many changes ;-)

Former-commit-id: cb4aea844e960e4af4dc673ebc8eec49a7d12b13

doc/book/.ipynb_checkpoints/Untitled-checkpoint.ipynb

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+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

doc/book/Untitled.ipynb

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+{
+ "cells": [],
+ "metadata": {},
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

doc/book/wolf_data/sort_gb_order.sh

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+#!/bin/bash
+#!/bin/bash
+#OAR -n gbsort
+##OAR --array 50
+##OAR --array-param-file 50_first.tsv
+#OAR --project phyloalps
+#OAR -l nodes=1/core=10,walltime=24:00:00
+#OAR -O gbsort.%jobid%.log
+#OAR -E gbsort.%jobid%.log
+
+
+# /silenus/PROJECTS/pr-phyloalps/coissac
+# /bettik/LECA/ENVIRONMENT/data/biodatabase/genbank
+
+#
+# Used resources URLs
+#
+
+NCBIURL="https://ftp.ncbi.nlm.nih.gov/"            # NCBI Web site URL
+GBURL="${NCBIURL}genbank/"                         # Directory of Genbank flat files 
+TAXOURL="${NCBIURL}pub/taxonomy/taxdump.tar.gz"    # NCBI Taxdump
+
+LOGFILE="download.log"
+
+#
+# List of downloaded Genbank divisions
+#
+
+DIV="bct|inv|mam|phg|pln|pri|rod|vrl|vrt"
+
+############################
+#
+#  Functions
+#
+############################
+
+pattern_at_rank() {
+   local taxo="$1"
+   local rank="$2"
+
+   echo "^($(awk -F "|" -v rank="$rank" 'BEGIN {
+                          ORS="|";
+                          rank="\t" rank "\t"
+                        } 
+            ($3 ~ rank) {sub(/^[ \t]+/,"",$1); 
+                         sub(/[ \t]+$/,"",$1); 
+                         print $1}
+           ' "${taxo}/nodes.dmp" \
+       | sed 's/|$//'))$"
+}
+
+
+GBDIR=$1
+
+#
+# Extrate from the web site the current Genbank release number
+# end create the corresponding directory
+#
+
+echo "Looking at current Genbank release number"
+GB_Release_Number=$(for r in $(ls -d "${GBDIR}/Release-"* ); do 
+                        basename $r; 
+                    done \
+                    | sort -r \
+                    | head -1 \
+                    | sed 's/^Release-//')
+
+GB_Release_Number=251
+
+echo "identified latest release number is : ${GB_Release_Number}"
+
+GBSOURCE="${GBDIR}/Release-${GB_Release_Number}"
+
+mkdir -p "Release-${GB_Release_Number}"
+cd "Release-${GB_Release_Number}" || exit
+
+#
+# Download the current NCBI taxonomy
+#
+mkdir -p "ncbitaxo"
+
+if [[ ! -f ncbitaxo/nodes.dmp ]] || [[ ! -f ncbitaxo/names.dmp ]] ; then
+   curl "${TAXOURL}" \
+      | tar -C "ncbitaxo" -zxf -
+fi
+
+
+for f in $(ls -1 "${GBSOURCE}/"*.seq.gz ) ; do
+
+   echo "PROCESSING : $f saved into $fasta" $(pwd)
+
+      obiannotate --genbank -t ncbitaxo \
+                                 --with-taxon-at-rank kingdom \
+                                 --with-taxon-at-rank superkingdom \
+                                 --with-taxon-at-rank phylum\
+                                 --with-taxon-at-rank order  \
+                                 --with-taxon-at-rank family  \
+                                 --with-taxon-at-rank genus  \
+                                 -S division='"misc-@-0"' \
+                                 -S section='"misc-@-0"' \
+                                 "$f" \
+      | obigrep -A genus_taxid -A family_taxid \
+      | obigrep -p 'annotations.genus_taxid > 0 && annotations.family_taxid > 0' \
+                -p 'annotations.phylum_taxid > 0 || annotations.order_taxid > 0' \
+      | obiannotate -p 'annotations.superkingdom_taxid > 0' \
+                -S division='printf("%s-S-%d",subspc(annotations.superkingdom_name),annotations.superkingdom_taxid)' \
+      | obiannotate -p 'annotations.kingdom_taxid > 0' \
+                -S division='printf("%s-K-%d",subspc(annotations.kingdom_name),annotations.kingdom_taxid)' \
+      | obiannotate -p 'annotations.phylum_taxid > 0' \
+                -S section='printf("%s-P-%d",subspc(annotations.phylum_name),annotations.phylum_taxid)' \
+      | obiannotate -p 'annotations.order_taxid > 0' \
+                -S section='printf("%s-O-%d",subspc(annotations.order_name),annotations.order_taxid)' \
+      | obidistribute -Z -A -p "%s.fasta" -c section -d division 
+
+
+
+done
+