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/dports/benchmarks/inferno/inferno-0.10.9/tests/
H A Ddiff-folded.rs14 infile1: &str, in test_diff_folded()
35 differential::from_files(options, infile1, infile2, &mut result)?; in test_diff_folded()
84 fn test_diff_folded_logs<F>(infile1: &str, infile2: &str, asserter: F) in test_diff_folded_logs()
92 infile1: &str, in test_diff_folded_logs_with_options()
100 let r1 = BufReader::new(File::open(infile1).unwrap()); in test_diff_folded_logs_with_options()
109 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_default() localVariable
118 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_normalize() localVariable
131 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_strip_hex() localVariable
144 let infile1 = "./tests/data/diff-folded/before_fractionals.txt"; in diff_folded_fractional_samples() localVariable
195 let infile1 = "./tests/data/diff-folded/before.txt"; in diff_folded_cli() localVariable
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/dports/science/dakota/dakota-6.13.0-release-public.src-UI/src/unit_test/
H A Dstat_utils.cpp48 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
69 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
74 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST()
90 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
95 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST()
111 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
115 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST()
133 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
137 infile1 >> Xmatrix[i][0]; in TEUCHOS_UNIT_TEST()
155 std::ifstream infile1("stat_util_test_files/Matrix1.txt"); in TEUCHOS_UNIT_TEST() local
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/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/Alignment/
H A DExonerate.pm226 my ($self,$infile1) = @_;
227 $self->{'input'} = $infile1 if(defined $infile1);
273 my ($fh,$infile1);
276 ($fh, $infile1) = $self->io->tempfile();
277 my $temp = Bio::SeqIO->new( -file => ">$infile1",
284 push @infilearr, $infile1;
288 ($fh, $infile1) = $self->io->tempfile();
289 my $temp = Bio::SeqIO->new( -file => ">$infile1",
294 $infile1 = $query;
296 return $infile1;
H A DSim4.pm249 my ($temp,$infile1, $infile2, $est_first,$seq);
253 ($est_first,$infile1,$infile2)= $self->_setinput($self->cdna_seq,$self->genomic_seq);
254 …if (!($infile1 && $infile2)) {$self->throw("Bad input data (sequences need an id ) or less than 2 …
260 my @exon_sets = $self->_run($est_first,$infile1,$infile2,$param_string);
280 my ($self,$estfirst,$infile1,$infile2,$param_string) = @_;
290 my $commandstring = $self->executable." $infile1 $infile2 $param_string > $outfile";
H A DLagan.pm197 my ($infile1, $infile2) = $self->_setinput($executable, $input1, $input2);
200 $infile1,
322 my ($fh, $infile1, $infile2, $temp1, $temp2, $seq1, $seq2);
333 ($fh, $infile1) = $self->io->tempfile();
342 push @infilearr, $infile1;
344 $infile1 = \@infilearr;
349 ($fh, $infile1) = $self->io->tempfile();
390 return ($infile1, $infile2);
H A DBlat.pm527 my ($self,$infile1) = @_;
528 if (defined $infile1) {
529 $self->{'input'} = $infile1;
546 my ($self,$infile1) = @_;
547 $self->{'db'} = $infile1 if(defined $infile1);
/dports/math/plplot-ada/plplot-5.15.0/scripts/
H A Dcompare.c53 FILE *infile1, *infile2; in main() local
65 infile1 = fopen( argv[1], "r" ); in main()
66 if ( infile1 == NULL ) { in main()
80 fseek( infile1, 0L, SEEK_END ); in main()
82 size1 = ftell( infile1 ); in main()
92 fseek( infile1, SKIPHEADER, SEEK_END ); in main()
98 fread( contents1, sizeof(char), (size_t)(size1-SKIPHEADER), infile1 ); in main()
/dports/math/plplot/plplot-5.15.0/scripts/
H A Dcompare.c53 FILE *infile1, *infile2; in main() local
65 infile1 = fopen( argv[1], "r" ); in main()
66 if ( infile1 == NULL ) { in main()
80 fseek( infile1, 0L, SEEK_END ); in main()
82 size1 = ftell( infile1 ); in main()
92 fseek( infile1, SKIPHEADER, SEEK_END ); in main()
98 fread( contents1, sizeof(char), (size_t)(size1-SKIPHEADER), infile1 ); in main()
/dports/math/gap/gap-4.11.0/pkg/digraphs-1.1.1/extern/edge-addition-planarity-suite-Version_3.0.0.5/c/
H A DplanarityUtils.c132 FILE *infile1 = NULL, *infile2 = NULL; in TextFilesEqual() local
135 infile1 = fopen(file1Name, "r"); in TextFilesEqual()
138 if (infile1 == NULL || infile2 == NULL) in TextFilesEqual()
145 while ((c1 = fgetc(infile1)) != EOF) in TextFilesEqual()
184 if (infile1 != NULL) fclose(infile1); in TextFilesEqual()
194 FILE *infile1 = NULL, *infile2 = NULL; in BinaryFilesEqual() local
197 infile1 = fopen(file1Name, "r"); in BinaryFilesEqual()
200 if (infile1 == NULL || infile2 == NULL) in BinaryFilesEqual()
207 while ((c1 = fgetc(infile1)) != EOF) in BinaryFilesEqual()
235 if (infile1 != NULL) fclose(infile1); in BinaryFilesEqual()
/dports/math/planarity/edge-addition-planarity-suite-Version_3.0.1.1/c/
H A DplanarityUtils.c143 FILE *infile1 = NULL, *infile2 = NULL; in TextFilesEqual() local
146 infile1 = fopen(file1Name, "r"); in TextFilesEqual()
149 if (infile1 == NULL || infile2 == NULL) in TextFilesEqual()
156 while ((c1 = fgetc(infile1)) != EOF) in TextFilesEqual()
195 if (infile1 != NULL) fclose(infile1); in TextFilesEqual()
205 FILE *infile1 = NULL, *infile2 = NULL; in BinaryFilesEqual() local
208 infile1 = fopen(file1Name, "r"); in BinaryFilesEqual()
211 if (infile1 == NULL || infile2 == NULL) in BinaryFilesEqual()
218 while ((c1 = fgetc(infile1)) != EOF) in BinaryFilesEqual()
246 if (infile1 != NULL) fclose(infile1); in BinaryFilesEqual()
/dports/graphics/mapserver/mapserver-7.6.4/mapscript/perl/examples/
H A DdistanceToShape.pl18 my ($infile1, $infile1_shpid, $infile2, $infile2_shpid, $distance);
20 GetOptions("infile1=s", \$infile1, "infile1_shpid=s", \$infile1_shpid, "infile2=s", \$infile2, "inf…
22 if(!$infile1 or !$infile1_shpid or !$infile2 or !$infile2_shpid) {
28 my $inshpf1 = new mapscript::shapefileObj($infile1, -1) or die "Unable to open shapefile $infile1.";
39 print "Distance between shape $infile1/$infile1_shpid and shape $infile2/$infile2_shpid is $distanc…
H A Dshp_in_shp.pl16 my ($infile1, $infile1_shpid, $infile2, $infile2_shpid, $within);
18 GetOptions("infile1=s", \$infile1, "infile1_shpid=s", \$infile1_shpid, "infile2=s", \$infile2, "inf…
21 if(!$infile1 or !defined($infile1_shpid) or !$infile2 or !defined($infile2_shpid)) {
27 my $inshpf1 = new mapscript::shapefileObj($infile1, -1) or die "Unable to open shapefile $infile1.";
45 print "Shape $infile1/$infile1_shpid is $within shape $infile2/$infile2_shpid\n";
/dports/biology/p5-BioPerl-Run/BioPerl-Run-1.007003/lib/Bio/Tools/Run/
H A DSignalp.pm196 my $infile1 = $self->_writeSeqFile($seq);
198 $self->_input($infile1);
201 unlink $infile1;
206 my $infile1;
209 $infile1 = $self->_writeSeqFile($tmpseq);
212 $self->_input($infile1);
231 my ($self,$infile1) = @_;
232 $self->{'input'} = $infile1 if(defined $infile1);
H A DCoil.pm211 my $infile1 = $self->_writeSeqFile($seq);
213 $self->_input($infile1);
216 unlink $infile1;
244 my ($self,$infile1) = @_;
245 if(defined $infile1){
247 $self->{'input'}=$infile1;
H A DSeg.pm182 my $infile1 = $self->_writeSeqFile($seq);
184 $self->_input($infile1);
187 unlink $infile1;
214 my ($self,$infile1) = @_;
215 if(defined $infile1){
217 $self->{'input'}=$infile1;
H A DPrints.pm190 my $infile1 = $self->_writeSeqFile($seq);
192 $self->_input($infile1);
195 unlink $infile1;
222 my ($self,$infile1) = @_;
224 if(defined $infile1){
226 $self->{'input'}=$infile1;
H A DProfile.pm189 my $infile1 = $self->_writeSeqFile($seq);
191 $self->_input($infile1);
194 unlink $infile1;
223 my ($self,$infile1) = @_;
224 if(defined $infile1){
225 $self->{'input'}=$infile1;
H A DTmhmm.pm233 my $infile1 = $self->_writeSeqFile($seq);
235 $self->_input($infile1);
238 unlink $infile1;
266 my ($self,$infile1) = @_;
267 if (defined $infile1){
269 $self->{'input'}=$infile1;
H A DInfernal.pm514 my $infile1 = $self->_writeSeqFile(@seq);
515 return $self->_run($infile1);
517 my $infile1 = $self->_writeAlignFile(@seq);
518 return $self->_run($infile1);
540 my $infile1 = $self->_writeSeqFile(@seq);
541 return $self->_run(-seq_files => [$infile1]);
562 my $infile1 = $self->_writeSeqFile(@seq);
563 return $self->_run(-seq_files => [$infile1]);
568 my $infile1 = $self->_writeAlignFile($seq[0]);
612 my $infile1 = $self->_writeAlignFile(@seq);
[all …]
H A DGenscan.pm175 my $infile1 = $self->_writeSeqFile($seq);
176 $self->_set_input($infile1);
230 my ($self,$infile1) = @_;
231 $self->{'input'}=$infile1;
/dports/biology/py-biopython/biopython-1.79/Tests/
H A Dtest_TCoffee_tool.py35 self.infile1 = "Fasta/fa01"
58 cmdline = TCoffeeCommandline(t_coffee_exe, infile=self.infile1)
63 records = list(SeqIO.parse(self.infile1, "fasta"))
74 cmdline.infile = self.infile1
86 records = list(SeqIO.parse(self.infile1, "fasta"))
97 cmdline.infile = self.infile1
112 records = list(SeqIO.parse(self.infile1, "fasta"))
124 infile=self.infile1,
138 records = list(SeqIO.parse(self.infile1, "fasta"))
151 infile=self.infile1,
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H A Dtest_Mafft_tool.py76 self.infile1 = "Fasta/f002"
85 cmdline = MafftCommandline(mafft_exe, input=self.infile1)
101 cmdline.set_parameter("input", self.infile1)
113 cmdline.input = self.infile1
126 cmdline = MafftCommandline(mafft_exe, input=self.infile1, phylipout=True)
143 mafft_exe, input=self.infile1, phylipout=True, namelength=50
160 cmdline.set_parameter("input", self.infile1)
H A Dtest_Dialign_tool.py49 self.infile1 = "Fasta/f002"
64 cmdline = DialignCommandline(dialign_exe, input=self.infile1)
74 cmdline.set_parameter("input", self.infile1)
87 cmdline.input = self.infile1
99 cmdline.set_parameter("input", self.infile1)
H A Dtest_BWA_tool.py77 self.infile1 = "BWA/HNSCC1_1_truncated.fastq"
150 self.do_aln(self.infile1, self.saifile1)
153 cmdline.set_parameter("read_file", self.infile1)
170 self.do_aln(self.infile1, self.saifile1)
177 cmdline.set_parameter("read_file1", self.infile1)
195 cmdline.set_parameter("read_file1", self.infile1)
/dports/biology/stringtie/stringtie-2.1.1/SuperReads_RNA/global-1/SuperReadsR/src/
H A Drename_filter_fastq.cc67 std::ifstream infile1(path1); in main() local
68 if(!infile1.good()) in main()
87 while(infile1.good()) { in main()
88 const char* res = parse_write(infile1, out, read_number++); in main()
91 …valid fastq format (" << res << ") in file '" << path1 << "' around position " << infile1.tellg()); in main()

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