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]))
Build a Maximum Likelihood tree:
ali.16SB<-as.phyDat(ssuAlignB[c(2:10,1),segSitB]) dist.16SB<-dist.ml(ali.16SB) tree.16S.njB<-root(NJ(dist.16SB),10) mod.16SB<-modelTest(ali.16SB,model="all",multicore=TRUE) env.16SB<-attr(mod.16SB,"env") fitStart.16SB<-eval(get(mod.16SB$Model[which.min(mod.16SB$BIC)],env.16SB),env.16SB) # mod.16SB$Model[which.min(mod.16SB$BIC)]="K80" fitNJ.16SB<-pml(tree.16S.njB,ali.16SB) fit.16SB<-optim.pml(fitNJ.16SB,rearrangement="stochastic",model="K80",optInv=FALSE,optGamma=FALSE) bs.16SB<-bootstrap.pml(fit.16SB,bs=1000,optNni=TRUE,multicore=TRUE) plotBS(fit.16SB$tree,bs.16SB,p=50,type="p",bs.adj=c(1.2,-.7)) add.scale.bar()