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Additional vector species added for IR and SpeciesID #85

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Additional vector species added for IR and SpeciesID #85

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4 changes: 4 additions & 0 deletions src/nomadic/start/commands.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,10 @@ class Organism:
_organisms = [
Organism("pfalciparum", "Pf3D7", "nomadsMVP", "delve"),
Organism("agambiae", "AgPEST", "nomadsIR", "bcftools"),
Organism("astephensi", "AsUCISS2018", "nomadsSID", "bcftools"),
Organism("acoluzzi", "AcolN3", "nomadsSID", "bcftools"),
Organism("afunestus", "AfunGA1", "nomadsSID", "bcftools"),
Organism("aarabiensis", "AaDONGOLA2021", "nomadsSID", "bcftools"),
]
ORGANISM_COLLECTION = {organism.name: organism for organism in _organisms}

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10 changes: 10 additions & 0 deletions src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
AgamP4_2R 10619030 10619900 AGAP001804
AgamP4_2R 10621813 10622772 AGAP001805
AgamP4_2R 16402726 16403552 AGAP002141
AgamP4_2R 16504349 16505159 AGAP002151
AgamP4_2R 34374885 34375935 AGAP003240
AgamP4_2R 34568699 34569745 AGAP003262
AgamP4_2R 55870012 55870866 AGAP004422
AgamP4_2R 57347774 57348653 AGAP004522
AgamP4_2L 10356592 10357629 AGAP005134
AgamP4_3R 1485490 1486392 AGAP007827
10 changes: 10 additions & 0 deletions src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
AgamP4_2R 10619030 10619900 AGAP001804
AgamP4_2R 10621813 10622772 AGAP001805
AgamP4_2R 16402726 16403552 AGAP002141
AgamP4_2R 16504349 16505159 AGAP002151
AgamP4_2R 34374885 34375935 AGAP003240
AgamP4_2R 34568699 34569745 AGAP003262
AgamP4_2R 55870012 55870866 AGAP004422
AgamP4_2R 57347774 57348653 AGAP004522
AgamP4_2L 10356592 10357629 AGAP005134
AgamP4_3R 1485490 1486392 AGAP007827
6 changes: 6 additions & 0 deletions src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed
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@@ -0,0 +1,6 @@
AgamP4_2R 3491270 3492332 Ace1-280S
AgamP4_2L 25428663 25429767 Gaba-296G
AgamP4_3R 28597892 28598734 Gste2-119V
AgamP4_2L 2422485 2423463 Vgsc-L995S
AgamP4_2L 2428804 2429878 Vgsc-N1570Y
AgamP4_2L 2390443 2391584 Vgsc-V402
10 changes: 10 additions & 0 deletions src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed
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@@ -0,0 +1,10 @@
AgamP4_2R 10619030 10619900 AGAP001804
AgamP4_2R 10621813 10622772 AGAP001805
AgamP4_2R 16402726 16403552 AGAP002141
AgamP4_2R 16504349 16505159 AGAP002151
AgamP4_2R 34374885 34375935 AGAP003240
AgamP4_2R 34568699 34569745 AGAP003262
AgamP4_2R 55870012 55870866 AGAP004422
AgamP4_2R 57347774 57348653 AGAP004522
AgamP4_2L 10356592 10357629 AGAP005134
AgamP4_3R 1485490 1486392 AGAP007827
6 changes: 6 additions & 0 deletions src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
AgamP4_2R 3491270 3492332 Ace1-280S
AgamP4_2L 25428663 25429767 Gaba-296G
AgamP4_3R 28597892 28598734 Gste2-119V
AgamP4_2L 2422485 2423463 Vgsc-L995S
AgamP4_2L 2428804 2429878 Vgsc-N1570Y
AgamP4_2L 2390443 2391584 Vgsc-V402
10 changes: 10 additions & 0 deletions src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,10 @@
AgamP4_2R 10619030 10619900 AGAP001804
AgamP4_2R 10621813 10622772 AGAP001805
AgamP4_2R 16402726 16403552 AGAP002141
AgamP4_2R 16504349 16505159 AGAP002151
AgamP4_2R 34374885 34375935 AGAP003240
AgamP4_2R 34568699 34569745 AGAP003262
AgamP4_2R 55870012 55870866 AGAP004422
AgamP4_2R 57347774 57348653 AGAP004522
AgamP4_2L 10356592 10357629 AGAP005134
AgamP4_3R 1485490 1486392 AGAP007827
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