ghostKOALA - Update README.md

README.md

@@ -11,4 +11,46 @@ ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_A_26_11_15_S1_all_R1_001.fastq.gz DATA/ra
 ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_A_26_11_15_S1_all_R2_001.fastq.gz DATA/raw/J80_A_R2.fastq.gz
 ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_B_26_11_15_S2_all_R1_001.fastq.gz DATA/raw/J80_B_R1.fastq.gz
 ln -s ~/DIGESTOMIC/DATA/DIGESTOMIC_J80_B_26_11_15_S2_all_R2_001.fastq.gz DATA/raw/J80_B_R2.fastq.gz
-```
+```
\ No newline at end of file
+
+## ghostKOALA
+
+### Submit analysis
+
+```bash
+awk 'NR<=2000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-1.faa 
+awk 'NR>=2000001&&NR<=4000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-2.faa 
+awk 'NR>=4000001&&NR<=6000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-3.faa 
+awk 'NR>=6000001&&NR<=8000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-4.faa 
+awk 'NR>=8000001&&NR<=10000000' work/FGS/coassembly_FGS.faa > work/FGS/coassembly_FGS-5.faa 
+awk 'NR>=10000001' work/FGS/coassembly_FGS.faa  > work/FGS/coassembly_FGS-6.faa 
+```
+
+* Download files
+* Upload on [GhostKOALA webserver](https://www.kegg.jp/ghostkoala/) with `genus_prokaryotes + family_eukaryotes + viruses ` database option
+* Submit
+* Download from webserver and group in order annotation files `user_ko.txt`
+* Join with other tables
+
+### KEGG orthology table
+
+[source](http://merenlab.org/2018/01/17/importing-ghostkoala-annotations/)
+
+```bash
+cd work/ghostKOALA
+wget 'https://www.genome.jp/kegg-bin/download_htext?htext=ko00001&format=htext&filedir=' -O ko00001.keg
+
+kegfile="ko00001.keg"
+
+while read -r prefix content
+do
+    case "$prefix" in A) col1="$content";; \
+                      B) col2="$content" ;; \
+                      C) col3="$content";; \
+                      D) echo -e "$col1\t$col2\t$col3\t$content";;
+    esac 
+done < <(sed '/^[#!+]/d;s/<[^>]*>//g;s/^./& /' < "$kegfile") > KO_Orthology_ko00001.txt
+
+rm ko00001.keg
+```
+