diff --git a/src/nomadic/start/commands.py b/src/nomadic/start/commands.py index f05b18e..78928e8 100644 --- a/src/nomadic/start/commands.py +++ b/src/nomadic/start/commands.py @@ -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} @@ -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: diff --git a/src/nomadic/start/data/beds/aarabiensis/nomadsIR.amplicons.bed b/src/nomadic/start/data/beds/aarabiensis/nomadsIR.amplicons.bed new file mode 100644 index 0000000..8fd3cc2 --- /dev/null +++ b/src/nomadic/start/data/beds/aarabiensis/nomadsIR.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed b/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed new file mode 100644 index 0000000..e20ceaa --- /dev/null +++ b/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed new file mode 100644 index 0000000..9aa5f21 --- /dev/null +++ b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons_KEMRI.bed b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons_KEMRI.bed new file mode 100644 index 0000000..da3fb35 --- /dev/null +++ b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons_KEMRI.bed @@ -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