/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Search/HSP/ |
H A D | PSLHSP.pm | 120 my ($self,$seqtype,$blocks) = @_; 121 if( ! defined $seqtype ) { $seqtype = 'query' } 122 $seqtype = lc($seqtype); 123 $seqtype = 'hit' if $seqtype eq 'sbjct'; 124 if( $seqtype !~ /query|hit/i ) { 129 return $self->{'_gap_blocks'}->{$seqtype}; 131 return $self->{'_gap_blocks'}->{$seqtype} = $blocks;
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_UniGene.py | 980 self.assertEqual(record.sequence[0].seqtype, "mRNA") 984 self.assertEqual(record.sequence[1].seqtype, "mRNA") 988 self.assertEqual(record.sequence[2].seqtype, "mRNA") 992 self.assertEqual(record.sequence[3].seqtype, "mRNA") 996 self.assertEqual(record.sequence[4].seqtype, "mRNA") 1000 self.assertEqual(record.sequence[5].seqtype, "mRNA") 1006 self.assertEqual(record.sequence[6].seqtype, "EST") 1013 self.assertEqual(record.sequence[7].seqtype, "EST") 1019 self.assertEqual(record.sequence[8].seqtype, "EST") 1026 self.assertEqual(record.sequence[9].seqtype, "EST") [all …]
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/dports/emulators/mess/mame-mame0226/src/frontend/mame/ui/ |
H A D | inputmap.cpp | 84 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in populate() local 89 item.seqtype = seqtype; in populate() 90 item.seq = machine().ioport().type_seq(entry.type(), entry.player(), seqtype); in populate() 91 item.defseq = &entry.defseq(seqtype); in populate() 110 item.seq = machine().ioport().type_seq(entry.type(), entry.player(), item.seqtype); in populate() 155 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in populate() local 160 item.seqtype = seqtype; in populate() 161 item.seq = field.seq(seqtype); in populate() 162 item.defseq = &field.defseq(seqtype); in populate() 217 item.seq = field.seq(item.seqtype); in populate() [all …]
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/dports/emulators/mame/mame-mame0226/src/frontend/mame/ui/ |
H A D | inputmap.cpp | 84 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in populate() local 89 item.seqtype = seqtype; in populate() 90 item.seq = machine().ioport().type_seq(entry.type(), entry.player(), seqtype); in populate() 91 item.defseq = &entry.defseq(seqtype); in populate() 110 item.seq = machine().ioport().type_seq(entry.type(), entry.player(), item.seqtype); in populate() 155 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in populate() local 160 item.seqtype = seqtype; in populate() 161 item.seq = field.seq(seqtype); in populate() 162 item.defseq = &field.defseq(seqtype); in populate() 217 item.seq = field.seq(item.seqtype); in populate() [all …]
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/ |
H A D | concat_alg.py | 74 self.seqtype = seqtype 79 if seqtype == "aa": 81 elif seqtype == "nt": 95 job = Msf(set(co), set(), seqtype = self.seqtype) 122 alg_seqtypes.add(job.seqtype) 133 clean_alg_seqtypes.add(job.seqtype) 156 seqtype = seqtypes.pop() 158 log.warning("Using %s concatenated alignment" %seqtype) 160 if seqtype == "aa": 162 elif seqtype == "nt": [all …]
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H A D | iqtree.py | 20 seqtype, conf, confname, parts_id=None): argument 29 base_args["-st"] = "AA" if seqtype == "aa" else "DNA" 32 if seqtype == "aa" or "aa" not in GLOBALS["seqtypes"]: 42 elif seqtype == "aa": 44 elif seqtype == "nt": 52 self.seqtype = seqtype
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H A D | phyml.py | 84 seqtype, conf, confname, parts_id=None): argument 113 conf[confname]["-f"] = "m" if seqtype == "nt" else "e" 115 conf[confname]["-f"] = '0.25,0.25,0.25,0.25' if seqtype == "nt" else "m" 118 if seqtype == "nt": 122 model = conf[confname]["_aa_model"] if seqtype == "aa" else conf[confname]["_nt_model"] 139 self.seqtype = seqtype 147 args["--datatype"] = self.seqtype
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H A D | fasttree.py | 55 def __init__(self, nodeid, alg_file, constrain_id, model, seqtype, argument 66 self.seqtype = seqtype 76 if self.seqtype == "nt": 78 elif self.seqtype == "aa": 81 raise ValueError("Unknown seqtype %s" %self.seqtype)
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H A D | raxml.py | 59 seqtype, conf, confname, parts_id=None): argument 62 model_string = "PROT" if seqtype == "aa" else "GTR" 66 if seqtype == "nt" and basemodel != "GTR": 77 if seqtype == "aa": 80 if seqtype == "aa": 92 if seqtype == "aa": 97 if "F" in conf[confname]["_model_suffix"] and seqtype == "aa": 102 if seqtype == "aa": 140 self.seqtype = seqtype 198 "-d": self.seqtype,
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H A D | meta_aligner.py | 67 def __init__(self, nodeid, seqtype, all_alg_files, conf, confname, parent_ids): argument 79 self.seqtype = seqtype 113 def __init__(self, nodeid, multiseq_file, seqtype, conf, confname): argument 120 self.seqtype = seqtype 160 task1 = _aligner(self.nodeid, self.multiseq_file, self.seqtype, 169 self.seqtype, self.conf, aligner_name) 186 mcoffee_task = MCoffee(self.nodeid, self.seqtype, all_alg_names,
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H A D | msf.py | 55 def __init__(self, target_seqs, out_seqs, seqtype): argument 70 self.seqtype = seqtype 83 fasta = '\n'.join([">%s\n%s" % (n, db.get_seq(n, self.seqtype))
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/dports/biology/mafft/mafft-7.267-without-extensions/core/ |
H A D | mafft.tmpl | 193 seqtype=" " 473 seqtype=" -D " 475 seqtype=" -P " 610 seqtype="-P" 1829 "$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1 1900 "$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile 1903 "$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile 1936 "$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1 1948 …"$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1 # yari… 1985 "$prefix/replaceu" $seqtype -i instr -o 0 > clean 2>>"$progressfile" || exit 1 [all …]
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/dports/emulators/mess/mame-mame0226/src/emu/ |
H A D | ioport.cpp | 631 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in ioport_field() local 883 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in get_user_settings() local 884 settings.seq[seqtype] = seq(seqtype); in get_user_settings() 914 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in set_user_settings() local 920 m_live->seq[seqtype] = settings.seq[seqtype]; in set_user_settings() 1345 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in ioport_field_live() local 2094 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in load_config() local 2122 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in load_config() local 2123 entry.defseq(seqtype) = entry.seq(seqtype); in load_config() 2242 entry.set_seq(seqtype, newseq[seqtype]); in load_default_config() [all …]
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/dports/emulators/mame/mame-mame0226/src/emu/ |
H A D | ioport.cpp | 631 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in ioport_field() local 883 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in get_user_settings() local 884 settings.seq[seqtype] = seq(seqtype); in get_user_settings() 914 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in set_user_settings() local 920 m_live->seq[seqtype] = settings.seq[seqtype]; in set_user_settings() 1345 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in ioport_field_live() local 2094 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in load_config() local 2122 for (input_seq_type seqtype = SEQ_TYPE_STANDARD; seqtype < SEQ_TYPE_TOTAL; ++seqtype) in load_config() local 2123 entry.defseq(seqtype) = entry.seq(seqtype); in load_config() 2242 entry.set_seq(seqtype, newseq[seqtype]); in load_default_config() [all …]
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/ |
H A D | seqio.py | 54 def load_sequences(args, seqtype, target_seqs, target_species, cached_seqs): argument 55 seqfile = getattr(args, "%s_seed_file" %seqtype) 59 log.log(28, "Reading %s sequences from %s...", seqtype, seqfile) 69 if seqtype == "aa": 130 db.add_seq(seqid, seq, seqtype) 186 for seqtype in GLOBALS["seqtypes"]: 187 missing_seq = target_seqs - set(seq2seq[seqtype].keys()) 189 error += "\nThe following %s sequences are missing:\n" %seqtype 193 for seqtype in GLOBALS["seqtypes"]: 194 if seq2unknown[seqtype]: [all …]
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/workflow/ |
H A D | genetree.py | 99 tree_seqtype=task.seqtype, 215 seqtype = task.seqtype 265 seqtype, conf, alignerconf) 269 seqtype, conf, alignerconf) 350 if seqtype == "aa" and \ 380 seqtype = "nt" 395 None, seqtype, 408 model, seqtype, 411 if task.seqtype != seqtype: 416 treemerge_task = splitterclass(nodeid, seqtype, [all …]
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/dports/biology/clustal-omega/clustal-omega-1.2.4/src/clustal/ |
H A D | seq.c | 507 prMSeq->seqtype = SEQTYPE_DNA; in ReadSequences() 510 prMSeq->seqtype = SEQTYPE_RNA; in ReadSequences() 513 prMSeq->seqtype = SEQTYPE_PROTEIN; in ReadSequences() 516 prMSeq->seqtype = SEQTYPE_UNKNOWN; in ReadSequences() 529 prMSeq->seqtype = iSeqType; in ReadSequences() 584 if (prMSeq->seqtype==SEQTYPE_DNA) in ReadSequences() 586 if (prMSeq->seqtype==SEQTYPE_RNA) in ReadSequences() 721 (*prMSeq)->seqtype = SEQTYPE_UNKNOWN; in NewMSeq() 752 (*prMSeqDest_p)->seqtype = prMSeqSrc->seqtype; in CopyMSeq() 856 (*mseq)->seqtype = SEQTYPE_UNKNOWN; in FreeMSeq() [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/ |
H A D | seqdbexpert.cpp | 39 ESeqType seqtype, in CSeqDBExpert() argument 41 : CSeqDB(dbname, seqtype, gi_list) in CSeqDBExpert() 46 ESeqType seqtype, in CSeqDBExpert() argument 51 : CSeqDB(dbname, seqtype, oid_begin, oid_end, use_mmap, gi_list) in CSeqDBExpert()
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H A D | seqdb.cpp | 64 switch(seqtype) { in s_GetSeqTypeChar() 156 ESeqType seqtype, in CSeqDB() argument 167 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 180 ESeqType seqtype, in CSeqDB() argument 202 ESeqType seqtype, in CSeqDB() argument 212 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 226 ESeqType seqtype, in CSeqDB() argument 238 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 339 ESeqType seqtype, in CSeqDB() argument 637 ESeqType seqtype) in GetDate() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/ |
H A D | seqdbexpert.cpp | 39 ESeqType seqtype, in CSeqDBExpert() argument 41 : CSeqDB(dbname, seqtype, gi_list) in CSeqDBExpert() 46 ESeqType seqtype, in CSeqDBExpert() argument 51 : CSeqDB(dbname, seqtype, oid_begin, oid_end, use_mmap, gi_list) in CSeqDBExpert()
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H A D | seqdb.cpp | 64 switch(seqtype) { in s_GetSeqTypeChar() 156 ESeqType seqtype, in CSeqDB() argument 167 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 180 ESeqType seqtype, in CSeqDB() argument 202 ESeqType seqtype, in CSeqDB() argument 212 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 226 ESeqType seqtype, in CSeqDB() argument 238 char seq_type = s_GetSeqTypeChar(seqtype); in CSeqDB() 339 ESeqType seqtype, in CSeqDB() argument 637 ESeqType seqtype) in GetDate() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/services/ |
H A D | blast_services.cpp | 184 char seqtype, // 'p' or 'n' in s_BuildGetSeqRequest() argument 192 EBlast4_residue_type rtype = s_SeqTypeToResidue(seqtype, errors); in s_BuildGetSeqRequest() 254 char seqtype, in s_GetSequences() argument 309 char seqtype, // 'p' or 'n' in s_BuildGetSeqPartsRequest() argument 317 EBlast4_residue_type rtype = s_SeqTypeToResidue(seqtype, errors); in s_BuildGetSeqPartsRequest() 559 char seqtype, // 'p' or 'n' in GetSequencesInfo() argument 566 s_GetSequences(seqids, database, seqtype, true, target_only, bioseqs, in GetSequencesInfo() 573 char seqtype, // 'p' or 'n' in GetSequences() argument 580 s_GetSequences(seqids, database, seqtype, false, target_only, bioseqs, in GetSequences() 619 char seqtype, // 'p' or 'n' in GetSequenceParts() argument [all …]
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/services/ |
H A D | blast_services.cpp | 184 char seqtype, // 'p' or 'n' in s_BuildGetSeqRequest() argument 192 EBlast4_residue_type rtype = s_SeqTypeToResidue(seqtype, errors); in s_BuildGetSeqRequest() 254 char seqtype, in s_GetSequences() argument 309 char seqtype, // 'p' or 'n' in s_BuildGetSeqPartsRequest() argument 317 EBlast4_residue_type rtype = s_SeqTypeToResidue(seqtype, errors); in s_BuildGetSeqPartsRequest() 559 char seqtype, // 'p' or 'n' in GetSequencesInfo() argument 566 s_GetSequences(seqids, database, seqtype, true, target_only, bioseqs, in GetSequencesInfo() 573 char seqtype, // 'p' or 'n' in GetSequences() argument 580 s_GetSequences(seqids, database, seqtype, false, target_only, bioseqs, in GetSequences() 619 char seqtype, // 'p' or 'n' in GetSequenceParts() argument [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_reader/ |
H A D | seqdb.hpp | 336 CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBGiList * gilist = 0, 353 ESeqType seqtype, 370 ESeqType seqtype, 388 ESeqType seqtype, 407 CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBIdSet ids); 421 ESeqType seqtype, 452 ESeqType seqtype, 485 ESeqType seqtype, 860 ESeqType seqtype); 1148 ESeqType seqtype,
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/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_reader/ |
H A D | seqdb.hpp | 336 CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBGiList * gilist = 0, 353 ESeqType seqtype, 370 ESeqType seqtype, 388 ESeqType seqtype, 407 CSeqDB(const string & dbname, ESeqType seqtype, CSeqDBIdSet ids); 421 ESeqType seqtype, 452 ESeqType seqtype, 485 ESeqType seqtype, 860 ESeqType seqtype); 1148 ESeqType seqtype,
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