search

GMOD / Apollo

Genome annotation editor with a Java Server backend and a Javascript client that runs in a web browser as a JBrowse plugin.
http://genomearchitect.readthedocs.io/
Other
128 stars 85 forks source link

Overlapper issue #34

Closed nathandunn closed 9 years ago

nathandunn commented 10 years ago
nathandunn commented 10 years ago

I'm a bit confused, i thought you guys where using one of the overlappers : org.bbop.apollo.web.overlap.SimpleOverlapper org.bbop.apollo.web.overlap.OrfOverlapper but there's a number of overlapping models:

Scaffold72 cap_1 gene 61337 103237 . -1 . ID=0A07543993DACE8960CC9629545337DA; Scaffold72 cap_1 mRNA 61337 103237 . -1 . ID=736A6FAB2711A89DF80DBD885018018D;Parent=0A07543993DACE8960CC9629545337DA;description=hypothetic Scaffold72 cap_1 exon 102422 103237 . -1 . ID=ED463816EEEB100EB248C73421C16270;Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 exon 67474 67696 . -1 . ID=354E342636A42D8970CF82FC40C2D529;Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 exon 66692 66914 . -1 . ID=FE6B728A7E01F28597F183D0D6168146;Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 exon 61337 62041 . -1 . ID=47549428943A0B48665E3F23A7761B79;Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 CDS 102422 103237 . - 0 Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 CDS 67474 67696 . - 0 Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 CDS 66692 66914 . - 2 Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 CDS 61747 62041 . - 1 Parent=736A6FAB2711A89DF80DBD885018018D; Scaffold72 cap_1 three_prime_utr 61337 61746 . - . Parent=736A6FAB2711A89DF80DBD885018018D

vs.

Scaffold72 cap_2 gene 61337 111778 . -1 . ID=24AEC9BEE634E7F79816137F5174AEA5; Scaffold72 cap_2 mRNA 61337 111778 . -1 . ID=68E3F185F28BE0EEB731B75A2A658725;Parent=24AEC9BEE634E7F79816137F5174AEA5;description=hypothetic Scaffold72 cap_2 exon 110969 111778 . -1 . ID=AC058E79BE0AEF8076A5D3FB84A447B3;Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 exon 67474 67696 . -1 . ID=1172DFD9559E544F2BBAAF2B559EB56D;Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 exon 66692 66914 . -1 . ID=7CAF1B65B5481734981C98A412F6A70D;Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 exon 61337 62041 . -1 . ID=B1865B0A8169B5207A4F86A187E0E8C5;Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 CDS 110969 111778 . - 0 Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 CDS 67474 67696 . - 0 Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 CDS 66692 66914 . - 2 Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 CDS 61747 62041 . - 1 Parent=68E3F185F28BE0EEB731B75A2A658725; Scaffold72 cap_2 three_prime_utr 61337 61746 . - . Parent=68E3F185F28BE0EEB731B75A2A658725

two others also overlap these :

Scaffold72 cap_2 gene 61337 91196 . -1 . ID=24C0AA2B26260CE88282B6F421D1EB05;

Scaffold72 cap_2 gene 61337 123423 . -1 . ID=A5FAA5FB4BA934E7320D3A07EC99DE21;

and :

Scaffold253 cap_1 gene 712496 728328 . 1 . ID=E9392BD95E082DAFDFC472EE5134314E; Scaffold253 cap_1 mRNA 721875 728328 . 1 . ID=4CE8F78E561F122CFA50599FE6E482B9;Parent=E9392BD95E082DAFDFC472EE5134314E;description=hypothetic Scaffold253 cap_1 exon 721875 722744 . 1 . ID=973FDEBC3026A0BF3DA7ADF158B4973D;Parent=4CE8F78E561F122CFA50599FE6E482B9; Scaffold253 cap_1 exon 727523 728328 . 1 . ID=ED3BAEC4827A6C5AC0C8FDF7745FEB67;Parent=4CE8F78E561F122CFA50599FE6E482B9; Scaffold253 cap_1 CDS 721875 722744 . + 0 Parent=4CE8F78E561F122CFA50599FE6E482B9; Scaffold253 cap_1 CDS 727523 727789 . + 0 Parent=4CE8F78E561F122CFA50599FE6E482B9; Scaffold253 cap_1 three_prime_utr 727790 728328 . + . Parent=4CE8F78E561F122CFA50599FE6E482B9 Scaffold253 cap_1 mRNA 724599 728328 . 1 . ID=60820AA4F2F8A0AD46FBD047B5003DF5;Parent=E9392BD95E082DAFDFC472EE5134314E;description=hypothetic Scaffold253 cap_1 exon 724599 725432 . 1 . ID=FECADB68CC0EB0AE77CDB39DB4EA2A4D;Parent=60820AA4F2F8A0AD46FBD047B5003DF5; Scaffold253 cap_1 exon 727523 728328 . 1 . ID=ED3BAEC4827A6C5AC0C8FDF7745FEB67;Parent=60820AA4F2F8A0AD46FBD047B5003DF5; Scaffold253 cap_1 CDS 724599 725432 . + 0 Parent=60820AA4F2F8A0AD46FBD047B5003DF5; Scaffold253 cap_1 CDS 727523 727789 . + 0 Parent=60820AA4F2F8A0AD46FBD047B5003DF5; Scaffold253 cap_1 three_prime_utr 727790 728328 . + . Parent=60820AA4F2F8A0AD46FBD047B5003DF5 Scaffold253 cap_1 mRNA 712496 728328 . 1 . ID=F62A7BCE25259DBCD5CFB720D7905F29;Parent=E9392BD95E082DAFDFC472EE5134314E;description=hypothetic Scaffold253 cap_1 exon 712496 713353 . 1 . ID=9C0E959BF112890F6288D82AA77CAC0F;Parent=F62A7BCE25259DBCD5CFB720D7905F29; Scaffold253 cap_1 exon 727523 728328 . 1 . ID=ED3BAEC4827A6C5AC0C8FDF7745FEB67;Parent=F62A7BCE25259DBCD5CFB720D7905F29; Scaffold253 cap_1 CDS 712496 713353 . + 0 Parent=F62A7BCE25259DBCD5CFB720D7905F29; Scaffold253 cap_1 CDS 727523 727789 . + 0 Parent=F62A7BCE25259DBCD5CFB720D7905F29; Scaffold253 cap_1 three_prime_utr 727790 728328 . + . Parent=F62A7BCE25259DBCD5CFB720D7905F29 Scaffold253 cap_1 mRNA 715185 728328 . 1 . ID=AEFDA4030D213D85A56727C3D380C047;Parent=E9392BD95E082DAFDFC472EE5134314E;description=hypothetic Scaffold253 cap_1 exon 715185 716003 . 1 . ID=99DBBAA73A7D0689A1149D079C85EF10;Parent=AEFDA4030D213D85A56727C3D380C047; Scaffold253 cap_1 exon 727523 728328 . 1 . ID=ED3BAEC4827A6C5AC0C8FDF7745FEB67;Parent=AEFDA4030D213D85A56727C3D380C047; Scaffold253 cap_1 CDS 715185 716003 . + 0 Parent=AEFDA4030D213D85A56727C3D380C047; Scaffold253 cap_1 CDS 727523 727789 . + 0 Parent=AEFDA4030D213D85A56727C3D380C047; Scaffold253 cap_1 three_prime_utr 727790 728328 . + . Parent=AEFDA4030D213D85A56727C3D380C047 #

Comparison cap gene_2:

# Scaffold253 cap_2 gene 720348 728328 . 1 . ID=B574E70F5CBFB92E086E33DB9A15D39F; Scaffold253 cap_2 mRNA 720348 728328 . 1 . ID=8954245B7FE605AE3CE8C9FCE965727A;Parent=B574E70F5CBFB92E086E33DB9A15D39F;description=hypothetic Scaffold253 cap_2 exon 720348 721199 . 1 . ID=52490E137AF3B6502F040C8198D0AF3A;Parent=8954245B7FE605AE3CE8C9FCE965727A; Scaffold253 cap_2 exon 727523 728328 . 1 . ID=BCE699E12F75F2EEFEDC3088C2E98A7A;Parent=8954245B7FE605AE3CE8C9FCE965727A; Scaffold253 cap_2 CDS 720348 721199 . + 0 Parent=8954245B7FE605AE3CE8C9FCE965727A; Scaffold253 cap_2 CDS 727523 727789 . + 0 Parent=8954245B7FE605AE3CE8C9FCE965727A; Scaffold253 cap_2 three_prime_utr 727790 728328 . + . Parent=8954245B7FE605AE3CE8C9FCE965727A

while this one i guess would indicate you're using the OrfOverlapper and not SimpleOveralapper

Scaffold47 cap_1 gene 555349 561633 . -1 . ID=A55D8834BEBA1336F794E99C4EE75959; Scaffold47 cap_1 mRNA 555349 561633 . -1 . ID=6A9FD626E6489952BCC8BC671415A075;Parent=A55D8834BEBA1336F794E99C4EE75959;description=hypothetic Scaffold47 cap_1 exon 561595 561633 . -1 . ID=6F48B53238FD3598B83F7B4BCBB4FD6B;Parent=6A9FD626E6489952BCC8BC671415A075; Scaffold47 cap_1 exon 561288 561472 . -1 . ID=B11C765A0CE3C50C85185F4C75B297A6;Parent=6A9FD626E6489952BCC8BC671415A075; Scaffold47 cap_1 exon 555349 555472 . -1 . ID=FA59A666FE1F7CB6FE52B310A339B608;Parent=6A9FD626E6489952BCC8BC671415A075; Scaffold47 cap_1 five_prime_utr 561607 561633 . - . Parent=6A9FD626E6489952BCC8BC671415A075 Scaffold47 cap_1 CDS 561595 561606 . - 0 Parent=6A9FD626E6489952BCC8BC671415A075; Scaffold47 cap_1 CDS 561288 561472 . - 0 Parent=6A9FD626E6489952BCC8BC671415A075; Scaffold47 cap_1 CDS 555349 555472 . - 1 Parent=6A9FD626E6489952BCC8BC671415A075;

Scaffold47 cap_2 gene 560941 566415 . -1 . ID=5607EC6CA6BE52483F589600D74E7738; Scaffold47 cap_2 mRNA 560941 566415 . -1 . ID=DCCC0F3F2BD93E8032ACDE3EEF48756E;Parent=5607EC6CA6BE52483F589600D74E7738;description=hypothetic Scaffold47 cap_2 exon 566379 566415 . -1 . ID=D95314599F12FD86C925608EF3BD7349;Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 exon 566076 566260 . -1 . ID=56CF11742374F9C2BF86A636504E0C4C;Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 exon 565764 566011 . -1 . ID=5B6CA65BB179BE1DA06F34973DD7DFCB;Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 exon 563133 563158 . -1 . ID=FC68BE3C9BE667D9CCC7B010B51360FC;Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 exon 560941 561223 . -1 . ID=17A5D18F41B9473575043309AD07EBB0;Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 five_prime_utr 566394 566415 . - . Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E Scaffold47 cap_2 CDS 566379 566393 . - 0 Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 CDS 566076 566260 . - 0 Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 CDS 565764 566011 . - 1 Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 CDS 563133 563158 . - 2 Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 CDS 561218 561223 . - 0 Parent=DCCC0F3F2BD93E8032ACDE3EEF48756E; Scaffold47 cap_2 three_prime_utr 560941 561217 . - . Parent=DCCC0F3F2BD93E8032ACDE3EEF48756

nathandunn commented 9 years ago

Probably just need to double-check or clarify.

monicacecilia commented 9 years ago

Unable to reproduce this. Should it arise again after 2.0, let's bring it back. I'm closing for now.