diff --git a/src/nomadic/start/commands.py b/src/nomadic/start/commands.py index f05b18e..e266c9f 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", "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} diff --git a/src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed new file mode 100644 index 0000000..e638f38 --- /dev/null +++ b/src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed new file mode 100644 index 0000000..e638f38 --- /dev/null +++ b/src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed @@ -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 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..1c87dcc --- /dev/null +++ b/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed new file mode 100644 index 0000000..e638f38 --- /dev/null +++ b/src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed @@ -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 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..1c87dcc --- /dev/null +++ b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed @@ -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 diff --git a/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed new file mode 100644 index 0000000..e638f38 --- /dev/null +++ b/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed @@ -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