diff --git a/bin/config/housekeeping.yaml b/bin/config/housekeeping.yaml index eddb8c6..33e6f1b 100644 --- a/bin/config/housekeeping.yaml +++ b/bin/config/housekeeping.yaml @@ -29,9 +29,7 @@ indexed_special_collections: db_key: id indexed_special_dbs: - cellz: - biosamples: location: db_key: provenance.geo_location.geometry @@ -40,10 +38,32 @@ indexed_special_dbs: location: db_key: provenance.geo_location.geometry type: 2dsphere - + variants: + variantbracketquery: + db_key: + variant_state.id: 1 + location.sequence_id: 1 + location.start: 1 + location.end: 1 + info.var_length: 1 + type: compound + variantallelequery: + db_key: + location.sequence_id: 1 + location.start: 1 + sequence: 1 + reference_sequence: 1 + type: compound + variantrangequery: + db_key: + location.sequence_id: 1 + location.start: 1 + location.end: 1 + variant_state.id: 1 + sequence: 1 + type: compound progenetix: - biosamples: location: db_key: provenance.geo_location.geometry @@ -52,6 +72,30 @@ indexed_special_dbs: location: db_key: provenance.geo_location.geometry type: 2dsphere + variants: + variantbracketquery: + db_key: + variant_state.id: 1 + location.sequence_id: 1 + location.start: 1 + location.end: 1 + info.var_length: 1 + type: compound + variantallelequery: + db_key: + location.sequence_id: 1 + location.start: 1 + sequence: 1 + reference_sequence: 1 + type: compound + variantrangequery: + db_key: + location.sequence_id: 1 + location.start: 1 + location.end: 1 + variant_state.id: 1 + sequence: 1 + type: compound publications: id: diff --git a/bin/lib/mongodb_utils.py b/bin/lib/mongodb_utils.py index 6f1757b..8c2c18d 100644 --- a/bin/lib/mongodb_utils.py +++ b/bin/lib/mongodb_utils.py @@ -13,12 +13,10 @@ def mongodb_update_indexes(ds_id, byc): data_db = mongo_client[ds_id] coll_names = data_db.list_collection_names() for r_t, r_d in b_rt_s.items(): - collname = r_d.get("collection", False) if collname not in coll_names: print(f"¡¡¡ Collection {collname} does not exist in {ds_id} !!!") continue - i_coll = data_db[ collname ] io_params = dt_m["definitions"][ r_t ]["parameters"] @@ -51,7 +49,6 @@ def mongodb_update_indexes(ds_id, byc): ################################################################################ def __index_by_colldef(ds_id, coll_defs): - mongo_client = MongoClient(host=DB_MONGOHOST) i_db = mongo_client[ds_id] coll_names = i_db.list_collection_names() @@ -61,7 +58,6 @@ def __index_by_colldef(ds_id, coll_defs): continue i_coll = i_db[ collname ] - for p_k, p_v in io_params.items(): special = p_v.get("type", "___none___") k = p_v["db_key"] @@ -69,6 +65,10 @@ def __index_by_colldef(ds_id, coll_defs): print(f'Creating GEOSPHERE index "{k}" in {collname} from {ds_id}') i_coll.create_index([(k, GEOSPHERE)]) pass + elif "compound" in special: + print(f'Creating compound index "{k}" in {collname} from {ds_id}') + i_coll.create_index(k) + pass else: print(f'Creating index "{k}" in {collname} from {ds_id}') try: @@ -77,7 +77,3 @@ def __index_by_colldef(ds_id, coll_defs): except Exception: print(f'¡¡¡ Index "{k}" in {collname} from {ds_id} has one with same id !!!') - - - - diff --git a/bin/pgxProbesPlotter.py b/bin/pgxProbesPlotter.py index c6fbe32..1d47650 100755 --- a/bin/pgxProbesPlotter.py +++ b/bin/pgxProbesPlotter.py @@ -18,9 +18,9 @@ ################################################################################ def main(): - pgx_probes_plotter() + ################################################################################ def pgx_probes_plotter(): @@ -34,7 +34,6 @@ def pgx_probes_plotter(): if not input_file: print("No input file specified (-i, --inputfile) => read_probedata_file(filepath, byc):quitting ...") exit() - if not "probe" in input_file: print('Only probe files are accepted (should have "...probes..." in name).') exit() @@ -43,7 +42,6 @@ def pgx_probes_plotter(): # TODO: method for multiple? cs_probes = pb.read_probedata_file(input_file) - plot_data_bundle = { "callsets_probes_bundles": [ {"id": "TBD", "probes": cs_probes }] } diff --git a/imports/variants.pgxseg b/imports/variants.pgxseg new file mode 100644 index 0000000..2ab0499 --- /dev/null +++ b/imports/variants.pgxseg @@ -0,0 +1,275 @@ +#meta=>id=progenetix +#meta=>assemblyId=GRCh38 +#meta=>pagination.skip=0;pagination.limit=200 +#sample=>id=pgxbs-kftviq25;biosample_id=pgxbs-kftviq25;individual_id=pgxind-kftx4g36;pubmed_id=PMID:20229506;pubmed_label=Ahmed AA, Etemadmoghadam D et al. (2010): Driver mutations in TP53 are ubiquitous...;external_references_id___PMID=PMID:20229506;group_id=NCIT:C4908;histological_diagnosis_id=NCIT:C4908;group_label=Ovarian Carcinoma;histological_diagnosis_label=Ovarian Carcinoma;icdo_morphology_id=pgx:icdom-80103;icdo_morphology_label=Carcinoma, NOS;icdo_topography_id=pgx:icdot-C56.9;icdo_topography_label=Ovary;pathological_stage_id=NCIT:C27970;pathological_stage_label=Stage III;biosample_status_id=EFO:0009656;biosample_status_label=neoplastic sample;sampled_tissue_id=UBERON:0000992;sampled_tissue_label=ovary;age_iso=P22Y;followup_state_id=EFO:0030039;followup_state_label=no followup status;experiment_id=geo:GSM482789;series_id=geo:GSE19416;platform_id=geo:GPL6801 +#meta=>pagination.skip=0;pagination.limit=200 +#sample=>id=pgxbs-kftviq25;biosample_id=pgxbs-kftviq25;individual_id=pgxind-kftx4g36;pubmed_id=PMID:20229506;pubmed_label=Ahmed AA, Etemadmoghadam D et al. (2010): Driver mutations in TP53 are ubiquitous...;external_references_id___PMID=PMID:20229506;group_id=NCIT:C4908;histological_diagnosis_id=NCIT:C4908;group_label=Ovarian Carcinoma;histological_diagnosis_label=Ovarian Carcinoma;icdo_morphology_id=pgx:icdom-80103;icdo_morphology_label=Carcinoma, NOS;icdo_topography_id=pgx:icdot-C56.9;icdo_topography_label=Ovary;pathological_stage_id=NCIT:C27970;pathological_stage_label=Stage III;biosample_status_id=EFO:0009656;biosample_status_label=neoplastic sample;sampled_tissue_id=UBERON:0000992;sampled_tissue_label=ovary;age_iso=P22Y;followup_state_id=EFO:0030039;followup_state_label=no followup status;experiment_id=geo:GSM482789;series_id=geo:GSE19416;platform_id=geo:GPL6801 +biosample_id reference_name start end log2 variant_type reference_bases alternate_bases +pgxbs-kftviq25 1 61736 785910 0.4964 DUP . . +pgxbs-kftviq25 1 787938 3830146 -0.3306 DEL . . +pgxbs-kftviq25 1 3830314 34272616 -0.4466 DEL . . +pgxbs-kftviq25 1 34273097 72284670 -0.4986 DEL . . +pgxbs-kftviq25 1 72290431 72297688 -2.1683 DEL . . +pgxbs-kftviq25 1 72302736 72345466 1.3714 DUP . . +pgxbs-kftviq25 1 72346221 105476689 -0.5249 DEL . . +pgxbs-kftviq25 1 105476749 105479754 -2.028 DEL . . +pgxbs-kftviq25 1 105481434 121614084 -0.4917 DEL . . +pgxbs-kftviq25 2 146107616 146109367 -1.9068 DEL . . +pgxbs-kftviq25 3 37940970 37945438 -2.506 DEL . . +pgxbs-kftviq25 3 68682878 68698263 1.1224 DUP . . +pgxbs-kftviq25 3 162790481 162908785 0.5325 DUP . . +pgxbs-kftviq25 3 188635218 188640802 -1.273 DEL . . +pgxbs-kftviq25 3 193160257 193165115 1.6213 DUP . . +pgxbs-kftviq25 3 193621122 193635572 -0.5441 DEL . . +pgxbs-kftviq25 4 12282 62089 0.417 DUP . . +pgxbs-kftviq25 4 3195921 4183759 0.1791 DUP . . +pgxbs-kftviq25 4 9459505 9477700 1.3033 DUP . . +pgxbs-kftviq25 4 34785334 34823104 -2.6071 DEL . . +pgxbs-kftviq25 4 114254168 114261020 -1.1073 DEL . . +pgxbs-kftviq25 4 171453734 171456783 1.4014 DUP . . +pgxbs-kftviq25 5 417800 424589 -0.6693 DEL . . +pgxbs-kftviq25 5 617982 619218 -1.1563 DEL . . +pgxbs-kftviq25 5 717265 806222 0.8096 DUP . . +pgxbs-kftviq25 5 46271829 46273401 -2.2328 DEL . . +pgxbs-kftviq25 5 118052916 118053390 -2.271 DEL . . +pgxbs-kftviq25 6 257354 291083 -0.4766 DEL . . +pgxbs-kftviq25 6 8338340 8339626 -3.9713 DEL . . +pgxbs-kftviq25 6 29869365 29931900 0.5651 DUP . . +pgxbs-kftviq25 6 29933788 29933800 2.0411 DUP . . +pgxbs-kftviq25 6 29937088 29950810 0.3524 DUP . . +pgxbs-kftviq25 6 29953298 29953447 1.1698 DUP . . +pgxbs-kftviq25 6 31512495 31526961 -0.5282 DEL . . +pgxbs-kftviq25 6 31888293 32139670 0.2792 DUP . . +pgxbs-kftviq25 6 32488907 32605995 1.0945 DUP . . +pgxbs-kftviq25 6 72156822 72157170 -2.4892 DEL . . +pgxbs-kftviq25 6 76730151 76743041 -0.6292 DEL . . +pgxbs-kftviq25 6 78262086 78329517 -0.5086 DEL . . +pgxbs-kftviq25 6 103290102 103314187 0.6139 DUP . . +pgxbs-kftviq25 6 104357840 104358666 -2.3152 DEL . . +pgxbs-kftviq25 8 7392859 7981253 0.3623 DUP . . +pgxbs-kftviq25 8 9198858 9204980 -0.635 DEL . . +pgxbs-kftviq25 8 12145208 12376892 0.2556 DUP . . +pgxbs-kftviq25 8 12382327 12464389 0.5822 DUP . . +pgxbs-kftviq25 8 12465084 12728923 0.2633 DUP . . +pgxbs-kftviq25 8 25117063 25126709 -2.6984 DEL . . +pgxbs-kftviq25 8 111282853 111283032 -2.3524 DEL . . +pgxbs-kftviq25 9 46431 216919 0.2866 DUP . . +pgxbs-kftviq25 9 23363118 23373487 -2.0406 DEL . . +pgxbs-kftviq25 9 75155918 75156169 -3.5214 DEL . . +pgxbs-kftviq25 9 103806416 103807010 -2.7156 DEL . . +pgxbs-kftviq25 9 114323991 114326043 1.3905 DUP . . +pgxbs-kftviq25 9 114330749 114465835 0.1944 DUP . . +pgxbs-kftviq25 9 124749761 124863449 0.3523 DUP . . +pgxbs-kftviq25 10 6357017 6357021 1.5867 DUP . . +pgxbs-kftviq25 10 43093463 43093496 1.1027 DUP . . +pgxbs-kftviq25 10 45653981 46154875 0.3154 DUP . . +pgxbs-kftviq25 10 50081225 50132161 -1.6537 DEL . . +pgxbs-kftviq25 10 50096999 50097501 2.3853 DUP . . +pgxbs-kftviq25 10 65548834 65551544 -0.7026 DEL . . +pgxbs-kftviq25 10 76497853 76500828 -2.2052 DEL . . +pgxbs-kftviq25 11 72841398 73128749 -0.1943 DEL . . +pgxbs-kftviq25 11 73129465 73402072 0.1731 DUP . . +pgxbs-kftviq25 12 11069769 11088934 -1.3244 DEL . . +pgxbs-kftviq25 12 30084564 30090682 -1.5179 DEL . . +pgxbs-kftviq25 14 25290708 25290944 -3.0642 DEL . . +pgxbs-kftviq25 14 26314706 26314713 1.5101 DUP . . +pgxbs-kftviq25 14 106294690 106370709 0.3717 DUP . . +pgxbs-kftviq25 15 20187569 22206805 0.3598 DUP . . +pgxbs-kftviq25 15 24258513 24473450 0.4824 DUP . . +pgxbs-kftviq25 15 53492998 53493083 -2.8753 DEL . . +pgxbs-kftviq25 15 76599401 76603435 -1.8775 DEL . . +pgxbs-kftviq25 16 32577581 32577589 -2.6669 DEL . . +pgxbs-kftviq25 16 33567298 33908314 -0.2893 DEL . . +pgxbs-kftviq25 16 78338544 78351105 0.6028 DUP . . +pgxbs-kftviq25 20 54062820 54062841 -1.7324 DEL . . +pgxbs-kftviq25 21 10775583 13384908 0.1527 DUP . . +pgxbs-kftviq25 22 38900536 38900900 -3.7248 DEL . . +pgxbs-kftviq27 1 61736 98603 -0.671 DEL . . +pgxbs-kftviq27 1 3619081 12799265 -0.3322 DEL . . +pgxbs-kftviq27 1 12802106 12823122 0.4283 DUP . . +pgxbs-kftviq27 1 12823234 16504326 -0.3443 DEL . . +pgxbs-kftviq27 1 16719267 30947040 -0.331 DEL . . +pgxbs-kftviq27 1 72280851 72345466 0.5836 DUP . . +pgxbs-kftviq27 1 95825289 97086687 0.2665 DUP . . +pgxbs-kftviq27 1 109683299 109697557 0.9263 DUP . . +pgxbs-kftviq27 1 112153052 112154769 -1.2532 DEL . . +pgxbs-kftviq27 1 143708230 143714440 0.1978 DUP . . +pgxbs-kftviq27 1 143714500 143796141 -0.4393 DEL . . +pgxbs-kftviq27 1 150880583 152583231 0.269 DUP . . +pgxbs-kftviq27 1 152583292 152614065 -1.1113 DEL . . +pgxbs-kftviq27 1 152614101 200726019 0.257 DUP . . +pgxbs-kftviq27 1 200731841 208267558 0.3127 DUP . . +pgxbs-kftviq27 1 208272376 248930190 0.2604 DUP . . +pgxbs-kftviq27 2 11957235 12020910 -0.4438 DEL . . +pgxbs-kftviq27 2 105677339 107305983 0.2583 DUP . . +pgxbs-kftviq27 2 122724153 122724666 -2.0056 DEL . . +pgxbs-kftviq27 2 139993332 190328371 0.235 DUP . . +pgxbs-kftviq27 2 234818101 242147306 -0.3366 DEL . . +pgxbs-kftviq27 3 18668 182920 0.2978 DUP . . +pgxbs-kftviq27 3 188340 193194 -1.7291 DEL . . +pgxbs-kftviq27 3 193348 1627341 0.1906 DUP . . +pgxbs-kftviq27 3 1629041 1879549 -1.2483 DEL . . +pgxbs-kftviq27 3 1881281 6035486 0.2061 DUP . . +pgxbs-kftviq27 3 6036310 6059864 -1.2296 DEL . . +pgxbs-kftviq27 3 6061586 40244996 0.2014 DUP . . +pgxbs-kftviq27 3 40248356 50110777 -0.4333 DEL . . +pgxbs-kftviq27 3 50115923 50649522 -0.1983 DEL . . +pgxbs-kftviq27 3 50651608 62972231 -0.4519 DEL . . +pgxbs-kftviq27 3 62975756 63005833 -1.5584 DEL . . +pgxbs-kftviq27 3 63009873 68682878 -0.449 DEL . . +pgxbs-kftviq27 3 68697014 68698263 1.221 DUP . . +pgxbs-kftviq27 3 68699608 77094426 -0.468 DEL . . +pgxbs-kftviq27 3 146625951 162790481 0.2342 DUP . . +pgxbs-kftviq27 3 162794870 162908193 1.1884 DUP . . +pgxbs-kftviq27 3 162908208 198169248 0.2308 DUP . . +pgxbs-kftviq27 4 9459505 9484441 0.9673 DUP . . +pgxbs-kftviq27 4 10227494 10229174 -1.4237 DEL . . +pgxbs-kftviq27 4 55337032 63831892 -0.4719 DEL . . +pgxbs-kftviq27 4 63832016 63841888 0.4118 DUP . . +pgxbs-kftviq27 4 63842037 68506286 -0.4893 DEL . . +pgxbs-kftviq27 4 68509224 68530749 0.4983 DUP . . +pgxbs-kftviq27 4 68544507 68548136 1.4442 DUP . . +pgxbs-kftviq27 4 68548223 68655692 0.617 DUP . . +pgxbs-kftviq27 4 68663242 171448196 -0.4538 DEL . . +pgxbs-kftviq27 4 171453734 171456783 1.3644 DUP . . +pgxbs-kftviq27 4 171459221 190106769 -0.4451 DEL . . +pgxbs-kftviq27 5 617982 621576 -0.863 DEL . . +pgxbs-kftviq27 5 717447 818427 0.6188 DUP . . +pgxbs-kftviq27 5 58030201 58037707 1.4829 DUP . . +pgxbs-kftviq27 5 104686163 123304418 0.2093 DUP . . +pgxbs-kftviq27 5 156049989 156055720 -1.0901 DEL . . +pgxbs-kftviq27 5 171671878 180260281 0.2762 DUP . . +pgxbs-kftviq27 5 180514677 180565696 -0.4892 DEL . . +pgxbs-kftviq27 6 271774 385785 0.2475 DUP . . +pgxbs-kftviq27 6 29906933 29931900 -0.528 DEL . . +pgxbs-kftviq27 6 29933788 29933800 1.1604 DUP . . +pgxbs-kftviq27 6 31888293 32218571 0.3094 DUP . . +pgxbs-kftviq27 6 32488907 32606605 0.9985 DUP . . +pgxbs-kftviq27 6 78252228 78332057 -0.3886 DEL . . +pgxbs-kftviq27 6 98787484 157146023 -0.4471 DEL . . +pgxbs-kftviq27 6 157161088 160765609 -0.3641 DEL . . +pgxbs-kftviq27 6 160765857 166491364 -0.4452 DEL . . +pgxbs-kftviq27 6 166491713 168773410 -0.3339 DEL . . +pgxbs-kftviq27 6 168774208 170741918 -0.4318 DEL . . +pgxbs-kftviq27 7 54183 3205266 -0.3153 DEL . . +pgxbs-kftviq27 7 3206507 3774253 -0.4826 DEL . . +pgxbs-kftviq27 7 57532934 63255714 0.1525 DUP . . +pgxbs-kftviq27 7 91730277 97756659 -0.1644 DEL . . +pgxbs-kftviq27 7 97766149 97766198 1.0859 DUP . . +pgxbs-kftviq27 7 126405429 126406828 1.3653 DUP . . +pgxbs-kftviq27 7 142346125 144682336 0.1667 DUP . . +pgxbs-kftviq27 7 149615067 159334315 0.1619 DUP . . +pgxbs-kftviq27 8 81255 8078334 -0.4032 DEL . . +pgxbs-kftviq27 8 8085661 8120666 0.333 DUP . . +pgxbs-kftviq27 8 8132442 8151683 -0.5907 DEL . . +pgxbs-kftviq27 8 8160409 8237241 0.4241 DUP . . +pgxbs-kftviq27 8 8245004 21250933 -0.4101 DEL . . +pgxbs-kftviq27 8 107377825 133189358 0.194 DUP . . +pgxbs-kftviq27 8 133189967 134039566 0.3255 DUP . . +pgxbs-kftviq27 8 134040527 138099993 0.2044 DUP . . +pgxbs-kftviq27 8 138101643 140703144 0.285 DUP . . +pgxbs-kftviq27 8 140984704 144932803 0.3151 DUP . . +pgxbs-kftviq27 9 41002397 41002400 1.3041 DUP . . +pgxbs-kftviq27 9 41569585 41569591 1.3251 DUP . . +pgxbs-kftviq27 9 64475171 64683568 0.5017 DUP . . +pgxbs-kftviq27 9 130830894 130838823 -0.4921 DEL . . +pgxbs-kftviq27 9 130882398 130894630 0.486 DUP . . +pgxbs-kftviq27 9 132298864 132531107 -0.3535 DEL . . +pgxbs-kftviq27 9 132994207 135322260 0.3439 DUP . . +pgxbs-kftviq27 9 135323777 135324567 -2.2617 DEL . . +pgxbs-kftviq27 9 135325951 138200945 0.3207 DUP . . +pgxbs-kftviq27 10 4248647 4248825 2.0536 DUP . . +pgxbs-kftviq27 10 6357017 6357023 1.3046 DUP . . +pgxbs-kftviq27 10 6362248 6369254 0.2163 DUP . . +pgxbs-kftviq27 10 6369396 6369520 1.212 DUP . . +pgxbs-kftviq27 10 6376792 6377513 0.2914 DUP . . +pgxbs-kftviq27 10 6377597 6377803 -0.9767 DEL . . +pgxbs-kftviq27 10 42844682 43093257 0.1882 DUP . . +pgxbs-kftviq27 10 43093463 43094419 0.8358 DUP . . +pgxbs-kftviq27 10 43117916 43118739 0.861 DUP . . +pgxbs-kftviq27 10 43118760 43120057 0.1648 DUP . . +pgxbs-kftviq27 10 46174453 46289813 -0.4711 DEL . . +pgxbs-kftviq27 10 51239227 51239818 -1.2864 DEL . . +pgxbs-kftviq27 11 198510 594558 -0.2405 DEL . . +pgxbs-kftviq27 11 20302808 20391206 -0.4346 DEL . . +pgxbs-kftviq27 11 97798301 132294762 -0.3765 DEL . . +pgxbs-kftviq27 12 45277 6737367 -0.2858 DEL . . +pgxbs-kftviq27 12 9474643 9561079 -1.0796 DEL . . +pgxbs-kftviq27 12 23791264 23809077 -0.3698 DEL . . +pgxbs-kftviq27 12 23811111 31499623 0.2838 DUP . . +pgxbs-kftviq27 12 58828199 58828436 1.1353 DUP . . +pgxbs-kftviq27 12 64372422 64450862 -0.5671 DEL . . +pgxbs-kftviq27 12 74242961 104120454 -0.3954 DEL . . +pgxbs-kftviq27 13 18452810 31957985 -0.3816 DEL . . +pgxbs-kftviq27 13 31958486 31967384 -1.745 DEL . . +pgxbs-kftviq27 13 31967567 57184256 -0.3937 DEL . . +pgxbs-kftviq27 13 57184493 57192666 -1.3344 DEL . . +pgxbs-kftviq27 13 57192688 63026004 -0.3938 DEL . . +pgxbs-kftviq27 13 68676648 68676904 1.9673 DUP . . +pgxbs-kftviq27 13 97560310 98095730 -0.9375 DEL . . +pgxbs-kftviq27 13 98099260 114342923 -0.3622 DEL . . +pgxbs-kftviq27 14 58429428 62511878 -0.1596 DEL . . +pgxbs-kftviq27 14 73534420 73563212 1.1356 DUP . . +pgxbs-kftviq27 14 101027349 101037969 -1.5505 DEL . . +pgxbs-kftviq27 15 24429605 24473027 -1.1037 DEL . . +pgxbs-kftviq27 15 35817002 42125237 -0.3842 DEL . . +pgxbs-kftviq27 15 42125270 42135595 -1.3675 DEL . . +pgxbs-kftviq27 15 42141604 73728296 -0.3877 DEL . . +pgxbs-kftviq27 15 73729773 74021633 -0.2687 DEL . . +pgxbs-kftviq27 15 74021721 74022120 0.7998 DUP . . +pgxbs-kftviq27 15 74022308 75172626 -0.2695 DEL . . +pgxbs-kftviq27 15 75173127 77882780 -0.3879 DEL . . +pgxbs-kftviq27 15 92510899 101928838 -0.3813 DEL . . +pgxbs-kftviq27 16 22547737 22773239 0.2943 DUP . . +pgxbs-kftviq27 16 32022066 33840933 0.2126 DUP . . +pgxbs-kftviq27 16 54597755 56859724 -0.3972 DEL . . +pgxbs-kftviq27 16 56864967 58808348 -0.2856 DEL . . +pgxbs-kftviq27 16 58809026 70816990 -0.3994 DEL . . +pgxbs-kftviq27 16 71168586 76504758 -0.3857 DEL . . +pgxbs-kftviq27 16 76506903 76507993 2.7288 DUP . . +pgxbs-kftviq27 16 76510861 83805081 -0.3768 DEL . . +pgxbs-kftviq27 16 83805690 86257971 -0.258 DEL . . +pgxbs-kftviq27 16 86258017 87423449 -0.37 DEL . . +pgxbs-kftviq27 16 87428363 89899865 -0.2509 DEL . . +pgxbs-kftviq27 16 89899949 90221128 -0.1682 DEL . . +pgxbs-kftviq27 17 150734 261308 0.2029 DUP . . +pgxbs-kftviq27 17 4978252 6456782 -0.3717 DEL . . +pgxbs-kftviq27 17 39705136 39726740 0.3894 DUP . . +pgxbs-kftviq27 17 39818468 39908152 -0.2765 DEL . . +pgxbs-kftviq27 17 39909987 40560309 0.1726 DUP . . +pgxbs-kftviq27 17 41266763 41277290 0.8558 DUP . . +pgxbs-kftviq27 17 45118332 46033304 0.2669 DUP . . +pgxbs-kftviq27 17 46717824 65490218 0.2291 DUP . . +pgxbs-kftviq27 17 65491282 72916326 0.4484 DUP . . +pgxbs-kftviq27 17 72916378 83091923 0.5257 DUP . . +pgxbs-kftviq27 18 47820589 47911483 -0.2594 DEL . . +pgxbs-kftviq27 18 47911695 47914981 -1.0676 DEL . . +pgxbs-kftviq27 18 47915134 51039144 -0.3289 DEL . . +pgxbs-kftviq27 18 51039163 51039263 -2.2242 DEL . . +pgxbs-kftviq27 18 51039402 53740492 -0.3889 DEL . . +pgxbs-kftviq27 18 53740728 53741023 1.0628 DUP . . +pgxbs-kftviq27 18 53741814 67292087 -0.361 DEL . . +pgxbs-kftviq27 18 67292136 67300029 -1.4804 DEL . . +pgxbs-kftviq27 18 67300482 68625166 -0.3663 DEL . . +pgxbs-kftviq27 18 68631748 68631875 1.1035 DUP . . +pgxbs-kftviq27 18 68638868 80257174 -0.3498 DEL . . +pgxbs-kftviq27 19 90911 5666325 -0.2316 DEL . . +pgxbs-kftviq27 19 17212722 17215053 -1.2006 DEL . . +pgxbs-kftviq27 19 17229591 19672824 0.3525 DUP . . +pgxbs-kftviq27 19 36395691 37142921 -0.1602 DEL . . +pgxbs-kftviq27 20 80665 81821 0.304 DUP . . +pgxbs-kftviq27 20 243487 249916 -0.7938 DEL . . +pgxbs-kftviq27 20 1590092 1601123 0.7412 DUP . . +pgxbs-kftviq27 20 62108227 62597350 0.1985 DUP . . +pgxbs-kftviq27 20 62598107 62604787 -2.7043 DEL . . +pgxbs-kftviq27 21 10775583 40294962 -0.3856 DEL . . +pgxbs-kftviq27 21 40554219 40554779 -2.4761 DEL . . +pgxbs-kftviq27 22 15471685 19581479 -0.3698 DEL . . +pgxbs-kftviq27 22 19584142 19585247 -3.3139 DEL . . +pgxbs-kftviq27 22 19585650 22131597 -0.2906 DEL . . +pgxbs-kftviq27 22 22131725 22131876 0.8016 DUP . . +pgxbs-kftviq27 22 22132160 24001028 -0.3206 DEL . . +pgxbs-kftviq27 22 24006763 36108529 -0.3925 DEL . . +pgxbs-kftviq27 22 36108631 39702839 -0.2449 DEL . . +pgxbs-kftviq27 22 39705228 41172374 -0.4834 DEL . . +pgxbs-kftviq27 22 41172393 50796028 -0.3128 DEL . . diff --git a/services/sampleplots.py b/services/sampleplots.py index b05358e..f8f7d19 100755 --- a/services/sampleplots.py +++ b/services/sampleplots.py @@ -43,14 +43,12 @@ def sampleplots(): run_beacon_init_stack(byc) generate_genome_bins(byc) - plot_type = byc["form_data"].get("plot_type", "___none___") - file_id = byc["form_data"].get("file_id", "___no-input-file___") + form = byc.get("form_data", {}) + plot_type = form.get("plot_type", "histoplot") + file_id = form.get("file_id", "___no-input-file___") + inputfile = Path( path.join( *byc["local_paths"][ "server_tmp_dir_loc" ], file_id ) ) pb = ByconBundler(byc) - - inputfile = Path( path.join( *byc["local_paths"][ "server_tmp_dir_loc" ], file_id ) ) - prdbug(inputfile.is_file()) - prdbug(inputfile) if inputfile.is_file(): pdb = pb.pgxseg_to_plotbundle(inputfile) else: