From 072a7413a6572beafae9dcd2a6a22d0db31a5785 Mon Sep 17 00:00:00 2001 From: Daniel Bridges Date: Mon, 18 May 2026 10:57:59 +0200 Subject: [PATCH 1/4] Initial commit of additional vector species --- src/nomadic/start/commands.py | 4 ++++ .../data/beds/aarabiensis/nomadsSID.amplicons.bed | 10 ++++++++++ .../start/data/beds/acoluzzi/nomadsSID.amplicons.bed | 10 ++++++++++ .../start/data/beds/afunestus/nomadsIR.amplicons.bed | 6 ++++++ .../start/data/beds/afunestus/nomadsSID.amplicons.bed | 10 ++++++++++ .../start/data/beds/astephensi/nomadsIR.amplicons.bed | 6 ++++++ .../start/data/beds/astephensi/nomadsSID.amplicons.bed | 10 ++++++++++ 7 files changed, 56 insertions(+) create mode 100644 src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed create mode 100644 src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed create mode 100644 src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed create mode 100644 src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed create mode 100644 src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed create mode 100644 src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed 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 From f10569bea49a04906b693658090209f27b87db97 Mon Sep 17 00:00:00 2001 From: Daniel Bridges Date: Thu, 28 May 2026 16:44:20 +0200 Subject: [PATCH 2/4] Added new options to help --- src/nomadic/start/commands.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/src/nomadic/start/commands.py b/src/nomadic/start/commands.py index e266c9f..31e4730 100644 --- a/src/nomadic/start/commands.py +++ b/src/nomadic/start/commands.py @@ -134,6 +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: From bfc022bd261654dc7d97c6d19515354f8e170e0b Mon Sep 17 00:00:00 2001 From: Daniel Bridges Date: Thu, 16 Jul 2026 14:56:25 +0200 Subject: [PATCH 3/4] Correct Astephensi bed file --- src/nomadic/start/commands.py | 2 +- .../data/beds/astephensi/nomadsIR.amplicons.bed | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/src/nomadic/start/commands.py b/src/nomadic/start/commands.py index 31e4730..78928e8 100644 --- a/src/nomadic/start/commands.py +++ b/src/nomadic/start/commands.py @@ -28,7 +28,7 @@ class Organism: _organisms = [ Organism("pfalciparum", "Pf3D7", "nomadsMVP", "delve"), Organism("agambiae", "AgPEST", "nomadsIR", "bcftools"), - Organism("astephensi", "AsUCISS2018", "nomadsSID", "bcftools"), + Organism("astephensi", "AsUCISS2018", "nomadsIR", "bcftools"), Organism("acoluzzi", "AcolN3", "nomadsSID", "bcftools"), Organism("afunestus", "AfunGA1", "nomadsSID", "bcftools"), Organism("aarabiensis", "AaDONGOLA2021", "nomadsSID", "bcftools"), diff --git a/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed index 1c87dcc..da3fb35 100644 --- a/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed +++ b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed @@ -1,6 +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 +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 From a0517f382a313128ffa96d019a50db3da506637b Mon Sep 17 00:00:00 2001 From: Daniel Bridges Date: Fri, 24 Jul 2026 07:28:56 +0100 Subject: [PATCH 4/4] Updated bed files --- .../data/beds/aarabiensis/nomadsIR.amplicons.bed | 6 ++++++ .../data/beds/aarabiensis/nomadsSID.amplicons.bed | 10 ---------- .../start/data/beds/acoluzzi/nomadsSID.amplicons.bed | 10 ---------- .../start/data/beds/afunestus/nomadsIR.amplicons.bed | 11 +++++------ .../data/beds/afunestus/nomadsSID.amplicons.bed | 10 ---------- .../data/beds/astephensi/nomadsIR.amplicons.bed | 12 ++++++------ .../beds/astephensi/nomadsIR.amplicons_KEMRI.bed | 6 ++++++ .../data/beds/astephensi/nomadsSID.amplicons.bed | 10 ---------- 8 files changed, 23 insertions(+), 52 deletions(-) create mode 100644 src/nomadic/start/data/beds/aarabiensis/nomadsIR.amplicons.bed delete mode 100644 src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed delete mode 100644 src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed delete mode 100644 src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed create mode 100644 src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons_KEMRI.bed delete mode 100644 src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed 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/aarabiensis/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed deleted file mode 100644 index e638f38..0000000 --- a/src/nomadic/start/data/beds/aarabiensis/nomadsSID.amplicons.bed +++ /dev/null @@ -1,10 +0,0 @@ -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 deleted file mode 100644 index e638f38..0000000 --- a/src/nomadic/start/data/beds/acoluzzi/nomadsSID.amplicons.bed +++ /dev/null @@ -1,10 +0,0 @@ -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 index 1c87dcc..e20ceaa 100644 --- a/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed +++ b/src/nomadic/start/data/beds/afunestus/nomadsIR.amplicons.bed @@ -1,6 +1,5 @@ -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 +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/afunestus/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed deleted file mode 100644 index e638f38..0000000 --- a/src/nomadic/start/data/beds/afunestus/nomadsSID.amplicons.bed +++ /dev/null @@ -1,10 +0,0 @@ -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 index da3fb35..9aa5f21 100644 --- a/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed +++ b/src/nomadic/start/data/beds/astephensi/nomadsIR.amplicons.bed @@ -1,6 +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 +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 diff --git a/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed b/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed deleted file mode 100644 index e638f38..0000000 --- a/src/nomadic/start/data/beds/astephensi/nomadsSID.amplicons.bed +++ /dev/null @@ -1,10 +0,0 @@ -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