From f91975eadfc113b64013f36e4c2dd6ca63b55b64 Mon Sep 17 00:00:00 2001 From: RSWilson1 Date: Thu, 1 Feb 2024 12:32:06 +0000 Subject: [PATCH] assembly data for pytest GH actions --- ...00001405.25_GRCh37.p13_assembly_report.txt | 334 ++++++++++++++++++ tests/test_gene_annotation2bed.py | 3 +- 2 files changed, 336 insertions(+), 1 deletion(-) create mode 100644 tests/test_data/GCF_000001405.25_GRCh37.p13_assembly_report.txt diff --git a/tests/test_data/GCF_000001405.25_GRCh37.p13_assembly_report.txt b/tests/test_data/GCF_000001405.25_GRCh37.p13_assembly_report.txt new file mode 100644 index 0000000..b8f5e27 --- /dev/null +++ b/tests/test_data/GCF_000001405.25_GRCh37.p13_assembly_report.txt @@ -0,0 +1,334 @@ +# Assembly name: GRCh37.p13 +# Description: Genome Reference Consortium Human Build 37 patch release 13 (GRCh37.p13) +# Organism name: Homo sapiens (human) +# Taxid: 9606 +# BioProject: PRJNA31257 +# Submitter: Genome Reference Consortium +# Date: 2013-06-28 +# Synonyms: hg19 +# Assembly type: haploid-with-alt-loci +# Release type: patch +# Assembly level: Chromosome +# Genome representation: full +# GenBank assembly accession: GCA_000001405.14 +# RefSeq assembly accession: GCF_000001405.25 +# RefSeq assembly and GenBank assemblies identical: yes +# +## Assembly-Units: +## GenBank Unit Accession RefSeq Unit Accession Assembly-Unit name +## GCA_000001305.1 GCF_000001305.13 Primary Assembly +## GCA_000005045.13 GCF_000005045.12 PATCHES +## GCA_000001315.1 GCF_000001315.1 ALT_REF_LOCI_1 +## GCA_000001325.1 GCF_000001325.2 ALT_REF_LOCI_2 +## GCA_000001335.1 GCF_000001335.1 ALT_REF_LOCI_3 +## GCA_000001345.1 GCF_000001345.1 ALT_REF_LOCI_4 +## GCA_000001355.1 GCF_000001355.1 ALT_REF_LOCI_5 +## GCA_000001365.1 GCF_000001365.2 ALT_REF_LOCI_6 +## GCA_000001375.1 GCF_000001375.1 ALT_REF_LOCI_7 +## GCA_000001385.1 GCF_000001385.1 ALT_REF_LOCI_8 +## GCA_000001395.1 GCF_000001395.1 ALT_REF_LOCI_9 +## GCA_000006015.1 GCF_000006015.1 non-nuclear +# +# Ordered by chromosome/plasmid; the chromosomes/plasmids are followed by +# unlocalized scaffolds. +# Unplaced scaffolds are listed at the end. +# RefSeq is equal or derived from GenBank object. +# +# Sequence-Name Sequence-Role Assigned-Molecule Assigned-Molecule-Location/Type GenBank-Accn Relationship RefSeq-Accn Assembly-Unit Sequence-Length UCSC-style-name +1 assembled-molecule 1 Chromosome CM000663.1 = NC_000001.10 Primary Assembly 249250621 chr1 +2 assembled-molecule 2 Chromosome CM000664.1 = NC_000002.11 Primary Assembly 243199373 chr2 +3 assembled-molecule 3 Chromosome CM000665.1 = NC_000003.11 Primary Assembly 198022430 chr3 +4 assembled-molecule 4 Chromosome CM000666.1 = NC_000004.11 Primary Assembly 191154276 chr4 +5 assembled-molecule 5 Chromosome CM000667.1 = NC_000005.9 Primary Assembly 180915260 chr5 +6 assembled-molecule 6 Chromosome CM000668.1 = NC_000006.11 Primary Assembly 171115067 chr6 +7 assembled-molecule 7 Chromosome CM000669.1 = NC_000007.13 Primary Assembly 159138663 chr7 +8 assembled-molecule 8 Chromosome CM000670.1 = NC_000008.10 Primary Assembly 146364022 chr8 +9 assembled-molecule 9 Chromosome CM000671.1 = NC_000009.11 Primary Assembly 141213431 chr9 +10 assembled-molecule 10 Chromosome CM000672.1 = NC_000010.10 Primary Assembly 135534747 chr10 +11 assembled-molecule 11 Chromosome CM000673.1 = NC_000011.9 Primary Assembly 135006516 chr11 +12 assembled-molecule 12 Chromosome CM000674.1 = NC_000012.11 Primary Assembly 133851895 chr12 +13 assembled-molecule 13 Chromosome CM000675.1 = NC_000013.10 Primary Assembly 115169878 chr13 +14 assembled-molecule 14 Chromosome CM000676.1 = NC_000014.8 Primary Assembly 107349540 chr14 +15 assembled-molecule 15 Chromosome CM000677.1 = NC_000015.9 Primary Assembly 102531392 chr15 +16 assembled-molecule 16 Chromosome CM000678.1 = NC_000016.9 Primary Assembly 90354753 chr16 +17 assembled-molecule 17 Chromosome CM000679.1 = NC_000017.10 Primary Assembly 81195210 chr17 +18 assembled-molecule 18 Chromosome CM000680.1 = NC_000018.9 Primary Assembly 78077248 chr18 +19 assembled-molecule 19 Chromosome CM000681.1 = NC_000019.9 Primary Assembly 59128983 chr19 +20 assembled-molecule 20 Chromosome CM000682.1 = NC_000020.10 Primary Assembly 63025520 chr20 +21 assembled-molecule 21 Chromosome CM000683.1 = NC_000021.8 Primary Assembly 48129895 chr21 +22 assembled-molecule 22 Chromosome CM000684.1 = NC_000022.10 Primary Assembly 51304566 chr22 +X assembled-molecule X Chromosome CM000685.1 = NC_000023.10 Primary Assembly 155270560 chrX +Y assembled-molecule Y Chromosome CM000686.1 = NC_000024.9 Primary Assembly 59373566 chrY +HSCHR1_RANDOM_CTG5 unlocalized-scaffold 1 Chromosome GL000191.1 = NT_113878.1 Primary Assembly 106433 chr1_gl000191_random +HSCHR1_RANDOM_CTG12 unlocalized-scaffold 1 Chromosome GL000192.1 = NT_167207.1 Primary Assembly 547496 chr1_gl000192_random +HSCHR4_RANDOM_CTG2 unlocalized-scaffold 4 Chromosome GL000193.1 = NT_113885.1 Primary Assembly 189789 chr4_gl000193_random +HSCHR4_RANDOM_CTG3 unlocalized-scaffold 4 Chromosome GL000194.1 = NT_113888.1 Primary Assembly 191469 chr4_gl000194_random +HSCHR7_RANDOM_CTG1 unlocalized-scaffold 7 Chromosome GL000195.1 = NT_113901.1 Primary Assembly 182896 chr7_gl000195_random +HSCHR8_RANDOM_CTG1 unlocalized-scaffold 8 Chromosome GL000196.1 = NT_113909.1 Primary Assembly 38914 chr8_gl000196_random +HSCHR8_RANDOM_CTG4 unlocalized-scaffold 8 Chromosome GL000197.1 = NT_113907.1 Primary Assembly 37175 chr8_gl000197_random +HSCHR9_RANDOM_CTG1 unlocalized-scaffold 9 Chromosome GL000198.1 = NT_113914.1 Primary Assembly 90085 chr9_gl000198_random +HSCHR9_RANDOM_CTG2 unlocalized-scaffold 9 Chromosome GL000199.1 = NT_113916.2 Primary Assembly 169874 chr9_gl000199_random +HSCHR9_RANDOM_CTG4 unlocalized-scaffold 9 Chromosome GL000200.1 = NT_113915.1 Primary Assembly 187035 chr9_gl000200_random +HSCHR9_RANDOM_CTG5 unlocalized-scaffold 9 Chromosome GL000201.1 = NT_113911.1 Primary Assembly 36148 chr9_gl000201_random +HSCHR11_RANDOM_CTG2 unlocalized-scaffold 11 Chromosome GL000202.1 = NT_113921.2 Primary Assembly 40103 chr11_gl000202_random +HSCHR17_RANDOM_CTG1 unlocalized-scaffold 17 Chromosome GL000203.1 = NT_113941.1 Primary Assembly 37498 chr17_gl000203_random +HSCHR17_RANDOM_CTG2 unlocalized-scaffold 17 Chromosome GL000204.1 = NT_113943.1 Primary Assembly 81310 chr17_gl000204_random +HSCHR17_RANDOM_CTG3 unlocalized-scaffold 17 Chromosome GL000205.1 = NT_113930.1 Primary Assembly 174588 chr17_gl000205_random +HSCHR17_RANDOM_CTG4 unlocalized-scaffold 17 Chromosome GL000206.1 = NT_113945.1 Primary Assembly 41001 chr17_gl000206_random +HSCHR18_RANDOM_CTG1 unlocalized-scaffold 18 Chromosome GL000207.1 = NT_113947.1 Primary Assembly 4262 chr18_gl000207_random +HSCHR19_RANDOM_CTG1 unlocalized-scaffold 19 Chromosome GL000208.1 = NT_113948.1 Primary Assembly 92689 chr19_gl000208_random +HSCHR19_RANDOM_CTG2 unlocalized-scaffold 19 Chromosome GL000209.1 = NT_113949.1 Primary Assembly 159169 chr19_gl000209_random +HSCHR21_RANDOM_CTG9 unlocalized-scaffold 21 Chromosome GL000210.1 = NT_113950.2 Primary Assembly 27682 chr21_gl000210_random +HSCHRUN_RANDOM_CTG1 unplaced-scaffold na na GL000211.1 = NT_113961.1 Primary Assembly 166566 chrUn_gl000211 +HSCHRUN_RANDOM_CTG2 unplaced-scaffold na na GL000212.1 = NT_113923.1 Primary Assembly 186858 chrUn_gl000212 +HSCHRUN_RANDOM_CTG3 unplaced-scaffold na na GL000213.1 = NT_167208.1 Primary Assembly 164239 chrUn_gl000213 +HSCHRUN_RANDOM_CTG4 unplaced-scaffold na na GL000214.1 = NT_167209.1 Primary Assembly 137718 chrUn_gl000214 +HSCHRUN_RANDOM_CTG5 unplaced-scaffold na na GL000215.1 = NT_167210.1 Primary Assembly 172545 chrUn_gl000215 +HSCHRUN_RANDOM_CTG6 unplaced-scaffold na na GL000216.1 = NT_167211.1 Primary Assembly 172294 chrUn_gl000216 +HSCHRUN_RANDOM_CTG7 unplaced-scaffold na na GL000217.1 = NT_167212.1 Primary Assembly 172149 chrUn_gl000217 +HSCHRUN_RANDOM_CTG9 unplaced-scaffold na na GL000218.1 = NT_113889.1 Primary Assembly 161147 chrUn_gl000218 +HSCHRUN_RANDOM_CTG10 unplaced-scaffold na na GL000219.1 = NT_167213.1 Primary Assembly 179198 chrUn_gl000219 +HSCHRUN_RANDOM_CTG11 unplaced-scaffold na na GL000220.1 = NT_167214.1 Primary Assembly 161802 chrUn_gl000220 +HSCHRUN_RANDOM_CTG13 unplaced-scaffold na na GL000221.1 = NT_167215.1 Primary Assembly 155397 chrUn_gl000221 +HSCHRUN_RANDOM_CTG14 unplaced-scaffold na na GL000222.1 = NT_167216.1 Primary Assembly 186861 chrUn_gl000222 +HSCHRUN_RANDOM_CTG15 unplaced-scaffold na na GL000223.1 = NT_167217.1 Primary Assembly 180455 chrUn_gl000223 +HSCHRUN_RANDOM_CTG16 unplaced-scaffold na na GL000224.1 = NT_167218.1 Primary Assembly 179693 chrUn_gl000224 +HSCHRUN_RANDOM_CTG17 unplaced-scaffold na na GL000225.1 = NT_167219.1 Primary Assembly 211173 chrUn_gl000225 +HSCHRUN_RANDOM_CTG19 unplaced-scaffold na na GL000226.1 = NT_167220.1 Primary Assembly 15008 chrUn_gl000226 +HSCHRUN_RANDOM_CTG20 unplaced-scaffold na na GL000227.1 = NT_167221.1 Primary Assembly 128374 chrUn_gl000227 +HSCHRUN_RANDOM_CTG21 unplaced-scaffold na na GL000228.1 = NT_167222.1 Primary Assembly 129120 chrUn_gl000228 +HSCHRUN_RANDOM_CTG22 unplaced-scaffold na na GL000229.1 = NT_167223.1 Primary Assembly 19913 chrUn_gl000229 +HSCHRUN_RANDOM_CTG23 unplaced-scaffold na na GL000230.1 = NT_167224.1 Primary Assembly 43691 chrUn_gl000230 +HSCHRUN_RANDOM_CTG24 unplaced-scaffold na na GL000231.1 = NT_167225.1 Primary Assembly 27386 chrUn_gl000231 +HSCHRUN_RANDOM_CTG25 unplaced-scaffold na na GL000232.1 = NT_167226.1 Primary Assembly 40652 chrUn_gl000232 +HSCHRUN_RANDOM_CTG26 unplaced-scaffold na na GL000233.1 = NT_167227.1 Primary Assembly 45941 chrUn_gl000233 +HSCHRUN_RANDOM_CTG27 unplaced-scaffold na na GL000234.1 = NT_167228.1 Primary Assembly 40531 chrUn_gl000234 +HSCHRUN_RANDOM_CTG28 unplaced-scaffold na na GL000235.1 = NT_167229.1 Primary Assembly 34474 chrUn_gl000235 +HSCHRUN_RANDOM_CTG29 unplaced-scaffold na na GL000236.1 = NT_167230.1 Primary Assembly 41934 chrUn_gl000236 +HSCHRUN_RANDOM_CTG30 unplaced-scaffold na na GL000237.1 = NT_167231.1 Primary Assembly 45867 chrUn_gl000237 +HSCHRUN_RANDOM_CTG31 unplaced-scaffold na na GL000238.1 = NT_167232.1 Primary Assembly 39939 chrUn_gl000238 +HSCHRUN_RANDOM_CTG32 unplaced-scaffold na na GL000239.1 = NT_167233.1 Primary Assembly 33824 chrUn_gl000239 +HSCHRUN_RANDOM_CTG33 unplaced-scaffold na na GL000240.1 = NT_167234.1 Primary Assembly 41933 chrUn_gl000240 +HSCHRUN_RANDOM_CTG34 unplaced-scaffold na na GL000241.1 = NT_167235.1 Primary Assembly 42152 chrUn_gl000241 +HSCHRUN_RANDOM_CTG35 unplaced-scaffold na na GL000242.1 = NT_167236.1 Primary Assembly 43523 chrUn_gl000242 +HSCHRUN_RANDOM_CTG36 unplaced-scaffold na na GL000243.1 = NT_167237.1 Primary Assembly 43341 chrUn_gl000243 +HSCHRUN_RANDOM_CTG37 unplaced-scaffold na na GL000244.1 = NT_167238.1 Primary Assembly 39929 chrUn_gl000244 +HSCHRUN_RANDOM_CTG38 unplaced-scaffold na na GL000245.1 = NT_167239.1 Primary Assembly 36651 chrUn_gl000245 +HSCHRUN_RANDOM_CTG39 unplaced-scaffold na na GL000246.1 = NT_167240.1 Primary Assembly 38154 chrUn_gl000246 +HSCHRUN_RANDOM_CTG40 unplaced-scaffold na na GL000247.1 = NT_167241.1 Primary Assembly 36422 chrUn_gl000247 +HSCHRUN_RANDOM_CTG41 unplaced-scaffold na na GL000248.1 = NT_167242.1 Primary Assembly 39786 chrUn_gl000248 +HSCHRUN_RANDOM_CTG42 unplaced-scaffold na na GL000249.1 = NT_167243.1 Primary Assembly 38502 chrUn_gl000249 +HG999_1_PATCH fix-patch 1 Chromosome GL383516.1 = NW_003315903.1 PATCHES 49316 na +HG999_2_PATCH fix-patch 1 Chromosome GL383517.1 = NW_003315904.1 PATCHES 49352 na +HG989_PATCH fix-patch 1 Chromosome GL949741.1 = NW_003571030.1 PATCHES 151551 na +HG1287_PATCH fix-patch 1 Chromosome JH636052.4 = NW_003871055.3 PATCHES 7283150 na +HG1292_PATCH fix-patch 1 Chromosome JH636053.3 = NW_003871056.3 PATCHES 1676126 na +HG1293_PATCH fix-patch 1 Chromosome JH636054.1 = NW_003871057.1 PATCHES 758378 na +HG1471_PATCH fix-patch 1 Chromosome JH806573.1 = NW_004070863.1 PATCHES 24680 na +HG1472_PATCH fix-patch 1 Chromosome JH806574.2 = NW_004070864.2 PATCHES 22982 na +HG1473_PATCH fix-patch 1 Chromosome JH806575.1 = NW_004070865.1 PATCHES 47409 na +HSCHR1_1_CTG31 novel-patch 1 Chromosome GL383518.1 = NW_003315905.1 PATCHES 182439 na +HSCHR1_2_CTG31 novel-patch 1 Chromosome GL383519.1 = NW_003315906.1 PATCHES 110268 na +HSCHR1_3_CTG31 novel-patch 1 Chromosome GL383520.1 = NW_003315907.1 PATCHES 366579 na +HG1007_PATCH fix-patch 2 Chromosome GL877870.2 = NW_003571031.1 PATCHES 66021 na +HG686_PATCH fix-patch 2 Chromosome GL877871.1 = NW_003571032.1 PATCHES 389939 na +HG953_PATCH fix-patch 2 Chromosome KB663603.1 = NW_004504299.1 PATCHES 599580 na +HSCHR2_1_CTG1 novel-patch 2 Chromosome GL383521.1 = NW_003315908.1 PATCHES 143390 na +HSCHR2_1_CTG12 novel-patch 2 Chromosome GL383522.1 = NW_003315909.1 PATCHES 123821 na +HSCHR2_2_CTG12 novel-patch 2 Chromosome GL582966.2 = NW_003571033.2 PATCHES 96131 na +HG186_PATCH fix-patch 3 Chromosome GL383523.1 = NW_003315910.1 PATCHES 171362 na +HG280_PATCH fix-patch 3 Chromosome GL383524.1 = NW_003315911.1 PATCHES 78793 na +HG991_PATCH fix-patch 3 Chromosome GL383525.1 = NW_003315912.1 PATCHES 65063 na +HG1091_PATCH fix-patch 3 Chromosome JH159131.1 = NW_003871058.1 PATCHES 393769 na +HG325_PATCH fix-patch 3 Chromosome JH159132.1 = NW_003871059.1 PATCHES 100694 na +HG957_PATCH fix-patch 3 Chromosome KE332495.1 = NW_004775426.1 PATCHES 263861 na +HSCHR3_1_CTG2_1 novel-patch 3 Chromosome GL383526.1 = NW_003315913.1 PATCHES 180671 na +HSCHR3_1_CTG1 novel-patch 3 Chromosome JH636055.1 = NW_003871060.1 PATCHES 173151 na +HG706_PATCH fix-patch 4 Chromosome GL582967.1 = NW_003571035.1 PATCHES 248177 na +HG1032_PATCH fix-patch 4 Chromosome GL877872.1 = NW_003571034.1 PATCHES 297485 na +HG174_HG254_PATCH fix-patch 4 Chromosome KE332496.1 = NW_004775427.1 PATCHES 503215 na +HSCHR4_1_CTG12 novel-patch 4 Chromosome GL383527.1 = NW_003315914.1 PATCHES 164536 na +HSCHR4_1_CTG6 novel-patch 4 Chromosome GL383528.1 = NW_003315915.1 PATCHES 376187 na +HSCHR4_2_CTG9 novel-patch 4 Chromosome GL383529.1 = NW_003315916.1 PATCHES 121345 na +HG1063_PATCH fix-patch 5 Chromosome JH159133.1 = NW_003871061.1 PATCHES 266316 na +HG1082_HG167_PATCH fix-patch 5 Chromosome KE332497.1 = NW_004775428.1 PATCHES 543325 na +HSCHR5_1_CTG1 novel-patch 5 Chromosome GL339449.2 = NW_003315917.2 PATCHES 1612928 na +HSCHR5_1_CTG2 novel-patch 5 Chromosome GL383530.1 = NW_003315918.1 PATCHES 101241 na +HSCHR5_1_CTG5 novel-patch 5 Chromosome GL383531.1 = NW_003315919.1 PATCHES 173459 na +HSCHR5_2_CTG1 novel-patch 5 Chromosome GL383532.1 = NW_003315920.1 PATCHES 82728 na +HSCHR5_3_CTG1 novel-patch 5 Chromosome GL949742.1 = NW_003571036.1 PATCHES 226852 na +HG1304_PATCH fix-patch 6 Chromosome JH636056.1 = NW_003871062.1 PATCHES 262912 na +HG1322_PATCH fix-patch 6 Chromosome JH636057.1 = NW_003871063.1 PATCHES 200195 na +HG27_PATCH fix-patch 6 Chromosome JH806576.1 = NW_004070866.1 PATCHES 273386 na +HG357_PATCH fix-patch 6 Chromosome KB663604.1 = NW_004504300.1 PATCHES 478993 na +HG193_PATCH fix-patch 6 Chromosome KE332498.1 = NW_004775429.1 PATCHES 149443 na +HSCHR6_1_CTG5 novel-patch 6 Chromosome GL383533.1 = NW_003315921.1 PATCHES 124736 na +HSCHR6_2_CTG5 novel-patch 6 Chromosome KB021644.1 = NW_004166862.1 PATCHES 187824 na +HG115_PATCH fix-patch 7 Chromosome GL582968.1 = NW_003571037.1 PATCHES 356330 na +HG14_PATCH fix-patch 7 Chromosome GL582969.1 = NW_003571038.1 PATCHES 251823 na +HG736_PATCH fix-patch 7 Chromosome GL582970.1 = NW_003571039.1 PATCHES 354970 na +HG7_PATCH fix-patch 7 Chromosome GL582971.1 = NW_003571040.1 PATCHES 1284284 na +HG946_PATCH fix-patch 7 Chromosome GL582972.1 = NW_003571041.1 PATCHES 327774 na +HG1257_PATCH fix-patch 7 Chromosome JH159134.2 = NW_003871064.1 PATCHES 3821770 na +HG1308_PATCH fix-patch 7 Chromosome JH636058.1 = NW_003871065.1 PATCHES 716227 na +HG444_PATCH fix-patch 7 Chromosome KE332499.1 = NW_004775430.1 PATCHES 274521 na +HSCHR7_1_CTG6 novel-patch 7 Chromosome GL383534.2 = NW_003315922.2 PATCHES 119183 na +HG104_HG975_PATCH fix-patch 8 Chromosome GL383535.1 = NW_003315923.1 PATCHES 429806 na +HG243_PATCH fix-patch 8 Chromosome GL383536.1 = NW_003315924.1 PATCHES 203777 na +HG19_PATCH fix-patch 8 Chromosome GL949743.1 = NW_003571042.1 PATCHES 608579 na +HG418_PATCH fix-patch 8 Chromosome JH159135.2 = NW_003871066.2 PATCHES 102251 na +HG1699_PATCH fix-patch 8 Chromosome KE332500.1 = NW_004775431.1 PATCHES 228602 na +HG79_PATCH fix-patch 9 Chromosome GL339450.1 = NW_003315925.1 PATCHES 330164 na +HG998_1_PATCH fix-patch 9 Chromosome GL383537.1 = NW_003315926.1 PATCHES 62435 na +HG998_2_PATCH fix-patch 9 Chromosome GL383538.1 = NW_003315927.1 PATCHES 49281 na +HG962_PATCH fix-patch 9 Chromosome JH636059.1 = NW_003871067.1 PATCHES 295379 na +HG1500_PATCH fix-patch 9 Chromosome JH806577.1 = NW_004070867.1 PATCHES 22394 na +HG1501_PATCH fix-patch 9 Chromosome JH806578.1 = NW_004070868.1 PATCHES 169437 na +HG1502_PATCH fix-patch 9 Chromosome JH806579.1 = NW_004070869.1 PATCHES 211307 na +HG50_PATCH fix-patch 9 Chromosome KB663605.1 = NW_004504301.1 PATCHES 155926 na +HSCHR9_1_CTG1 novel-patch 9 Chromosome GL383539.1 = NW_003315928.1 PATCHES 162988 na +HSCHR9_1_CTG35 novel-patch 9 Chromosome GL383540.1 = NW_003315929.1 PATCHES 71551 na +HSCHR9_2_CTG35 novel-patch 9 Chromosome GL383541.1 = NW_003315930.1 PATCHES 171286 na +HSCHR9_3_CTG35 novel-patch 9 Chromosome GL383542.1 = NW_003315931.1 PATCHES 60032 na +HG544_PATCH fix-patch 10 Chromosome GL383543.1 = NW_003315932.1 PATCHES 392792 na +HG995_PATCH fix-patch 10 Chromosome GL383544.1 = NW_003315933.1 PATCHES 128378 na +HG905_PATCH fix-patch 10 Chromosome GL877873.1 = NW_003571043.1 PATCHES 168465 na +HG1211_PATCH fix-patch 10 Chromosome JH591181.2 = NW_003871068.1 PATCHES 2281126 na +HG311_PATCH fix-patch 10 Chromosome JH591182.1 = NW_003871069.1 PATCHES 196262 na +HG339_PATCH fix-patch 10 Chromosome JH591183.1 = NW_003871070.1 PATCHES 177920 na +HG871_PATCH fix-patch 10 Chromosome JH636060.1 = NW_003871071.1 PATCHES 437946 na +HG1479_PATCH fix-patch 10 Chromosome JH806580.1 = NW_004070870.1 PATCHES 93149 na +HG1074_PATCH fix-patch 10 Chromosome KB663606.1 = NW_004504302.1 PATCHES 305900 na +HG979_PATCH fix-patch 10 Chromosome KE332501.1 = NW_004775432.1 PATCHES 1020827 na +HSCHR10_1_CTG2 novel-patch 10 Chromosome GL383545.1 = NW_003315934.1 PATCHES 179254 na +HSCHR10_1_CTG5 novel-patch 10 Chromosome GL383546.1 = NW_003315935.1 PATCHES 309802 na +HG281_PATCH fix-patch 11 Chromosome GL582973.1 = NW_003571045.1 PATCHES 321004 na +HG536_PATCH fix-patch 11 Chromosome GL949744.1 = NW_003571046.1 PATCHES 276448 na +HG299_PATCH fix-patch 11 Chromosome JH159138.1 = NW_003871076.1 PATCHES 108875 na +HG305_PATCH fix-patch 11 Chromosome JH159139.1 = NW_003871077.1 PATCHES 120441 na +HG306_PATCH fix-patch 11 Chromosome JH159140.1 = NW_003871078.1 PATCHES 546435 na +HG348_PATCH fix-patch 11 Chromosome JH159141.2 = NW_003871079.1 PATCHES 240775 na +HG388_HG400_PATCH fix-patch 11 Chromosome JH159142.2 = NW_003871080.1 PATCHES 326647 na +HG414_PATCH fix-patch 11 Chromosome JH159143.1 = NW_003871081.1 PATCHES 191402 na +HG256_PATCH fix-patch 11 Chromosome JH591184.1 = NW_003871075.1 PATCHES 462282 na +HG873_PATCH fix-patch 11 Chromosome JH591185.1 = NW_003871082.1 PATCHES 167437 na +HG122_PATCH fix-patch 11 Chromosome JH720443.2 = NW_003871072.2 PATCHES 408430 na +HG865_PATCH fix-patch 11 Chromosome JH806581.1 = NW_004070871.1 PATCHES 872115 na +HSCHR11_1_CTG1_1 novel-patch 11 Chromosome GL383547.1 = NW_003315936.1 PATCHES 154407 na +HG142_HG150_NOVEL_TEST novel-patch 11 Chromosome JH159136.1 = NW_003871073.1 PATCHES 200998 na +HG151_NOVEL_TEST novel-patch 11 Chromosome JH159137.1 = NW_003871074.1 PATCHES 191409 na +HG996_PATCH fix-patch 12 Chromosome GL383548.1 = NW_003315937.1 PATCHES 165247 na +HG858_PATCH fix-patch 12 Chromosome GL582974.1 = NW_003571048.1 PATCHES 163298 na +HG344_PATCH fix-patch 12 Chromosome JH720444.2 = NW_003871083.2 PATCHES 273128 na +HG1595_PATCH fix-patch 12 Chromosome KB663607.2 = NW_004504303.2 PATCHES 334922 na +HSCHR12_1_CTG2 novel-patch 12 Chromosome GL383549.1 = NW_003315938.1 PATCHES 120804 na +HSCHR12_1_CTG2_1 novel-patch 12 Chromosome GL383550.1 = NW_003315939.1 PATCHES 169178 na +HSCHR12_1_CTG5 novel-patch 12 Chromosome GL383551.1 = NW_003315940.1 PATCHES 184319 na +HSCHR12_2_CTG2_1 novel-patch 12 Chromosome GL383552.1 = NW_003315941.1 PATCHES 138655 na +HSCHR12_3_CTG2_1 novel-patch 12 Chromosome GL383553.2 = NW_003315942.2 PATCHES 152874 na +HSCHR12_1_CTG1 novel-patch 12 Chromosome GL877875.1 = NW_003571049.1 PATCHES 167313 na +HSCHR12_2_CTG2 novel-patch 12 Chromosome GL877876.1 = NW_003571050.1 PATCHES 408271 na +HG1133_PATCH novel-patch 12 Chromosome GL949745.1 = NW_003571047.1 PATCHES 372609 na +HG531_PATCH fix-patch 13 Chromosome GL582975.1 = NW_003571051.1 PATCHES 34662 na +HG1592_PATCH fix-patch 14 Chromosome KB021645.1 = NW_004166863.1 PATCHES 1523386 na +HG971_PATCH fix-patch 15 Chromosome JH720445.1 = NW_003871084.1 PATCHES 170033 na +HSCHR15_1_CTG4 novel-patch 15 Chromosome GL383554.1 = NW_003315943.1 PATCHES 296527 na +HSCHR15_1_CTG8 novel-patch 15 Chromosome GL383555.1 = NW_003315944.1 PATCHES 388773 na +HG1208_PATCH fix-patch 16 Chromosome JH720446.1 = NW_003871085.1 PATCHES 97345 na +HSCHR16_1_CTG3_1 novel-patch 16 Chromosome GL383556.1 = NW_003315945.1 PATCHES 192462 na +HSCHR16_2_CTG3_1 novel-patch 16 Chromosome GL383557.1 = NW_003315946.1 PATCHES 89672 na +HG183_PATCH fix-patch 17 Chromosome GL383558.1 = NW_003315947.1 PATCHES 457041 na +HG745_PATCH fix-patch 17 Chromosome GL383559.2 = NW_003315948.2 PATCHES 338640 na +HG75_PATCH fix-patch 17 Chromosome GL383560.1 = NW_003315949.1 PATCHES 534288 na +HG987_PATCH fix-patch 17 Chromosome GL383561.2 = NW_003315950.2 PATCHES 644425 na +HG990_PATCH fix-patch 17 Chromosome GL383562.1 = NW_003315951.1 PATCHES 45551 na +HG185_PATCH fix-patch 17 Chromosome GL582976.1 = NW_003571052.1 PATCHES 412535 na +HG747_PATCH fix-patch 17 Chromosome JH159144.1 = NW_003871088.1 PATCHES 388340 na +HG883_PATCH fix-patch 17 Chromosome JH159145.1 = NW_003871090.1 PATCHES 194862 na +HG748_PATCH fix-patch 17 Chromosome JH591186.1 = NW_003871089.1 PATCHES 376223 na +HG271_PATCH fix-patch 17 Chromosome JH636061.1 = NW_003871087.1 PATCHES 186059 na +HG1146_PATCH fix-patch 17 Chromosome JH720447.1 = NW_003871086.1 PATCHES 454385 na +HG417_PATCH fix-patch 17 Chromosome JH806582.2 = NW_004070872.2 PATCHES 342635 na +HG385_PATCH fix-patch 17 Chromosome KB021646.2 = NW_004166864.2 PATCHES 211416 na +HG1591_PATCH fix-patch 17 Chromosome KE332502.1 = NW_004775433.1 PATCHES 341712 na +HSCHR17_1_CTG1 novel-patch 17 Chromosome GL383563.2 = NW_003315952.2 PATCHES 270261 na +HSCHR17_1_CTG4 novel-patch 17 Chromosome GL383564.1 = NW_003315953.1 PATCHES 133151 na +HSCHR17_2_CTG4 novel-patch 17 Chromosome GL383565.1 = NW_003315954.1 PATCHES 223995 na +HSCHR17_3_CTG4 novel-patch 17 Chromosome GL383566.1 = NW_003315955.1 PATCHES 90219 na +HSCHR17_4_CTG4 novel-patch 17 Chromosome JH159146.1 = NW_003871091.1 PATCHES 278131 na +HSCHR17_5_CTG4 novel-patch 17 Chromosome JH159147.1 = NW_003871092.1 PATCHES 70345 na +HSCHR17_6_CTG4 novel-patch 17 Chromosome JH159148.1 = NW_003871093.1 PATCHES 88070 na +HSCHR18_1_CTG1_1 novel-patch 18 Chromosome GL383567.1 = NW_003315956.1 PATCHES 289831 na +HSCHR18_1_CTG2 novel-patch 18 Chromosome GL383568.1 = NW_003315957.1 PATCHES 104552 na +HSCHR18_1_CTG2_1 novel-patch 18 Chromosome GL383569.1 = NW_003315958.1 PATCHES 167950 na +HSCHR18_2_CTG1_1 novel-patch 18 Chromosome GL383570.1 = NW_003315959.1 PATCHES 164789 na +HSCHR18_2_CTG2 novel-patch 18 Chromosome GL383571.1 = NW_003315960.1 PATCHES 198278 na +HSCHR18_2_CTG2_1 novel-patch 18 Chromosome GL383572.1 = NW_003315961.1 PATCHES 159547 na +HG730_PATCH fix-patch 19 Chromosome GL582977.2 = NW_003571053.2 PATCHES 580393 na +HG729_PATCH fix-patch 19 Chromosome JH159149.1 = NW_003871094.1 PATCHES 245473 na +HG1079_PATCH fix-patch 19 Chromosome KB021647.1 = NW_004166865.1 PATCHES 1058686 na +HG1350_HG959_PATCH fix-patch 19 Chromosome KE332505.1 = NW_004775434.1 PATCHES 579598 na +HSCHR19_1_CTG3 novel-patch 19 Chromosome GL383573.1 = NW_003315962.1 PATCHES 385657 na +HSCHR19_1_CTG3_1 novel-patch 19 Chromosome GL383574.1 = NW_003315963.1 PATCHES 155864 na +HSCHR19_2_CTG3 novel-patch 19 Chromosome GL383575.2 = NW_003315964.2 PATCHES 170222 na +HSCHR19_3_CTG3 novel-patch 19 Chromosome GL383576.1 = NW_003315965.1 PATCHES 188024 na +HSCHR19LRC_COX1_CTG1 novel-patch 19 Chromosome GL949746.1 = NW_003571054.1 PATCHES 987716 na +HSCHR19LRC_COX2_CTG1 novel-patch 19 Chromosome GL949747.1 = NW_003571055.1 PATCHES 729519 na +HSCHR19LRC_LRC_I_CTG1 novel-patch 19 Chromosome GL949748.1 = NW_003571056.1 PATCHES 1064303 na +HSCHR19LRC_LRC_J_CTG1 novel-patch 19 Chromosome GL949749.1 = NW_003571057.1 PATCHES 1091840 na +HSCHR19LRC_LRC_S_CTG1 novel-patch 19 Chromosome GL949750.1 = NW_003571058.1 PATCHES 1066389 na +HSCHR19LRC_LRC_T_CTG1 novel-patch 19 Chromosome GL949751.1 = NW_003571059.1 PATCHES 1002682 na +HSCHR19LRC_PGF1_CTG1 novel-patch 19 Chromosome GL949752.1 = NW_003571060.1 PATCHES 987100 na +HSCHR19LRC_PGF2_CTG1 novel-patch 19 Chromosome GL949753.1 = NW_003571061.1 PATCHES 796478 na +HG506_HG507_HG1000_PATCH fix-patch 20 Chromosome GL582979.2 = NW_003571063.2 PATCHES 179899 na +HG144_PATCH fix-patch 20 Chromosome JH720448.1 = NW_003871095.1 PATCHES 70483 na +HG944_PATCH fix-patch 20 Chromosome KB663608.1 = NW_004504304.1 PATCHES 283551 na +HSCHR20_1_CTG1 novel-patch 20 Chromosome GL383577.1 = NW_003315966.1 PATCHES 128385 na +HG237_PATCH fix-patch 21 Chromosome KE332506.1 = NW_004775435.1 PATCHES 307252 na +HSCHR21_1_CTG1_1 novel-patch 21 Chromosome GL383578.1 = NW_003315967.1 PATCHES 63917 na +HSCHR21_2_CTG1_1 novel-patch 21 Chromosome GL383579.1 = NW_003315968.1 PATCHES 201198 na +HSCHR21_3_CTG1_1 novel-patch 21 Chromosome GL383580.1 = NW_003315969.1 PATCHES 74652 na +HSCHR21_4_CTG1_1 novel-patch 21 Chromosome GL383581.1 = NW_003315970.1 PATCHES 116690 na +HG329_PATCH fix-patch 22 Chromosome JH720449.1 = NW_003871096.1 PATCHES 212298 na +HG1486_PATCH fix-patch 22 Chromosome JH806583.1 = NW_004070873.1 PATCHES 167183 na +HG1487_PATCH fix-patch 22 Chromosome JH806584.1 = NW_004070874.1 PATCHES 70876 na +HG1488_PATCH fix-patch 22 Chromosome JH806585.1 = NW_004070875.1 PATCHES 73505 na +HG497_PATCH fix-patch 22 Chromosome JH806586.1 = NW_004070876.1 PATCHES 43543 na +HSCHR22_1_CTG1 novel-patch 22 Chromosome GL383582.2 = NW_003315971.2 PATCHES 162811 na +HSCHR22_1_CTG2 novel-patch 22 Chromosome GL383583.1 = NW_003315972.1 PATCHES 96924 na +HSCHR22_2_CTG1 novel-patch 22 Chromosome KB663609.1 = NW_004504305.1 PATCHES 74013 na +HG480_HG481_PATCH fix-patch X Chromosome GL877877.2 = NW_003571064.2 PATCHES 284527 na +HG1497_PATCH fix-patch X Chromosome JH159150.3 = NW_003871103.3 PATCHES 3110903 na +HG1423_PATCH fix-patch X Chromosome JH720451.1 = NW_003871098.1 PATCHES 898979 na +HG1424_PATCH fix-patch X Chromosome JH720452.1 = NW_003871099.1 PATCHES 522319 na +HG1425_PATCH fix-patch X Chromosome JH720453.1 = NW_003871100.1 PATCHES 1461188 na +HG1426_PATCH fix-patch X Chromosome JH720454.3 = NW_003871101.3 PATCHES 752267 na +HG375_PATCH fix-patch X Chromosome JH720455.1 = NW_003871102.1 PATCHES 65034 na +HG1433_PATCH fix-patch X Chromosome JH806587.1 = NW_004070877.1 PATCHES 4110759 na +HG1434_PATCH fix-patch X Chromosome JH806588.1 = NW_004070878.1 PATCHES 862483 na +HG1435_PATCH fix-patch X Chromosome JH806589.1 = NW_004070879.1 PATCHES 270630 na +HG1436_HG1432_PATCH fix-patch X Chromosome JH806590.2 = NW_004070880.2 PATCHES 2418393 na +HG1437_PATCH fix-patch X Chromosome JH806591.1 = NW_004070881.1 PATCHES 882083 na +HG1438_PATCH fix-patch X Chromosome JH806592.1 = NW_004070882.1 PATCHES 835911 na +HG1439_PATCH fix-patch X Chromosome JH806593.1 = NW_004070883.1 PATCHES 389631 na +HG1440_PATCH fix-patch X Chromosome JH806594.1 = NW_004070884.1 PATCHES 390496 na +HG1441_PATCH fix-patch X Chromosome JH806595.1 = NW_004070885.1 PATCHES 444074 na +HG1442_PATCH fix-patch X Chromosome JH806596.1 = NW_004070886.1 PATCHES 413927 na +HG1443_HG1444_PATCH fix-patch X Chromosome JH806597.1 = NW_004070887.1 PATCHES 1045622 na +HG1453_PATCH fix-patch X Chromosome JH806598.1 = NW_004070888.1 PATCHES 899320 na +HG1458_PATCH fix-patch X Chromosome JH806599.1 = NW_004070889.1 PATCHES 1214327 na +HG1459_PATCH fix-patch X Chromosome JH806600.2 = NW_004070890.2 PATCHES 6530008 na +HG1462_PATCH fix-patch X Chromosome JH806601.1 = NW_004070891.1 PATCHES 1389764 na +HG1463_PATCH fix-patch X Chromosome JH806602.1 = NW_004070892.1 PATCHES 713266 na +HG1490_PATCH fix-patch X Chromosome JH806603.1 = NW_004070893.1 PATCHES 182949 na +HG29_PATCH fix-patch X Chromosome KB021648.1 = NW_004166866.1 PATCHES 469972 na +HSCHR6_MHC_APD_CTG1 alt-scaffold 6 Chromosome GL000250.1 = NT_167244.1 ALT_REF_LOCI_1 4622290 chr6_apd_hap1 +HSCHR6_MHC_COX_CTG1 alt-scaffold 6 Chromosome GL000251.1 = NT_113891.2 ALT_REF_LOCI_2 4795371 chr6_cox_hap2 +HSCHR6_MHC_DBB_CTG1 alt-scaffold 6 Chromosome GL000252.1 = NT_167245.1 ALT_REF_LOCI_3 4610396 chr6_dbb_hap3 +HSCHR6_MHC_MANN_CTG1 alt-scaffold 6 Chromosome GL000253.1 = NT_167246.1 ALT_REF_LOCI_4 4683263 chr6_mann_hap4 +HSCHR6_MHC_MCF_CTG1 alt-scaffold 6 Chromosome GL000254.1 = NT_167247.1 ALT_REF_LOCI_5 4833398 chr6_mcf_hap5 +HSCHR6_MHC_QBL_CTG1 alt-scaffold 6 Chromosome GL000255.1 = NT_167248.1 ALT_REF_LOCI_6 4611984 chr6_qbl_hap6 +HSCHR6_MHC_SSTO_CTG1 alt-scaffold 6 Chromosome GL000256.1 = NT_167249.1 ALT_REF_LOCI_7 4928567 chr6_ssto_hap7 +HSCHR4_1_CTG9 alt-scaffold 4 Chromosome GL000257.1 = NT_167250.1 ALT_REF_LOCI_8 590426 chr4_ctg9_hap1 +HSCHR17_1_CTG5 alt-scaffold 17 Chromosome GL000258.1 = NT_167251.1 ALT_REF_LOCI_9 1680828 chr17_ctg5_hap1 +MT assembled-molecule MT Mitochondrion J01415.2 = NC_012920.1 non-nuclear 16569 chrM diff --git a/tests/test_gene_annotation2bed.py b/tests/test_gene_annotation2bed.py index bb202e3..51e9a8f 100644 --- a/tests/test_gene_annotation2bed.py +++ b/tests/test_gene_annotation2bed.py @@ -25,6 +25,7 @@ os.path.join(os.path.dirname(__file__), 'test_data') ) +IN_GITHUB_ACTIONS = os.getenv("GITHUB_ACTIONS") == "true" class TestParseGFF(unittest.TestCase): """ @@ -451,7 +452,7 @@ class TestWriteBed(unittest.TestCase): """ def setUp(self) -> None: - self.assembly_file = "data/GCF_000001405.25_GRCh37.p13_assembly_report.txt" + self.assembly_file = "tests/test_data/GCF_000001405.25_GRCh37.p13_assembly_report.txt" self.annotation_df = pd.read_csv( f"{TEST_DATA_DIR}/example_final_merged_df.csv") self.coordinates_df = pd.read_csv(