() 134 stats[motif].push_back(0); in update_stats() 151 std::string motif = i->first; in print_dist() local [all …]
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/dports/print/lilypond-devel/lilypond-2.23.5/input/regression/ |
H A D | modal-transforms.ly | 4 \modalInversion work for an octatonic motif." 11 motif = { 21 \motif 22 \modalTranspose c' f' \cOctatonicScale \motif 23 \retrograde \motif 25 \inversion aes' b' \motif 28 s1-"Octatonic motif" | 29 s1-"motif transposed from c to f" | 30 s1-"motif in retrograde" | 31 s1-"motif inverted around aes to b" | [all …]
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/dports/print/lilypond/lilypond-2.22.1/input/regression/ |
H A D | modal-transforms.ly | 4 \modalInversion work for an octatonic motif." 11 motif = { 21 \motif 22 \modalTranspose c' f' \cOctatonicScale \motif 23 \retrograde \motif 25 \inversion aes' b' \motif 28 s1-"Octatonic motif" | 29 s1-"motif transposed from c to f" | 30 s1-"motif in retrograde" | 31 s1-"motif inverted around aes to b" | [all …]
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/dports/science/py-pymatgen/pymatgen-2022.0.15/pymatgen/analysis/magnetism/ |
H A D | jahnteller.py | 151 motif = "oct" 154 motif = "tet" 157 motif = "unknown" 160 if motif in ["oct", "tet"]: 162 motif = cast(Literal["oct", "tet"], motif) # mypy needs help 193 "motif": motif, 404 if motif in self.spin_configs: 431 if motif == "oct": 438 elif motif == "tet": 463 mu_so_high = JahnTellerAnalyzer.mu_so(species, motif=motif, spin_state="high") [all …]
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/dports/converters/wkhtmltopdf/qt-5db36ec/doc/src/widgets-and-layouts/ |
H A D | gallery-motif.qdoc | 29 \page gallery-motif.html 50 \o \image motif-checkbox.png 60 \o \image motif-groupbox.png 64 \o \image motif-frame.png 66 \o \image motif-toolbox.png 74 \o \image motif-listview.png 76 \o \image motif-treeview.png 89 \o \image motif-label.png 111 \o \image motif-slider.png 115 \o \image motif-spinbox.png [all …]
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/dports/biology/emboss/EMBOSS-6.6.0/doc/programs/master/emboss/apps/inc/ |
H A D | epestfind.output | 12 Potential PEST motif with 34 amino acids between position 238 and 273. 18 Potential PEST motif with 14 amino acids between position 206 and 221. 24 Poor PEST motif with 18 amino acids between position 363 and 382. 28 Poor PEST motif with 17 amino acids between position 409 and 427. 32 Poor PEST motif with 19 amino acids between position 22 and 42. 36 Poor PEST motif with 10 amino acids between position 440 and 451. 40 Poor PEST motif with 13 amino acids between position 279 and 293. 44 Poor PEST motif with 13 amino acids between position 349 and 363. 48 Invalid PEST motif with 20 amino acids between position 1 and 22. 51 Invalid PEST motif with 13 amino acids between position 43 and 57. [all …]
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/dports/lang/elk/elk-3.99.8/examples/ |
H A D | Makefile.am | 90 motif/scroll-bar.scm \ 91 motif/radio.scm \ 93 motif/drawing-area.scm \ 94 motif/radio-stuff.scm \ 95 motif/popup-menu.scm \ 96 motif/pulldown-menu.scm \ 97 motif/main-window.scm \ 98 motif/menu-stuff.scm \ 99 motif/vcr.scm \ 100 motif/option-menu.scm \ [all …]
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/dports/biology/py-biopython/biopython-1.79/Bio/motifs/jaspar/ |
H A D | __init__.py | 145 for motif in self: 146 dic[motif.matrix_id] = motif 175 motif = motifs[0] 176 counts = motif.counts 216 motif.mask = "*" * motif.length 218 record.append(motif) 243 motif.mask = "*" * motif.length 245 record.append(motif) 329 alphabet = motif.alphabet 330 background = motif.background [all …]
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H A D | db.py | 139 motif = None 143 return motif 286 num_sites = sum(motif.counts[nt][0] for nt in motif.alphabet) 290 record.append(motif) 389 motif.species = tax_ids 401 motif.acc = accs 410 motif.tf_class = val 418 motif.pazar_id = val 420 motif.medline = val 422 motif.comment = val [all …]
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/dports/biology/py-biopython/biopython-1.79/Doc/Tutorial/ |
H A D | chapter_motifs.tex | 502 >>> motif.pseudocounts = motifs.jaspar.calculate_pseudocounts(motif) 626 >>> motif = record[0] 639 >>> motif.length 644 >>> motif.name 646 >>> motif.id 766 >>> motif["ID"] # Using motif as a dictionary 1017 in the motif: 1285 >>> print(motif.pwm) 1324 >>> print(motif.pwm) 1400 >>> print("%f" % motif.pssm.mean(motif.background)) [all …]
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