reinit

00-scripts/step2/format_bold.sh

@@ -40,5 +40,20 @@ cat $NO_SEQ_BOLD $GEONAMES_ASSIGNED_REG_BOLD > $ALL_FORMAT_BOLD
 COI_BOLD=${ALL_FORMAT_BOLD/.tsv/_coi.tsv}
 awk -F "\t" '{ if($70 == "COI-5P" || $70 == "markercode") print $0 }' $ALL_FORMAT_BOLD > $COI_BOLD
 
-COI_LENGHT_BOLD=${COI_BOLD/.tsv/_length499.tsv}
-awk -F "\t" 'NR == 1 {print; next} { if(length($72) > 499) print $0 }' $COI_BOLD > $COI_LENGHT_BOLD
\ No newline at end of file
+## keep sequence with a length greater than 420 bases
+COI_LENGHT_BOLD=${COI_BOLD/.tsv/_length420.tsv}
+awk -F "\t" 'NR == 1 {print; next} { if(length($72) > 420) print $0 }' $COI_BOLD > $COI_LENGHT_BOLD
+
+## keep species with at least 2 sequences
+SPECIES_WITH_A_SINGLE_SEQUENCE="02-bold_format/species_with_a_single_sequence.txt"
+COI_2SEQ_SPECIES=${COI_LENGHT_BOLD/.tsv/_atleast2seqbyspecies.tsv}
+sort -k22 -t$'\t' $COI_LENGHT_BOLD | awk -F "\t" '{ print $22 }' | uniq -c | awk '{ if($1 < 2) print $2" "$3 }' > $SPECIES_WITH_A_SINGLE_SEQUENCE
+
+
+grep -wvf $SPECIES_WITH_A_SINGLE_SEQUENCE $COI_LENGHT_BOLD > $COI_2SEQ_SPECIES
+
+
+sort -k22 -t$'\t' $COI_LENGHT_BOLD | awk -F "\t" '{ print $22 }' | uniq -c | awk '{ if($1 < 2) print $2" "$3" "$4" "$5 }'
+
+
+sed 's/ /[[:space:]]/g' $SPECIES_WITH_A_SINGLE_SEQUENCE
\ No newline at end of file

README.md

@@ -3,17 +3,58 @@
 Here we go again to investigate genetic patterns at different scale
 
 
-# Prerequisites
+# Installation
 
-* python2
+## Prerequisites
+
+* python3
 * bash
 * lynx
 * awk
 
 
+
+### CONDA
+
+Instructions to install CONDA are [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/linux.html)
+
+
+### JUPYTER NOTEBOOK
+
+* install jupyter notebook using CONDA
+
+```
+conda install -c conda-forge notebook
+```
+
+### R 
+
+```
+conda env create -f conda/env_ubuntu.yml
+conda activate mapmarine2
+
+```
+
+If you haven’t done this already, you will have to make Jupyter see the newly installed R kernel by installing a kernel spec. The kernel spec can be installed for the current user with the following line from R: 
+
+```
+IRkernel::installspec()
+```
+
+### geogendiv
+
+
+Into R session:
+```
+devtools::install_github("grelot/geogendivr", force = TRUE)
+```
+
+
+
+
 # 1 Donwload and format BOLD database
 
-1. I type the word 'actinopterygii' on [BOLD website](http://www.boldsystems.org).
+1. I seek the term 'actinopterygii' on [BOLD website](http://www.boldsystems.org).
 2. I download Combined TSV files on **monday the 6th january 2020**.
 3. The original file is stored into [01-bold_raw](01-bold_raw) folder.
 
@@ -26,9 +67,8 @@ Here we go again to investigate genetic patterns at different scale
 4. File with COI georeferenced sequences is stored as [02-bold_format/all_format_bold_coi.tsv](02-bold_format/all_format_bold_coi.tsv)
 
 ```
-bash 00-scripts/step1/format_bold.sh
+bash 00-scripts/step2/format_bold.sh
 ```
 
-# Cluster individual sequences by region/tile
-
+# 3 
 

conda/env_jupyter.yml

+name: mapmarine2
+channels:
+  - r
+  - conda-forge
+  - conda-forge/label/gcc7
+  - bioconda
+dependencies:
+  - jupyter=1.0.0
+  - r-taxize=0.9.91
+  - r-irkernel=0.8.12
+  - r-rgdal=1.4.4
+  - r-rgeos=0.5.1
+  - r-dplyr=0.8.3
+  - r-leaflet=2.0.3
+  - r-htmlwidgets=1.3
+  - r-htmltools=0.3.6
+  - r-sf=0.8
+  - r-classint=0.4.2
+  - r-tidyverse=1.2.1
+  - r-xfun=0.5
+  - r-biocmanager=1.30.4 
+  - r-bold=0.9.0
+  - bioconductor-sangerseqr=1.22.0 
+

conda/env_ubuntu.yml

+name: mapmarine2
+channels:  
+  - conda-forge
+  - conda-forge/label/gcc7
+  - bioconda
+  - bioconda/label/gcc7
+  - r
+dependencies:
+  - libblas
+  - r=3.6.*
+  - r-rcpp=1.0.1
+  - r-geonames=0.999
+  - r-data.table=1.12.2
+  - r-stringi=1.4.5
+  - r-mclust=5.4.5
+  - bioconductor-preprocesscore=1.48.0
+  - r-classint 0.4.1
+  - r-taxize=0.9.*
+  - r-rgdal=1.4.4
+  - r-rgeos=0.5.1
+  - r-dplyr=0.8.3
+  - r-sf=0.8
+  - r-tidyverse=1.2.1
+  - r-biocmanager=1.30.4
+  - r-bold=0.9.0
+  - bioconductor-sangerseqr=1.22.0
+  - r-ggplot2=3.1.1
+  - muscle=3.8.1551
+  - r-raster=3.*
+  - r-countrycode=1.1.0
+  - r-mass
+  - r-lme4
+  - r-shape
+  - r-visreg
+  - r-betareg=3.*
+  - r-spatial=7.*
+  - r-hier.part
+  - r-gridextra=2.3 

96-descriptions/filter_bold.tsv → report/filter_bold.tsv

@@ -6,5 +6,7 @@ no seq & no spec & notlatlon	02-bold_format/bold_nolatlon_nospec_noseq.tsv	10089
 add geonames assignment	02-bold_format/all_format_bold.tsv	102599
 select COI sequences	02-bold_format/all_format_bold_coi.tsv	97146
 select 499 baseslength sequences	02-bold_format/all_format_bold_coi_length499.tsv	95609
+select 420 baseslength sequences	02-bold_format/all_format_bold_coi_length420.tsv	96127
+keep species with a least 2 sequences 91168
 
 

src/01_download_bold.R

+library("bold")
+
+taxonRequest <- "Actinopterygii"
+
+resBold <- bold_seqspec(taxon=taxonRequest, sepfasta=TRUE)
+
+## Saving object in RData format
+resboldObjFile=paste("rdata/bold_res_",taxonRequest,".RData",sep="")
+save(resBold, file = resboldObjFile)
+

src/02_filter_bold.R

+## load request bold data sequence+specimens
+taxonRequest <- "Actinopterygii"
+resboldObjFile=paste("rdata/bold_res_",taxonRequest,".RData",sep="")
+
+load(resboldObjFile)
\ No newline at end of file