Lots of interval_list file utility scripts
1. findGenes : Parses the Genetic Association Database (from NIH) into an annotated 'genes of interest' interval_list file. 2. sortGenesByCoverage : combines the interval_list of the genes of interest with the report from GATK's DepthOfCoverage, generating an annotated interval_list with total and average coverages on each gene. 3. hasTheseTargets : Give it a list of targets (example: exon targets) and any interval_list (example: genes of interest) and it will generate an annotated interval_list of all the exons that are contained in the list of genes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5894 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro
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-- This script parses the table of genes from http://geneticassociationdb.nih.gov/
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-- and generates an annotated interval list for use with the GATK
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--
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-- Author: carneiro
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-- Date: 5/24/2011
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ref_table = {
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"ID",
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"AS",
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"PH",
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"DI",
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"DC",
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"DT",
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"CH",
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"CB",
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"GE",
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"ST",
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"SP",
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"PV",
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"RE",
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"PI",
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"AA",
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"AF",
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"PC",
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"GN",
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"RS",
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"PO",
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"GO",
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"SU",
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"LN",
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"UN",
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"NP",
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"MP",
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"JO",
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"TI",
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"RN",
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"OM",
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"YR",
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"CN",
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"SI",
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"EF",
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"GIGA",
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"GIAA",
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"GIGB",
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"GIAB",
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"GIGC",
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"GIAC",
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"GIAS",
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"GIEF"
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}
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chr_limits = {
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249250621,
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243199373,
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198022430,
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191154276,
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180915260,
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171115067,
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159138663,
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146364022,
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141213431,
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135534747,
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135006516,
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133851895,
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115169878,
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107349540,
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102531392,
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90354753,
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81195210,
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78077248,
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59128983,
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63025520,
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48129895,
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51304566,
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155270560,
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59373566,
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16569
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}
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local header = [[@HD VN:1.0 SO:coordinate
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@SQ SN:1 LN:249250621 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens
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@SQ SN:2 LN:243199373 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens
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@SQ SN:3 LN:198022430 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens
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@SQ SN:4 LN:191154276 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens
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@SQ SN:5 LN:180915260 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapiens
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@SQ SN:6 LN:171115067 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapiens
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@SQ SN:7 LN:159138663 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapiens
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@SQ SN:8 LN:146364022 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:96f514a9929e410c6651697bded59aec SP:Homo Sapiens
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@SQ SN:9 LN:141213431 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapiens
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@SQ SN:10 LN:135534747 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapiens
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@SQ SN:11 LN:135006516 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapiens
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@SQ SN:12 LN:133851895 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapiens
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@SQ SN:13 LN:115169878 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapiens
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@SQ SN:14 LN:107349540 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapiens
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@SQ SN:15 LN:102531392 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapiens
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@SQ SN:16 LN:90354753 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapiens
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@SQ SN:17 LN:81195210 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapiens
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@SQ SN:18 LN:78077248 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapiens
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@SQ SN:19 LN:59128983 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapiens
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@SQ SN:20 LN:63025520 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens
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@SQ SN:21 LN:48129895 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapiens
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@SQ SN:22 LN:51304566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens
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@SQ SN:X LN:155270560 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens
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@SQ SN:Y LN:59373566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens
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@SQ SN:MT LN:16569 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens
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@SQ SN:GL000207.1 LN:4262 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens
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@SQ SN:GL000226.1 LN:15008 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens
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@SQ SN:GL000229.1 LN:19913 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo Sapiens
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@SQ SN:GL000231.1 LN:27386 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo Sapiens
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@SQ SN:GL000210.1 LN:27682 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:851106a74238044126131ce2a8e5847c SP:Homo Sapiens
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@SQ SN:GL000239.1 LN:33824 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo Sapiens
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@SQ SN:GL000235.1 LN:34474 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo Sapiens
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@SQ SN:GL000201.1 LN:36148 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo Sapiens
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@SQ SN:GL000247.1 LN:36422 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo Sapiens
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@SQ SN:GL000245.1 LN:36651 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo Sapiens
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@SQ SN:GL000197.1 LN:37175 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo Sapiens
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@SQ SN:GL000203.1 LN:37498 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo Sapiens
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@SQ SN:GL000246.1 LN:38154 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo Sapiens
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@SQ SN:GL000249.1 LN:38502 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo Sapiens
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@SQ SN:GL000196.1 LN:38914 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo Sapiens
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@SQ SN:GL000248.1 LN:39786 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo Sapiens
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@SQ SN:GL000244.1 LN:39929 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:0996b4475f353ca98bacb756ac479140 SP:Homo Sapiens
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@SQ SN:GL000238.1 LN:39939 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:131b1efc3270cc838686b54e7c34b17b SP:Homo Sapiens
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@SQ SN:GL000202.1 LN:40103 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:06cbf126247d89664a4faebad130fe9c SP:Homo Sapiens
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@SQ SN:GL000234.1 LN:40531 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:93f998536b61a56fd0ff47322a911d4b SP:Homo Sapiens
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@SQ SN:GL000232.1 LN:40652 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3e06b6741061ad93a8587531307057d8 SP:Homo Sapiens
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@SQ SN:GL000206.1 LN:41001 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo Sapiens
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@SQ SN:GL000240.1 LN:41933 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo Sapiens
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@SQ SN:GL000236.1 LN:41934 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo Sapiens
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@SQ SN:GL000241.1 LN:42152 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens
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@SQ SN:GL000243.1 LN:43341 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens
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@SQ SN:GL000242.1 LN:43523 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens
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@SQ SN:GL000230.1 LN:43691 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens
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@SQ SN:GL000237.1 LN:45867 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens
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@SQ SN:GL000233.1 LN:45941 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo Sapiens
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@SQ SN:GL000204.1 LN:81310 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo Sapiens
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@SQ SN:GL000198.1 LN:90085 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:868e7784040da90d900d2d1b667a1383 SP:Homo Sapiens
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@SQ SN:GL000208.1 LN:92689 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo Sapiens
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@SQ SN:GL000191.1 LN:106433 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo Sapiens
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@SQ SN:GL000227.1 LN:128374 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo Sapiens
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@SQ SN:GL000228.1 LN:129120 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo Sapiens
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@SQ SN:GL000214.1 LN:137718 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo Sapiens
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@SQ SN:GL000221.1 LN:155397 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens
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@SQ SN:GL000209.1 LN:159169 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens
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@SQ SN:GL000218.1 LN:161147 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens
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@SQ SN:GL000220.1 LN:161802 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens
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@SQ SN:GL000213.1 LN:164239 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens
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@SQ SN:GL000211.1 LN:166566 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens
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@SQ SN:GL000199.1 LN:169874 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens
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@SQ SN:GL000217.1 LN:172149 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens
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@SQ SN:GL000216.1 LN:172294 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens
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@SQ SN:GL000215.1 LN:172545 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens
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@SQ SN:GL000205.1 LN:174588 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens
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@SQ SN:GL000219.1 LN:179198 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens
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@SQ SN:GL000224.1 LN:179693 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens
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@SQ SN:GL000223.1 LN:180455 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens
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@SQ SN:GL000195.1 LN:182896 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens
|
||||
@SQ SN:GL000212.1 LN:186858 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens
|
||||
@SQ SN:GL000222.1 LN:186861 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens
|
||||
@SQ SN:GL000200.1 LN:187035 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens
|
||||
@SQ SN:GL000193.1 LN:189789 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens
|
||||
@SQ SN:GL000194.1 LN:191469 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens
|
||||
@SQ SN:GL000225.1 LN:211173 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens
|
||||
@SQ SN:GL000192.1 LN:547496 AS:GRCh37 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens
|
||||
@SQ SN:NC_007605 LN:171823 AS:NC_007605.1 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus]]
|
||||
|
||||
local function comp(a, b)
|
||||
if a.chr == b.chr then return a.start < b.start end
|
||||
local x = tonumber(a.chr)
|
||||
local y = tonumber(b.chr)
|
||||
if x and y then
|
||||
return x < y end
|
||||
return a.chr < b.chr
|
||||
end
|
||||
|
||||
local function cleanNumber (x)
|
||||
local t = x:gsub(",","")
|
||||
return tonumber(t)
|
||||
end
|
||||
|
||||
local function cleanDisease (x)
|
||||
local d = x:gsub("[^%w%s]", "")
|
||||
return d:gsub(" ", "_")
|
||||
end
|
||||
|
||||
local function isSameGene (g1, g2)
|
||||
return g1.chr == g2.chr and
|
||||
g1.start == g2.start and
|
||||
g1.finish == g2.finish
|
||||
end
|
||||
|
||||
local function isValidGene(gene)
|
||||
local x
|
||||
if gene.chr == "X" then x = 23
|
||||
elseif gene.chr == "Y" then x = 24
|
||||
elseif gene.chr == "MT" then x = 25
|
||||
else x = tonumber(gene.chr) end
|
||||
|
||||
return x >= 1 and x <= 25 and gene.start < gene.finish and chr_limits[x] > gene.finish
|
||||
end
|
||||
|
||||
|
||||
local function addGene(geneTable, gene)
|
||||
if isValidGene(gene) then -- only adds valid genes
|
||||
local geneAdded = false
|
||||
for _, g in ipairs(geneTable) do
|
||||
if isSameGene(gene, g) then
|
||||
geneAdded = true
|
||||
if g.disease ~= gene.disease then
|
||||
g.disease = g.disease .. ","..gene.disease
|
||||
end
|
||||
end
|
||||
end
|
||||
if (not geneAdded) then
|
||||
table.insert(geneTable, gene)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
local function cleanIntervals(f, t)
|
||||
for l in io.lines(f) do
|
||||
local counter = 1
|
||||
local id, c, b, e, disease
|
||||
for match in l:gmatch("(.-);;") do
|
||||
-- print("DEBUG: ", counter, match)
|
||||
if counter == 1 then id = match
|
||||
elseif counter == 3 then disease = cleanDisease(match)
|
||||
elseif counter == 7 then c = match
|
||||
elseif counter == 10 then b = cleanNumber(match)
|
||||
elseif counter == 11 then e = cleanNumber(match)
|
||||
end
|
||||
counter = counter + 1
|
||||
end
|
||||
if id and c and b and e and c~= "" then
|
||||
addGene(t, {id=id, chr=c, start=b, finish=e, disease=disease})
|
||||
end
|
||||
end
|
||||
return table.sort(t, comp)
|
||||
end
|
||||
|
||||
local function printIntervals(t)
|
||||
print(header)
|
||||
for _,interval in ipairs(t) do
|
||||
print(interval.chr,interval.start,interval.finish, "+", interval.id..":::"..interval.disease)
|
||||
end
|
||||
end
|
||||
|
||||
t = {}
|
||||
cleanIntervals(arg[1], t)
|
||||
printIntervals(t)
|
||||
|
||||
--[[
|
||||
-- REFERENCE TABLE
|
||||
|
||||
1 ID
|
||||
2 Association(Y/N)
|
||||
3 Broad Phenotype
|
||||
4 Disease Class
|
||||
5 Disease Class Code
|
||||
6 MeSH Disease Terms
|
||||
7 Chromosom
|
||||
8 Chr-Band
|
||||
9 Gene
|
||||
10 DNA Start
|
||||
11 DNA End
|
||||
12 P Value
|
||||
13 Reference
|
||||
14 Pubmed ID
|
||||
15 Allele Author Description
|
||||
16 Allele Functional Effects
|
||||
17 Polymophism Class
|
||||
18 Gene Name
|
||||
19 RefSeq
|
||||
20 Population
|
||||
21 MeSH Geolocation
|
||||
22 Submitter
|
||||
23 Locus Number
|
||||
24 Unigene
|
||||
25 Narrow Phenotype
|
||||
26 Mole. Phenotype
|
||||
27 Journal
|
||||
28 Title
|
||||
29 rs Number
|
||||
30 OMIM ID
|
||||
31 Year
|
||||
32 Conclusion
|
||||
33 Study Info
|
||||
34 Env. Factor
|
||||
35 GI Gene A
|
||||
36 GI Allele of Gene A
|
||||
37 GI Gene B
|
||||
38 GI Allele of Gene B
|
||||
39 GI Gene C
|
||||
40 GI Allele of Gene C
|
||||
41 GI Association?
|
||||
42 GI combine Env. Factor
|
||||
--]]
|
||||
|
|
@ -0,0 +1,147 @@
|
|||
-- This script takes two interval lists (a and b) and creates another interval list (c) with the intervals in a that are
|
||||
-- inside the targets in b. For example, if a is a list of exon targets and b a list of genes, then c would be all exons
|
||||
-- covered by the genes in file b.
|
||||
--
|
||||
-- Author: carneiro
|
||||
-- Date: 5/26/2011
|
||||
|
||||
local targetList = arg[1] -- list of targets to check if they are part of the set
|
||||
local targetSet = arg[2] -- set of targets
|
||||
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Parses a line from an interval list file (not a header line!)
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: chromosome
|
||||
-- 2: interval start
|
||||
-- 3: interval end
|
||||
-- 4: strand (+/-)
|
||||
-- 5: info field
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function parseIntervalLine(l)
|
||||
return l:match("(%w+)%s+(%d+)%s+(%d+)%s+([%+%-])%s+(.*)")
|
||||
end
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Reads an interval list file into a table
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: index pairs table with each interval (each interval is a table of the form {c, s, e, strand, info})
|
||||
-- 2: header string
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function readIntervals(filename)
|
||||
t = {}
|
||||
header = ""
|
||||
for l in io.lines(filename) do
|
||||
if l:sub(1,1) == "@" then header = header .. l .."\n"
|
||||
else
|
||||
local c, s, e, strand, info = parseIntervalLine(l)
|
||||
table.insert(t, {c=c, s=tonumber(s), e=tonumber(e), strand=strand, info=info})
|
||||
end
|
||||
end
|
||||
return t, header
|
||||
end
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Checks if two intervals have the same chromosome, start and end.
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: true/false
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function isSameInterval(i, c, s, e)
|
||||
return i.c == c and s == i.s and e == i.e
|
||||
end
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Checks if the line from an interval list file is a header line
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: true/false
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function isIntervalHeaderLine(l)
|
||||
return l:sub(1,1) == "@"
|
||||
end
|
||||
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Compares the start position of two intervals
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: -1, 0 or 1 (respectively for a < b, a == b, a > b)
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function compIntervals(a, b)
|
||||
|
||||
local function c(x,y)
|
||||
if x < y then return -1
|
||||
elseif x > y then return 1
|
||||
else return 0 end
|
||||
end
|
||||
-- same chromosomes
|
||||
if a.c == b.c then return c(a.s, b.s)
|
||||
else
|
||||
x = tonumber(a.c)
|
||||
y = tonumber(b.c)
|
||||
if x and y then return c(x,y)
|
||||
else return c(a.c, b.c) end
|
||||
end
|
||||
end
|
||||
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
-- Creates a new interval
|
||||
--
|
||||
-- Return values:
|
||||
-- 1: interval table {c, s, e, st, info}
|
||||
------------------------------------------------------------------------------------------------------------------------
|
||||
local function newInterval(c,s,e,st,info)
|
||||
return {c=c, s=tonumber(s), e=tonumber(e), st=st, info=info }
|
||||
end
|
||||
|
||||
local function printInterval(i)
|
||||
print(i.c, i.s, i.e, i.st, i.info)
|
||||
end
|
||||
|
||||
local function intervalContainsInterval(a, b)
|
||||
return a.c == b.c and a.s <= b.s and a.e >= b.e
|
||||
end
|
||||
|
||||
local function isInterceptingInterval(a, b)
|
||||
return a.s < b.s and a.e < b.e and a.e > b.s
|
||||
end
|
||||
|
||||
local function findInterval(i, intervals)
|
||||
local start = 1
|
||||
local finish = table.getn(intervals)
|
||||
local current = math.floor((start + finish) / 2)
|
||||
|
||||
-- print("findInterval: ", start, finish, current, intervals[current].c, intervals[current].s, intervals[current].e)
|
||||
|
||||
while start < finish and not intervalContainsInterval(i, intervals[current]) and not isInterceptingInterval(i, intervals[current]) do
|
||||
if compIntervals(i, intervals[current]) < 0 then
|
||||
finish = current - 1
|
||||
else
|
||||
start = current + 1
|
||||
end
|
||||
current = math.floor((start + finish) / 2)
|
||||
-- print("findInterval: ", start, finish, current, intervals[current].c, intervals[current].s, intervals[current].e)
|
||||
end
|
||||
return intervalContainsInterval(i, intervals[current]), current
|
||||
end
|
||||
|
||||
|
||||
|
||||
|
||||
local a, header = readIntervals(targetList)
|
||||
io.write(header)
|
||||
|
||||
for l in io.lines(targetSet) do
|
||||
if not isIntervalHeaderLine(l) then
|
||||
local c, s, e, st, info = parseIntervalLine(l)
|
||||
local intA = newInterval(c,s,e,st,info)
|
||||
-- print("Debug: ", c,s,e,info)
|
||||
local intervalExists, i = findInterval(intA, a)
|
||||
if intervalExists then
|
||||
print(a[i].c, a[i].s, a[i].e, st, info)
|
||||
end
|
||||
end
|
||||
end
|
||||
|
|
@ -0,0 +1,66 @@
|
|||
-- This script takes the interval summary output from GATK's Depth of Coverage and the
|
||||
-- interval list for 'genes of interest' and generates an intervals file sorted by
|
||||
-- coverage.
|
||||
--
|
||||
-- Author: carneiro
|
||||
-- Date: 5/26/2011
|
||||
-------------------------------------------------------------------------------
|
||||
-- Global script variables
|
||||
-------------------------------------------------------------------------------
|
||||
local coverage = arg[1]
|
||||
local genesOfInterest= arg[2] or "/Volumes/humgen/gsa-hpprojects/dev/carneiro/top_genes/data/disease.genes.annotated.interval_list"
|
||||
|
||||
local genes = {}
|
||||
local header = ""
|
||||
|
||||
-------------------------------------------------------------------------------
|
||||
-- Helper functions
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
local function isSameGene(i, c, s, e)
|
||||
return genes[i].c == c and s == genes[i].s and e == genes[i].e
|
||||
end
|
||||
|
||||
local function isMergedGene(i, c, s, e)
|
||||
return genes[i].c == c and s <= genes[i].s and e >= genes[i].e
|
||||
end
|
||||
|
||||
local function comp(a,b)
|
||||
return a.avgCoverage < b.avgCoverage
|
||||
end
|
||||
|
||||
for l in io.lines(genesOfInterest) do
|
||||
if l:sub(1,1) == "@" then header = header .. l .."\n"
|
||||
else
|
||||
local c, s, e, info = l:match("(%w+)%s+(%d+)%s+(%d+)%s+%+%s+(.*)")
|
||||
-- print("Debug: adding gene: ",c,s,e,info)
|
||||
table.insert(genes, {c=c, s=tonumber(s), e=tonumber(e), info=info})
|
||||
end
|
||||
end
|
||||
|
||||
local i = 1
|
||||
for l in io.lines(coverage) do
|
||||
local geneOk = false
|
||||
if l:match("(%w+)") ~= "Target" then -- skip the first line (header)
|
||||
local c, s, e, totalCoverage, avgCoverage = l:match("(%w+):(%d+)%-(%d+)%s+(%d+)%s+([%d%.]+)")
|
||||
s = tonumber(s)
|
||||
e = tonumber(e)
|
||||
while genes[i] ~= nil and (isSameGene(i, c, s, e) or isMergedGene(i, c, s, e)) do
|
||||
-- print("Debug: ", c, s, e, "--",genes[i].c, genes[i].s, genes[i].e)
|
||||
genes[i].totalCoverage = tonumber(totalCoverage)
|
||||
genes[i].avgCoverage = tonumber(avgCoverage)
|
||||
geneOk = true
|
||||
i = i + 1
|
||||
end
|
||||
if not geneOk then
|
||||
error("Warning: Gene mismatch! Crazy!", c,s,e,"--",genes[i].c, genes[i].s, genes[i].e)
|
||||
break
|
||||
end
|
||||
end
|
||||
end
|
||||
|
||||
table.sort(genes, comp)
|
||||
io.write(header)
|
||||
for _, g in ipairs(genes) do
|
||||
print(g.c,g.s,g.e,"+",g.avgCoverage..":::"..g.totalCoverage..":::"..g.info)
|
||||
end
|
||||
Loading…
Reference in New Issue