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/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Search/HSP/
H A DPSLHSP.pm120 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;
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_UniGene.py980 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 …]
/dports/emulators/mess/mame-mame0226/src/frontend/mame/ui/
H A Dinputmap.cpp84 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 …]
/dports/emulators/mame/mame-mame0226/src/frontend/mame/ui/
H A Dinputmap.cpp84 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 …]
/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/
H A Dconcat_alg.py74 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 …]
H A Diqtree.py20 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
H A Dphyml.py84 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
H A Dfasttree.py55 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)
H A Draxml.py59 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,
H A Dmeta_aligner.py67 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,
H A Dmsf.py55 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))
/dports/biology/mafft/mafft-7.267-without-extensions/core/
H A Dmafft.tmpl193 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 …]
/dports/emulators/mess/mame-mame0226/src/emu/
H A Dioport.cpp631 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 …]
/dports/emulators/mame/mame-mame0226/src/emu/
H A Dioport.cpp631 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 …]
/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/
H A Dseqio.py54 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 …]
/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/workflow/
H A Dgenetree.py99 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 …]
/dports/biology/clustal-omega/clustal-omega-1.2.4/src/clustal/
H A Dseq.c507 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/seqdb_reader/
H A Dseqdbexpert.cpp39 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()
H A Dseqdb.cpp64 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/seqdb_reader/
H A Dseqdbexpert.cpp39 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()
H A Dseqdb.cpp64 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/blast/services/
H A Dblast_services.cpp184 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 …]
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/src/objtools/blast/services/
H A Dblast_services.cpp184 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 …]
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/include/objtools/blast/seqdb_reader/
H A Dseqdb.hpp336 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,
/dports/biology/ncbi-blast+/ncbi-blast-2.12.0+-src/c++/include/objtools/blast/seqdb_reader/
H A Dseqdb.hpp336 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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