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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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072a741
Initial commit of additional vector species
danieljbridges May 18, 2026
f10569b
Added new options to help
danieljbridges May 28, 2026
bfc022b
Correct Astephensi bed file
danieljbridges Jul 16, 2026
a0517f3
Updated bed files
danieljbridges Jul 24, 2026
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8 changes: 8 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", "nomadsIR", "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}

Expand Down Expand Up @@ -130,6 +134,10 @@ def start(organism, workspace_path) -> None:
Currently supported organisms:
- Plasmodium falciparum (pfalciparum)
- Anopheles gambiae (agambiae)
- Anopheles stephensi (astephensi)
- Anopheles coluzzii (acoluzzi)
- Anopheles funestus (afunestus)
- Anopheles arabiensis (aarabiensis)

"""
if organism is None:
Expand Down
6 changes: 6 additions & 0 deletions src/nomadic/start/data/beds/aarabiensis/nomadsIR.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
CM029352 3438922 3439981 Ace1-280S
CM029352 100183501 100184589 Gaba-296G
CM029353 28218141 28218982 Gste2-119V
CM029352 63292475 63293453 Vgsc-L995S
CM029352 63298780 63299852 Vgsc-N1570Y
CM029352 63261150 63262282 Vgsc-V402
5 changes: 5 additions & 0 deletions src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
AfunGA1_2RL 19479972 19480896 Ace1-280S
AfunGA1_3RL 13548985 13549488 Gaba-296G
AfunGA1_3RL 44125191 44125639 Vgsc-L995S
AfunGA1_3RL 44117230 44117949 Vgsc-N1570Y
AfunGA1_3RL 44137653 44138544 Vgsc-V402
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 @@
CM023248 60913392 60914310 Ace1-280S
CM023249 8352807 8353407 Gaba-296G
CM023249 70580367 70581005 Gste2-119V
CM023249 42817353 42817873 Vgsc-L995S
CM023249 42809923 42810648 Vgsc-N1570Y
CM023249 42830282 42831000 Vgsc-V402
6 changes: 6 additions & 0 deletions src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons_KEMRI.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
CM023248 60913370 60914332 Ace1-280S
CM023249 8352786 8353577 Gaba-296G
CM023249 70580365 70581064 Gste2-119V
CM023249 42817337 42817882 Vgsc-L995S
CM023249 42830276 42831003 Vgsc-N1570Y
CM023249 42809908 42810660 Vgsc-V402
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