Initial commit

Commands

+augur import beast --mcc WA261_mcct --output-tree OUTPUT_TREE --output-node-data OUTPUT_NODE_DATA --tip-date-regex [0-9]{4}
+
+augur export v2 -t scripts/OUTPUT_TREE --node-data scripts/output_node_data_without_jitter.json scripts/branch_length.json --auspice-config config/auspice_config.json --metadata data/metadata_updated_country.tsv --lat-longs config/lat_longs.tsv --description scripts/description.md --output auspice/outputtest.json 
+
+

README.md

+# RYMV-WA
+The sequences analysed in this study are available on Genbank. The articles referenced below list the scientists who obtained these sequences.
+
+
+Rivers and landscape ecology of a plant virus, Rice yellow mottle virus along the Niger Valley 
+Issaka S, Traore S, Longue DRS, Pinel-Galzi A, Gill MS, Dellicour S, Bastide P, Guindon S, Hebrard E, Dugue MJ, Sere Y, Semballa S, Ake S, Lemey P, Fargette D
+Virus Evol. 2021. veab072, doi.org/10.1093/ve/veab072
+
+Near-Complete Genome Sequences of Rice Yellow Mottle Virus Isolates from Senegal.
+Tall H, Aribi J, Camara S, Pinel-Galzi A, Poulicard N, Fargette D, Hebrard E.
+Microbiol Resour Announc. 2020;9(2):e00937-19. doi: 10.1128/MRA.00937-19.
+
+First Report of Rice yellow mottle virus in Rice in the Central African Republic.
+Longue DRS, Galzi-Pinel A, Semballa S, Zinga I, Fargette D, Traore O.
+Plant Dis. 2014;98(1):162. doi: 10.1094/PDIS-04-13-0418-PDN.
+
+A reassessment of the epidemiology of Rice yellow mottle virus following recent advances in field and molecular studies.
+Traore O, Pinel-Galzi A, Sorho F, Sarra S, Rakotomalala M, Sangu E, Kanyeka Z, Sere Y, Konate G, Fargette D.
+Virus Res. 2009;141(2):258-67. doi: 10.1016/j.virusres.2009.01.011.
+
+First Report of Rice yellow mottle virus in Rice in The Gambia.
+Sere Y, Sorho F, Onasanya A, Jobe L, Darboe S, Bojang Y, Touray ML, Pinel-Galzi A, Fargette D.
+Plant Dis. 2008;92(2):316. doi: 10.1094/PDIS-92-2-0316B.
+
+Processes of diversification and dispersion of rice yellow mottle virus inferred from large-scale and high-resolution phylogeographical studies.
+Traore O, Sorho F, Pinel A, Abubakar Z, Banwo O, Maley J, Hebrard E, Winter S, Sere Y, Konate G, Fargette D.
+Mol Ecol. 2005;14(7):2097-110. doi: 10.1111/j.1365-294X.2005.02578.x.
+
+Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies.
+Fargette D, Pinel A, Abubakar Z, Traore O, Brugidou C, Fatogoma S, Hebrard E, Choisy M, Sere Y, Fauquet C, Konate G.
+J Virol. 2004;78(7):3252-61. doi: 10.1128/jvi.78.7.3252-3261.2004.
+
+Occurrence of Resistance-Breaking Isolates of Rice yellow mottle virus in West and Central Africa.
+Traore O, Pinel A, Hebrard E, Gumedzoe MY, Fargette D, Traore AS, Konate G.
+Plant Dis. 2006;90(3):259-263. doi: 10.1094/PD-90-0259.
+
+Phylogeography of Rice yellow mottle virus in Africa.
+Abubakar Z, Ali F, Pinel A, Traore O, N'Guessan P, Notteghem JL, Kimmins F, Konate G, Fargette D.
+J Gen Virol. 2003;84(Pt 3):733-743. doi: 10.1099/vir.0.18759-0.
+
+First Report and Characterization of Rice yellow mottle virus in Central Africa.
+Traore O, Pinel A, Fargette D, Konate G.
+Plant Dis. 2001;85(8):920. doi: 10.1094/PDIS.2001.85.8.920A.
+
+Molecular variability of geographically distinct isolates of Rice yellow mottle virus in Africa.
+Pinel A, N'Guessan P, Bousalem M, Fargette D.
+Arch Virol. 2000;145(8):1621-38. doi: 10.1007/s007050070080.

config/.~lock.lat_longs.tsv#

+,aurorecomte,MPLCLTLP0236,18.10.2023 15:39,file:///home/aurorecomte/.config/libreoffice/4;
\ No newline at end of file

config/auspice_config.json

+{
+  "title": "Rice yellow mottle virus in Madagascar discrete first submission",
+  "maintainers": [
+    {"name": "Aurore Comte", "mail": "aurore.comte@ird.fr"}
+  ],
+  "colorings": [
+    {
+      "key": "location",
+      "title": "Location",
+      "type": "categorical"
+    },
+    {
+      "key": "strain",
+      "title": "Strain",
+      "type": "categorical"
+    }
+  ],
+  "geo_resolutions": [
+    "location"
+  ],
+  "panels": [
+     "tree",
+     "map"
+  ],
+  "display_defaults": {
+    "color_by" : "location"
+  },
+  "filters": [
+    "region"
+  ]
+}

config/lat_longs.tsv

+region	Diana	-13.408653	49.203085
+region	Sava	-14.440717	49.854727
+region	Itasy	-18.954096	46.902837
+region	Analamanga	-18.382333	47.292389
+region	Vakinankaratra	-19.811019	46.980510
+region	Bongolava	-18.633686	46.056321
+region	Sofia	-15.208663	48.205261
+region	Boeny	-15.907780	45.929111
+region	Betsiboka	-17.283356	47.136212
+region	Melaky	-17.967368	44.700614
+region	Alaotra-Mangoro	-18.028491	48.239353
+region	Atsinanana	-18.813148	48.879997
+region	Analanjirofo	-16.507537	49.528000
+region	Amoron'i Mania 	-20.514513	47.292389
+region	Haute Matsiatra	-21.540796	46.670534
+region	Vatovavy-Fitovinany	-21.320565	47.921820
+region	Atsimo-Atsinanana 	-23.274782	47.292389
+region	Ihorombe 	-22.348450	45.903969
+region	Menabe	-20.344631	44.700614
+region	Atsimo-Andrefana	-22.953069	44.096031
+region	Androy	-24.749783	45.449807
+region	Anosy	-24.382869	46.516262
+location	Diana	-13.408653	49.203085
+location	Sava	-14.440717	49.854727
+location	Itasy	-18.954096	46.902837
+location	Analamanga	-18.382333	47.292389
+location	Vakinankaratra	-19.811019	46.980510
+location	Bongolava	-18.633686	46.056321
+location	Sofia	-15.208663	48.205261
+location	Boeny	-15.907780	45.929111
+location	Betsiboka	-17.283356	47.136212
+location	Melaky	-17.967368	44.700614
+location	Alaotra-Mangoro	-18.028491	48.239353
+location	Atsinanana	-18.813148	48.879997
+location	Analanjirofo	-16.507537	49.528000
+location	Amoron'i Mania 	-20.514513	47.292389
+location	Haute Matsiatra	-21.540796	46.670534
+location	Vatovavy-Fitovinany	-21.320565	47.921820
+location	Atsimo-Atsinanana	-23.274782	47.292389
+location	Ihorombe 	-22.348450	45.903969
+location	Menabe	-20.344631	44.700614
+location	Atsimo-Andrefana	-22.953069	44.096031
+location	Androy	-24.749783	45.449807
+location	Anosy	-24.382869	46.516262

data/.~lock.metadata_updated_country_loc.tsv#

+,aurorecomte,MPLCLTLP0236,18.10.2023 14:55,file:///home/aurorecomte/.config/libreoffice/4;
\ No newline at end of file

data/Location_Mg94.txt

+traits	latMg	longMg
+1989Mg1cp.seq	-17.8	48.1
+1991Mg2cp.seq	-16.1	46.8
+1991Mg3cp.seq	-18.5	47.3
+1991Mg4cp.seq	-18.5	47.3		
+1991Mg5cp.seq	-16.1	46.8
+1991Mg6cp.seq	-17.8	48.1
+2003Mg10cp.seq	-15.6	47.6
+2003Mg11cp.seq	-16.1	46.6
+2003Mg12cp.seq	-16.0	46.6
+2003Mg13cp.seq	-14.6	49.7
+2003Mg14cp.seq	-13.9	50.1
+2003Mg15cp.seq	-14.4	49.7
+2003Mg16cp.seq	-16.1	46.8
+2003Mg35cp.seq	-16.5	46.8
+2003Mg40cp.seq	-15.8	46.4
+2003Mg41cp.seq	-15.0	48.0
+2003Mg42cp.seq	-16.2	47.7
+2003Mg43cp.seq	-15.8	46.8
+2003Mg44cp.seq	-16.1	47.6
+2003Mg45cp.seq	-16.4	46.7
+2003Mg46cp.seq	-15.9	47.3
+2003Mg47cp.seq	-15.9	46.6
+2003Mg48cp.seq	-15.8	46.9
+2003Mg49cp.seq	-15.7	46.6
+2003Mg50cp.seq	-14.6	50.0
+2003Mg51cp.seq	-14.3	49.8
+2003Mg52cp.seq	-14.2	49.8
+2003Mg53cp.seq	-14.2	49.6
+2003Mg54cp.seq	-14.4	49.6
+2003Mg55cp.seq	-14.4	49.6
+2003Mg56cp.seq	-13.7	49.9
+2003Mg57cp.seq	-13.9	49.8
+2003Mg68cp.seq	-16.2	46.4
+2003Mg69cp.seq	-14.2	50.1
+2003Mg70cp.seq	-13.9	49.8
+2003Mg71cp.seq	-14.3	50.1
+2003Mg410cp.seq	-16.1	46.8
+2003Mg419cp.seq	-16.1	46.8
+2004Mg67cp.seq	-19.6	45.4
+2004Mg17cp.seq	-14.9	50.1
+2004Mg18cp.seq	-14.4	50.1
+2004Mg19cp.seq	-21.7	43.6
+2004Mg20cp.seq	-19.6	45.4
+2004Mg21cp.seq	-17.9	48.4
+2004Mg22cp.seq	-18.0	48.2
+2004Mg23cp.seq	-21.7	48.1
+2004Mg24cp.seq	-22.2	48.0
+2004Mg25cp.seq	-21.5	47.7
+2004Mg26cp.seq	-21.3	47.7
+2004Mg27cp.seq	-20.4	44.3
+2004Mg28cp.seq	-20.5	44.8
+2004Mg29cp.seq	-20.0	45.6
+2004Mg30cp.seq	-17.9	48.6
+2004Mg31cp.seq	-17.9	48.3
+2004Mg32cp.seq	-21.1	48.2
+2004Mg33cp.seq	-21.3	48.2
+2004Mg34cp.seq	-21.9	47.7
+2004Mg58cp.seq	-17.5	48.5
+2004Mg59cp.seq	-18.0	48.5
+2004Mg60cp.seq	-17.9	48.2
+2004Mg61cp.seq	-17.6	48.1
+2004Mg62cp.seq	-17.8	48.1
+2004Mg63cp.seq	-21.5	48.1
+2004Mg64cp.seq	-21.7	47.7
+2004Mg65cp.seq	-22.4	47.8
+2004Mg66cp.seq	-21.4	47.6
+2008Mg201cp.seq	-15.8	46.8
+2008Mg202cp.seq	-16.1	46.8
+2010Mg105cp.seq	-16.7	49.6
+2010Mg108cp.seq	-17.4	49.3
+2010Mg119cp.seq	-12.5	49.3
+2010Mg123cp.seq	-12.3	49.1
+2010Mg124cp.seq	-13.1	49.0
+2010Mg125cp.seq	-13.6	48.7
+2010Mg126cp.seq	-13.9	48.2
+2010Mg127cp.seq	-14.9	47.9
+2010Mg128cp.seq	-15.2	47.9
+2010Mg147cp.seq	-25.0	46.3
+2010Mg150cp.seq	-25.1	46.5
+2010Mg155cp.seq	-24.3	45.7
+2010Mg163cp.seq	-23.7	45.8
+2010Mg165cp.seq	-16.9	47.0
+2010Mg210cp.seq	-16.1	46.8
+2014Mg301cp.seq	-18.5	47.3
+2014Mg302cp.seq	-18.5	47.3
+2014Mg303cp.seq	-18.5	47.3
+2014Mg304cp.seq	-18.5	47.3
+2014Mg341cp.seq	-18.5	47.3
+2014Mg342cp.seq	-18.5	47.3
+2014Mg343cp.seq	-18.5	47.3
+2014Mg344cp.seq	-18.5	47.3
+2017Mg401cp.seq	-16.1	46.6
+2017Mg402cp.seq	-16.1	46.6
+2017Mg403cp.seq	-16.1	46.6
\ No newline at end of file

data/beast.sh

+#!/bin/bash
+#SBATCH -J Beast-GPU
+#SBATCH -p gpu
+#SBATCH -A gpu_group
+#SBATCH -c 1
+#SBATCH --gres=gpu:1
+INPUT=$1
+
+# sbatch BeastGPU.sh A01_WA287.xml 
+
+#loading modules
+module load bioinfo/beagle-lib-gpu/3.1.2
+module load bioinfo/BEAST/1.10.5pre
+
+#running beast
+beast -beagle_cuda -beagle_gpu ${INPUT} > ${INPUT}.out

data/find.py

+#!/usr/bin/env python
+#First of all you need to install geopy with : pip install geopy or conda install -c conda-forge geopy 
+
+# Import the required library
+from geopy.geocoders import Nominatim
+import re
+
+# Initialize Nominatim API
+geolocator = Nominatim(user_agent="MyScript")
+
+def get_city_country(coord):
+    location = geolocator.reverse(coord, language='en') #get all address from coordinates
+    address = location.raw['address']  #to get address
+    #state = address.get('state', '')
+    #province = address.get('province', '')
+    country = address.get('country', '')  #extract country from the address
+    if "Côte d'Ivoire" in country:
+        country = "Ivory Coast"
+    if "The Gambia" in country:
+        country = "Gambia"
+    #conc = country+'\t'+country+'/'+state
+    #if state =='':
+    #    conc = country+'\t'+country
+    #elif province !='':
+    #    conc = country+'/'+province
+    #else:
+    #    region = address.get('region', '')
+    #    conc = country+'/'+region
+
+    return country
+
+
+with open('Location_Mg94.txt', 'r') as f, open('metadata_updated_country.tsv','w') as file:
+    raw = f.read().splitlines()
+    header = raw[0].split("\t")
+
+    header.append('location\tdate')
+    #updated_header = str(header).replace('[','')
+    #updated_header = str(header).replace(']','')
+    #updated_header = str(header).replace(',','')
+    #updated_header = str(header).replace("'",'')
+    file.write('\t'.join(header)+'\n')
+    #column_nb = 0
+    #for i in header:
+        #column_nb+=1
+        #if i == 'state':
+    for line in raw[1:]:
+        col = line.split("\t")
+        date = re.search('^\d{4}', col[0]).group(0)
+        line +='\t'+str(get_city_country(col[1:3]))+'\t'+date+'\n'
+        file.write(line)
+#print(get_city_country("14.4,1.2"))

data/location-lat-long-mada_loc.txt

+A	-12.5	49.3	Diana
+B	-13.9	50.1	Sava
+C	-14.9	47.9	Sofia
+D	-17.8	48.1	Alaotra-Mangoro
+F	-16.1	46.8	Boeny
+G	-19.6	45.4	Menabe
+H	-21.7	48.1	Vatovavy-Fitovinany
+I	-25.0	46.3	Anosy

data/metadata_updated_country_loc.tsv

+strain	latMg	longMg	location	date
+1989Mg1cp.seq	-17.8	48.1	Alaotra-Mangoro	1989
+1991Mg2cp.seq	-16.1	46.8	Boeny	1991
+1991Mg3cp.seq	-18.5	47.3	Analamanga	1991
+1991Mg4cp.seq	-18.5	47.3	Analamanga	1991
+1991Mg5cp.seq	-16.1	46.8	Boeny	1991
+1991Mg6cp.seq	-17.8	48.1	Alaotra-Mangoro	1991
+2003Mg10cp.seq	-15.6	47.6	Sofia	2003
+2003Mg11cp.seq	-16.1	46.6	Boeny	2003
+2003Mg12cp.seq	-16.0	46.6	Boeny	2003
+2003Mg13cp.seq	-14.6	49.7	Sava	2003
+2003Mg14cp.seq	-13.9	50.1	Sava	2003
+2003Mg15cp.seq	-14.4	49.7	Sava	2003
+2003Mg16cp.seq	-16.1	46.8	Boeny	2003
+2003Mg35cp.seq	-16.5	46.8	Boeny	2003
+2003Mg40cp.seq	-15.8	46.4	Boeny	2003
+2003Mg41cp.seq	-15.0	48.0	Sofia	2003
+2003Mg42cp.seq	-16.2	47.7	Sofia	2003
+2003Mg43cp.seq	-15.8	46.8	Boeny	2003
+2003Mg44cp.seq	-16.1	47.6	Sofia	2003
+2003Mg45cp.seq	-16.4	46.7	Boeny	2003
+2003Mg46cp.seq	-15.9	47.3	Sofia	2003
+2003Mg47cp.seq	-15.9	46.6	Boeny	2003
+2003Mg48cp.seq	-15.8	46.9	Boeny	2003
+2003Mg49cp.seq	-15.7	46.6	Boeny	2003
+2003Mg50cp.seq	-14.6	50.0	Sava	2003
+2003Mg51cp.seq	-14.3	49.8	Sava	2003
+2003Mg52cp.seq	-14.2	49.8	Sava	2003
+2003Mg53cp.seq	-14.2	49.6	Sava	2003
+2003Mg54cp.seq	-14.4	49.6	Sava	2003
+2003Mg55cp.seq	-14.4	49.6	Sava	2003
+2003Mg56cp.seq	-13.7	49.9	Sava	2003
+2003Mg57cp.seq	-13.9	49.8	Sava	2003
+2003Mg68cp.seq	-16.2	46.4	Boeny	2003
+2003Mg69cp.seq	-14.2	50.1	Sava	2003
+2003Mg70cp.seq	-13.9	49.8	Sava	2003
+2003Mg71cp.seq	-14.3	50.1	Sava	2003
+2003Mg410cp.seq	-16.1	46.8	Boeny	2003
+2003Mg419cp.seq	-16.1	46.8	Boeny	2003
+2004Mg67cp.seq	-19.6	45.4	Menabe	2004
+2004Mg17cp.seq	-14.9	50.1	Sava	2004
+2004Mg18cp.seq	-14.4	50.1	Sava	2004
+2004Mg19cp.seq	-21.7	43.6	Atsimo-Andrefana 	2004
+2004Mg20cp.seq	-19.6	45.4	Menabe	2004
+2004Mg21cp.seq	-17.9	48.4	Alaotra-Mangoro	2004
+2004Mg22cp.seq	-18.0	48.2	Alaotra-Mangoro	2004
+2004Mg23cp.seq	-21.7	48.1	Vatovavy-Fitovinany 	2004
+2004Mg24cp.seq	-22.2	48.0	Vatovavy-Fitovinany 	2004
+2004Mg25cp.seq	-21.5	47.7	Vatovavy-Fitovinany 	2004
+2004Mg26cp.seq	-21.3	47.7	Vatovavy-Fitovinany 	2004
+2004Mg27cp.seq	-20.4	44.3	Menabe	2004
+2004Mg28cp.seq	-20.5	44.8	Menabe	2004
+2004Mg29cp.seq	-20.0	45.6	Menabe	2004
+2004Mg30cp.seq	-17.9	48.6	Alaotra-Mangoro	2004
+2004Mg31cp.seq	-17.9	48.3	Alaotra-Mangoro	2004
+2004Mg32cp.seq	-21.1	48.2	Vatovavy-Fitovinany 	2004
+2004Mg33cp.seq	-21.3	48.2	Vatovavy-Fitovinany 	2004
+2004Mg34cp.seq	-21.9	47.7	Vatovavy-Fitovinany 	2004
+2004Mg58cp.seq	-17.5	48.5	Alaotra-Mangoro	2004
+2004Mg59cp.seq	-18.0	48.5	Alaotra-Mangoro	2004
+2004Mg60cp.seq	-17.9	48.2	Alaotra-Mangoro	2004
+2004Mg61cp.seq	-17.6	48.1	Alaotra-Mangoro	2004
+2004Mg62cp.seq	-17.8	48.1	Alaotra-Mangoro	2004
+2004Mg63cp.seq	-21.5	48.1	Vatovavy-Fitovinany 	2004
+2004Mg64cp.seq	-21.7	47.7	Vatovavy-Fitovinany 	2004
+2004Mg65cp.seq	-22.4	47.8	Vatovavy-Fitovinany 	2004
+2004Mg66cp.seq	-21.4	47.6	Vatovavy-Fitovinany 	2004
+2008Mg201cp.seq	-15.8	46.8	Boeny	2008
+2008Mg202cp.seq	-16.1	46.8	Boeny	2008
+2010Mg105cp.seq	-16.7	49.6	Analanjirofo	2010
+2010Mg108cp.seq	-17.4	49.3	Analanjirofo	2010
+2010Mg119cp.seq	-12.5	49.3	Diana	2010
+2010Mg123cp.seq	-12.3	49.1	Diana	2010
+2010Mg124cp.seq	-13.1	49.0	Diana	2010
+2010Mg125cp.seq	-13.6	48.7	Diana	2010
+2010Mg126cp.seq	-13.9	48.2	Sofia	2010
+2010Mg127cp.seq	-14.9	47.9	Sofia	2010
+2010Mg128cp.seq	-15.2	47.9	Sofia	2010
+2010Mg147cp.seq	-25.0	46.3	Anosy	2010
+2010Mg150cp.seq	-25.1	46.5	Anosy	2010
+2010Mg155cp.seq	-24.3	45.7	Androy 	2010
+2010Mg163cp.seq	-23.7	45.8	Anosy	2010
+2010Mg165cp.seq	-16.9	47.0	Betsiboka	2010
+2010Mg210cp.seq	-16.1	46.8	Boeny	2010
+2014Mg301cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg302cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg303cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg304cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg341cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg342cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg343cp.seq	-18.5	47.3	Analamanga	2014
+2014Mg344cp.seq	-18.5	47.3	Analamanga	2014
+2017Mg401cp.seq	-16.1	46.6	Boeny	2017
+2017Mg402cp.seq	-16.1	46.6	Boeny	2017
+2017Mg403cp.seq	-16.1	46.6	Boeny	2017