HowTo
From salvaEwiki
Successful tiny examples.
In bash, at Moria
Generate the md5 signatures of the files in a folder:
for file in /Volumes/MBL21/A_TREASURY/012_A_TRASURY_ThiobiosGenomes/* ; do md5 -q $file >> resultsQ.out ; done
Generate the sizes of the files in a folder:
for file in /Volumes/MBL21/A_TREASURY/012_A_TRASURY_ThiobiosGenomes/* ; do wc -c $file >> sizes.out ; done
Extract the first column:
awk '{print $1}' sizes.out > sizesQ.out
At CUBE
GC contents of the files in a folder:
for file in /proj/genomes/Thiobios/data/ThiobiosMAGs/* ; do gc $file >> gc.out ; done awk '{print $4}' gc.out > gcQ.out
Assess completeness, contamination and heterogeneity of the genomes in a folder:
checkm lineage_wf -t 8 /proj/genomes/Thiobios/results/2017_08_24_checkM/data /proj/genomes/Thiobios/results/2017_08_24_checkM/therest.checkm --tab_table --file therest.checkm.out
Check for tRNAs of the genomes in a folder:
cd /proj/genomes/Thiobios/data/ThiobiosMAGs for file in ./* ; do tRNAscan-SE -B $file -o /proj/genomes/Thiobios/results/2017_08_25_tRNAscan-SE/$file.tRNAscan-SE.out ; done
With R (and RStudio)
extract a part of a sequence, using ape:
s2c(c2s(as.matrix(g43Z2[1])[44214:47213]))