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Searched refs:qualfile (Results 1 – 25 of 28) sorted by relevance

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/dports/biology/mothur/mothur-1.46.1/source/commands/
H A Dmakefastqcommand.cpp93 qualfile = validParameter.validFile(parameters, "qfile"); in MakeFastQCommand()
94 if (qualfile == "not open") { abort = true; qualfile = ""; } in MakeFastQCommand()
95 else if (qualfile == "not found") { in MakeFastQCommand()
96 qualfile = current->getQualFile(); in MakeFastQCommand()
97 …if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter.… in MakeFastQCommand()
99 }else { current->setQualFile(qualfile); } in MakeFastQCommand()
133 util.openInputFile(qualfile, qFile); in execute()
H A Dsummaryqualcommand.cpp82 qualfile = validParameter.validFile(parameters, "qfile"); in SummaryQualCommand()
83 if (qualfile == "not open") { qualfile = ""; abort = true; } in SummaryQualCommand()
84 else if (qualfile == "not found") { in SummaryQualCommand()
85 qualfile = current->getQualFile(); in SummaryQualCommand()
86 …if (qualfile != "") { m->mothurOut("Using " + qualfile + " as input file for the qfile parameter.\… in SummaryQualCommand()
88 }else { current->setQualFile(qualfile); } in SummaryQualCommand()
102 if (outputdir == ""){ outputdir += util.hasPath(qualfile); } in SummaryQualCommand()
109 vector<string> files; files.push_back(qualfile); in SummaryQualCommand()
144 numSeqs = createProcessesCreateSummary(position, averageQ, scores, qualfile); in execute()
150 variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(qualfile)); in execute()
[all …]
H A Dchopseqscommand.cpp123 qualfile = validParameter.validFile(parameters, "qfile"); in ChopSeqsCommand()
124 if (qualfile == "not open") { qualfile = ""; abort = true; } in ChopSeqsCommand()
125 else if (qualfile == "not found") { qualfile = ""; } in ChopSeqsCommand()
126 else { current->setQualFile(qualfile); } in ChopSeqsCommand()
158 …lidParameter.valid(parameters, "keepn"); if (temp == "not found") { if (qualfile!= "") { temp = "t… in ChopSeqsCommand()
161 …if (((!keepN) && (qualfile != "")) || ((countGaps) && (qualfile != ""))){ m->mothurOut("[ERROR]: Y… in ChopSeqsCommand()
190 if (qualfile != "") { fastafileTemp = outputFileName + ".qualFile.Positions.temp"; } in execute()
195 if (qualfile != "") { in execute()
197 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in execute()
198 … variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in execute()
[all …]
H A Dsortseqscommand.cpp122 qualfile = validParameter.validFile(parameters, "qfile"); in SortSeqsCommand()
123 if (qualfile == "not open") { abort = true; } in SortSeqsCommand()
124 else if (qualfile == "not found") { qualfile = ""; } in SortSeqsCommand()
125 else { current->setQualFile(qualfile); } in SortSeqsCommand()
162 if (qualfile != "") { readQual(); } in execute()
572 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in readQual()
574 variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in readQual()
575 variables["[extension]"] = util.getExtension(qualfile); in readQual()
583 util.openInputFile(qualfile, in); in readQual()
630 util.openInputFile(qualfile, in2); in readQual()
[all …]
H A Drenamefilecommand.cpp175 qualfile = validParameter.validFile(parameters, "qfile"); in RenameFileCommand()
176 …if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLin… in RenameFileCommand()
177 else if (qualfile == "not found") { qualfile = ""; } in RenameFileCommand()
178 if (qualfile != "") { numFiles++; } in RenameFileCommand()
272 if (qualfile != "") { in execute()
273 newName = getNewName(qualfile, "qfile"); in execute()
274 renameOrCopy(qualfile, newName); in execute()
H A Drenameseqscommand.cpp157 qualfile = validParameter.validFile(parameters, "qfile"); in RenameSeqsCommand()
158 if (qualfile == "not open") { abort = true; } in RenameSeqsCommand()
159 else if (qualfile == "not found"){ qualfile =""; } in RenameSeqsCommand()
160 else { current->setQualFile(qualfile); } in RenameSeqsCommand()
186 …= "") || (nameFile != "") || (fastqfile != "") || (groupfile != "") || (qualfile != "") || (contig… in RenameSeqsCommand()
188 …= "") && (nameFile == "") && (fastqfile == "") && (groupfile == "") && (qualfile == "") && (contig… in RenameSeqsCommand()
240 if (qualfile != "") { readQual(old2NewNameMap); } in execute()
668 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in readQual()
670 variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in readQual()
671 variables["[extension]"] = util.getExtension(qualfile); in readQual()
[all …]
H A Dgetseqscommand.cpp205 qualfile = validParameter.validFile(parameters, "qfile"); in GetSeqsCommand()
206 if (qualfile == "not open") { abort = true; } in GetSeqsCommand()
207 else if (qualfile == "not found") { qualfile = ""; } in GetSeqsCommand()
208 else { current->setQualFile(qualfile); } in GetSeqsCommand()
271 if (qualfile != "") { readQual(); } in execute()
461 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in readQual()
463 variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in readQual()
464 variables["[extension]"] = util.getExtension(qualfile); in readQual()
470 util.openInputFile(qualfile, in); in readQual()
1030 if (qualfile != "") { in runSanityCheck()
[all …]
H A Dremoveseqscommand.cpp190 qualfile = validParameter.validFile(parameters, "qfile"); in RemoveSeqsCommand()
191 if (qualfile == "not open") { abort = true; } in RemoveSeqsCommand()
192 else if (qualfile == "not found") { qualfile = ""; } in RemoveSeqsCommand()
193 else { current->setQualFile(qualfile); } in RemoveSeqsCommand()
220 … == "") && (alignfile == "") && (listfile == "") && (taxfile == "") && (qualfile == "") && (contig… in RemoveSeqsCommand()
269 if (qualfile != "") { readQual(); } in execute()
453 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in readQual()
455 variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in readQual()
456 variables["[extension]"] = util.getExtension(qualfile); in readQual()
463 util.openInputFile(qualfile, in); in readQual()
H A Dsetcurrentcommand.cpp196 qualfile = validParameter.validFile(parameters, "qfile"); in SetCurrentCommand()
197 …if (qualfile == "not open") { m->mothurOut("Ignoring: " + parameters["qfile"]); m->mothurOutEndLin… in SetCurrentCommand()
198 else if (qualfile == "not found") { qualfile = ""; } in SetCurrentCommand()
199 if (qualfile != "") { current->setQualFile(qualfile); } in SetCurrentCommand()
H A Dscreenseqscommand.cpp189 qualfile = validParameter.validFile(parameters, "qfile"); in ScreenSeqsCommand()
190 if (qualfile == "not open") { abort = true; } in ScreenSeqsCommand()
191 else if (qualfile == "not found") { qualfile = ""; } in ScreenSeqsCommand()
192 else { current->setQualFile(qualfile); } in ScreenSeqsCommand()
376 …if ((countfile != "") || (namefile != "") || (groupfile != "") || (qualfile != "") || (taxonomy !=… in execute()
386 if(qualfile != "") { inputString += ", qfile=" + qualfile; } in execute()
434 if (qualfile != "") { in execute()
436 if (outputdir == "") { thisOutputDir += util.hasPath(qualfile); } in execute()
437 … variables["[filename]"] = thisOutputDir + util.getRootName(util.getSimpleName(qualfile)); in execute()
438 variables["[extension]"] = util.getExtension(qualfile); in execute()
H A Dmakefastqcommand.h39 string fastafile, qualfile, format;
H A Dsortseqscommand.h40 string accnosfile, fastafile, namefile, taxfile, qualfile, flowfile; variable
H A Dsummaryqualcommand.h39 string qualfile, namefile, countfile; variable
H A Dchopseqscommand.h39 string fastafile, keep, namefile, groupfile, countfile, qualfile;
H A Dsetcurrentcommand.h43 …string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile… variable
H A Dremoveseqscommand.h37 …astqfile, namefile, groupfile, countfile, alignfile, listfile, taxfile, qualfile, format, contigs… variable
H A Drenamefilecommand.h40 …string treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfil… variable
H A Dgetseqscommand.h40 …astqfile, namefile, countfile, groupfile, alignfile, listfile, taxfile, qualfile, format, contigs… variable
H A Drenameseqscommand.h41 …string fastaFile, fastqfile, listfile, nameFile, groupfile, placement, delim, countfile, qualfile…
/dports/biology/py-bx-python/bx-python-0.8.13/lib/bx/align/sitemask/
H A Dquality.py40 for species, qualfile in self.qualfiles.items():
44 open(qualfile + "." + chrom + ".bqv", "rb"),
103 for species, qualfile in self.qualfiles.items():
107 open(qualfile + "." + chrom + ".bqv", "rb"),
/dports/biology/mothur/mothur-1.46.1/source/
H A Dcurrentfile.cpp73 … if (qualfile != "") { m->mothurOut("qfile=" + qualfile, out); m->mothurOutEndLine(out); } in printCurrentFiles()
106 if (qualfile != "") { m->mothurOut("qfile=" + qualfile); m->mothurOutEndLine(); } in printCurrentFiles()
150 if (qualfile != "") { return true; } in hasCurrentFiles()
201 qualfile = ""; in clearCurrentFiles()
H A Dcurrentfile.h47 string getQualFile() { lock_guard<std::mutex> guard(currentProtector); return qualfile; } in getQualFile()
81 …void setQualFile(string f) { lock_guard<std::mutex> guard(currentProtector); qualfile = util.get… in setQualFile()
142 …string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile… variable
179 qualfile = ""; in CurrentFile()
190 qualfile = ""; in CurrentFile()
/dports/biology/p5-BioPerl/BioPerl-1.7.7/lib/Bio/Tools/
H A DLucy.pm295 if ($self->{qualfile}) {
296 …open my $QUAL, '<', $self->{qualfile} or $self->throw("Could not read quality file '$self->{qualfi…
301 $self->qualfile("$file.qual");
/dports/biology/mothur/mothur-1.46.1/TestMothur/testcommands/
H A Dtestrenameseqscommand.h33 using RenameSeqsCommand::qualfile;
/dports/biology/p5-BioPerl/BioPerl-1.7.7/t/Seq/
H A DPrimaryQual.t106 -file => test_input_file('qualfile.qual'),
128 -file => test_input_file('qualfile.qual'),

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