/dports/biology/bbmap/bbmap/current/dna/ |
H A D | Exon.java | 56 public static Exon merge(Exon exon1, Exon exon2){ in merge() argument 57 assert(canMerge(exon1, exon2)); in merge() 58 …return new Exon(min(exon1.a, exon2.a), max(exon1.b, exon2.b), exon1.chromosome, exon1.strand, exon… in merge() 61 public static boolean canMerge(Exon exon1, Exon exon2){ in canMerge() argument 62 if(exon1.chromosome!=exon2.chromosome){return false;} in canMerge() 63 return overlap(exon1.a, exon1.b, exon2.a, exon2.b); in canMerge()
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/dports/biology/emboss/EMBOSS-6.6.0/ajax/ensembl/ |
H A D | ensexon.c | 3493 if (!exon1) in ensExonMatch() 3499 if (exon1 == exon2) in ensExonMatch() 3575 if (!exon1) in ensExonSimilarity() 3581 if (exon1 == exon2) in ensExonSimilarity() 3676 exon1, in listExonCompareEndAscending() 3682 if (exon1 && (!exon2)) in listExonCompareEndAscending() 3688 if ((!exon1) && exon2) in listExonCompareEndAscending() 3727 exon1, in listExonCompareEndDescending() 3778 exon1, in listExonCompareIdentifierAscending() 3835 exon1, in listExonCompareStartAscending() [all …]
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H A D | ensexon.h | 251 AjBool ensExonMatch(const EnsPExon exon1, const EnsPExon exon2); 253 AjBool ensExonSimilarity(const EnsPExon exon1, const EnsPExon exon2);
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H A D | ensintron.c | 252 EnsPIntron ensIntronNewIni(EnsPExon exon1, in ensIntronNewIni() argument 279 exon1, in ensIntronNewIni() 283 ensExonTrace(exon1, 1); in ensIntronNewIni() 287 if (!exon1) in ensIntronNewIni() 293 feature1 = ensExonGetFeature(exon1); in ensIntronNewIni() 376 intron->PreviousExon = ensExonNewRef(exon1); in ensIntronNewIni()
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H A D | ensintron.h | 69 EnsPIntron ensIntronNewIni(EnsPExon exon1,
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H A D | ensgene.c | 2719 EnsPExon exon1 = *(EnsOExon *const *) item1; in listExonCompareAddressAscending() local 2727 exon1, in listExonCompareAddressAscending() 2731 if (ensExonSimilarity(exon1, exon2) == ajTrue) in listExonCompareAddressAscending() 2734 if (exon1 < exon2) in listExonCompareAddressAscending() 2737 if (exon1 > exon2) in listExonCompareAddressAscending()
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/dports/biology/p5-transdecoder/TransDecoder-TransDecoder-v5.4.0/__testing/ |
H A D | longest_orfs.gff3 | 4 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p1.exon1;Parent=CUFF.38.1.p1 11 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p2.exon1;Parent=CUFF.38.1.p2 18 CUFF.38.1 transdecoder exon 1 7903 . - . ID=CUFF.38.1.p3.exon1;Parent=CUFF.38.1.p3 25 CUFF.38.1 transdecoder exon 1 7903 . - . ID=CUFF.38.1.p4.exon1;Parent=CUFF.38.1.p4 31 CUFF.38.1 transdecoder exon 1 7903 . + . ID=CUFF.38.1.p5.exon1;Parent=CUFF.38.1.p5 38 CUFF.24.1 transdecoder exon 1 2538 . + . ID=CUFF.24.1.p1.exon1;Parent=CUFF.24.1.p1 45 CUFF.35.1 transdecoder exon 1 1885 . + . ID=CUFF.35.1.p1.exon1;Parent=CUFF.35.1.p1 52 CUFF.17.1 transdecoder exon 1 1368 . + . ID=CUFF.17.1.p1.exon1;Parent=CUFF.17.1.p1 121 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1 169 CUFF.6.1 transdecoder exon 1 1717 . + . ID=CUFF.6.1.p1.exon1;Parent=CUFF.6.1.p1 [all …]
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H A D | __test.simplest.expected | 3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1 9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1 16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1 23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2 29 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1 35 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1 40 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1 47 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1 87 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1 148 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1 [all …]
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H A D | __test.single_best.expected | 3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1 9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1 16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1 23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1 29 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1 34 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1 41 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1 81 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1 136 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1 211 CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1.p1.exon1;Parent=CUFF.4.1.p1 [all …]
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H A D | __test.wBlastNPfam.expected | 3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1 9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1 16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1 23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2 29 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p1.exon1;Parent=CUFF.13.1.p1 35 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1 40 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1 47 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1 87 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1 148 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1 [all …]
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H A D | __test.best_w_homology.expected | 3 CUFF.1.1 transdecoder exon 1 503 . + . ID=CUFF.1.1.p1.exon1;Parent=CUFF.1.1.p1 9 CUFF.11.1 transdecoder exon 1 938 . + . ID=CUFF.11.1.p1.exon1;Parent=CUFF.11.1.p1 16 CUFF.12.1 transdecoder exon 1 2733 . + . ID=CUFF.12.1.p1.exon1;Parent=CUFF.12.1.p1 23 CUFF.13.1 transdecoder exon 1 1770 . + . ID=CUFF.13.1.p2.exon1;Parent=CUFF.13.1.p2 28 CUFF.13.2 transdecoder exon 1 875 . + . ID=CUFF.13.2.p1.exon1;Parent=CUFF.13.2.p1 33 CUFF.13.3 transdecoder exon 1 822 . + . ID=CUFF.13.3.p1.exon1;Parent=CUFF.13.3.p1 40 CUFF.14.1 transdecoder exon 1 1275 . + . ID=CUFF.14.1.p1.exon1;Parent=CUFF.14.1.p1 80 CUFF.2.1 transdecoder exon 1 1060 . + . ID=CUFF.2.1.p1.exon1;Parent=CUFF.2.1.p1 135 CUFF.3.1 transdecoder exon 1 1353 . + . ID=CUFF.3.1.p1.exon1;Parent=CUFF.3.1.p1 210 CUFF.4.1 transdecoder exon 1 555 . + . ID=CUFF.4.1.p1.exon1;Parent=CUFF.4.1.p1 [all …]
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases_genbank/ |
H A D | rw-451.gff3 | 3 scaffold_944 JAMg exon 32926 33084 . - . ID=J14826.1.exon1;Parent=J14826.1 8 scaffold_944 JAMg exon 32926 33084 . - . ID=J24826.1.exon1;Parent=J24826.1 13 scaffold_944 JAMg exon 32926 33084 . - . ID=J34826.1.exon1;Parent=J34826.1
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H A D | mss-528.gff3 | 14 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
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/dports/biology/py-gffutils/gffutils-0.10.1/gffutils/test/data/ |
H A D | gff_example1.gff3 | 6 … 4772649 4772814 . - . Name=ENSMUST00000045689.exon1;Parent=ENSMUST00000045689;ID=ENSMUST000000456…
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/dports/biology/hyphy/hyphy-2.5.33/Examples/MoreComplexModels/ |
H A D | ExonIntron.bf | 47 DataSetFilter exon1 = CreateFilter (sequences,3,"0-98", "","TAA,TAG,TGA"); 59 HarvestFrequencies (observedFreq1, exon1, 1, 1, 1); 132 LikelihoodFunction theLnLik = (exon1, exon1Tree,
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/dports/biology/bedtools/bedtools2-2.30.0/test/intersect/ |
H A D | exons.issue750.bed | 1 chr1 0 100 exon1 1 +
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/dports/biology/ncbi-toolkit/ncbi/tools/ |
H A D | suggadj.c | 229 static Int4 overlap_aas (struct match *exon1, struct match *exon2) in overlap_aas() argument 235 if ( exon1 -> p_pos >= exon2 -> p_pos){ in overlap_aas() 236 if ( exon1 -> p_pos <= (end2=exon2 -> p_pos +exon2 ->length -1) ){ in overlap_aas() 237 if ( (diff= exon1 -> p_pos - exon2 -> p_pos) > 0 ){ in overlap_aas() 244 if ( exon2 -> p_pos <= (end1=exon1 -> p_pos +exon1 ->length -1) ){ in overlap_aas() 255 retval, exon1 -> p_pos, exon1 -> length, in overlap_aas()
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/dports/biology/primer3/primer3-2.3.6/test/ |
H A D | primer_mispriming_input | 1 SEQUENCE_ID=exon1
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H A D | primer_mispriming_th_input | 7 SEQUENCE_ID=exon1
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/dports/biology/py-biopython/biopython-1.79/Tests/ |
H A D | test_SeqIO_features.py | 231 exon1 = FeatureLocation(1148, 1188, strand=-1) 233 expected_loc = exon1 + exon2 241 exon1 = FeatureLocation(69610, 69724, strand=-1) 244 expected_loc = exon1 + exon2 + exon3 248 exon1 = FeatureLocation(69610, 69724, strand=+1) 251 expected_loc = exon1 + exon2 + exon3 255 exon1 = FeatureLocation(69610, 69724, strand=+1) 258 expected_loc = exon1 + exon2 + exon3 264 exon1 = FeatureLocation(69610, 69724, strand=-1) 267 expected_loc = exon1 + exon2 + exon3
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/align/util/ |
H A D | best_placement.cpp | 289 const CSpliced_exon& exon1, in GetGapLengthOnRow() 293 const auto r1 = exon1.GetRowSeq_range(row, true); in GetGapLengthOnRow()
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/tools/funcotator/dataSources/gencode/ |
H A D | DataProviderForExampleGencodeGtfGene.java | 46 final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); in createGencodeGtfGeneFeature() local 317 exon1.setUcscGenomeVersion(FuncotatorTestConstants.REFERENCE_VERSION_HG38); in createGencodeGtfGeneFeature() 356 exon1.setStartCodon(startCodon1); in createGencodeGtfGeneFeature() 362 transcript1.addExon(exon1); in createGencodeGtfGeneFeature()
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/import/unit_test/data/input/ |
H A D | test-multi-rna.gff3 | 14 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/objtools/readers/unit_test/gff3reader_test_cases/ |
H A D | mss-528.gff3 | 14 U00096.3 EcoCyc exon 337 2799 . + . ID=exon1;Parent=mrna1
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/dports/biology/gatk/gatk-4.2.0.0/src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/ |
H A D | GencodeGtfCodecUnitTest.java | 188 final GencodeGtfExonFeature exon1 = (GencodeGtfExonFeature) GencodeGtfFeature.create(data); in createGencodeGtfGene_gencode_valid_gencode_file2() local 1131 exon1.setUcscGenomeVersion("hg38"); in createGencodeGtfGene_gencode_valid_gencode_file2() 1175 exon1.setCds(cds1); in createGencodeGtfGene_gencode_valid_gencode_file2() 1176 exon1.setStartCodon(start_codon1); in createGencodeGtfGene_gencode_valid_gencode_file2() 1190 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_valid_gencode_file2() 2189 exon1.setUcscGenomeVersion("hg38"); in createGencodeGtfGene_gencode_and_this_is_a_valid_one_too_table() 2253 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_and_this_is_a_valid_one_too_table() 2981 exon1.setUcscGenomeVersion("hg19"); in createGencodeGtfGene_gencode_v19_valid_gencode_file2() 3023 transcript1.addExon(exon1); in createGencodeGtfGene_gencode_v19_valid_gencode_file2() 3263 exon1.setUcscGenomeVersion("hg19"); in createGencodeGtfGene_gencode_v19_and_this_is_a_valid_one_too() [all …]
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