Team:NYC Software/Protocols

Unix Pipe for Genome CDS Comparisons

This is the bash shell script we developed to predict genes in our genomes, align them to the D. rad genome, filter poorer quality hits, and build BED files we could use for visualization.
From it you can learn what commands to use to do the various operations.

# Unix Code scratch for Shell Scripting Gene Predictions + Alignment
# Will predict genes in foreign Deinos, extract predicted sequences, align them to the Drad genome and finally make a BED file to visualize tracks


genomes=~/Deinos/genomes
glimmer=~/Deinos/glimmer
predicts=~/Deinos/glimmer/script_predicts
CDSs=~/Deinos/glimmer/CDSs
alignments_root=~/Deinos/CDS_alignments/All_CDSs_to_Drad_genome
SAMs=~/Deinos/CDS_alignments/All_CDSs_to_Drad_genome/SAMs
BAMs=~/Deinos/CDS_alignments/All_CDSs_to_Drad_genome/BAMs
BEDs=~/Deinos/CDS_alignments/All_CDSs_to_Drad_genome/BEDs

#EMPTY ALL DIRECTORIES
for y in $predicts $CDSs $SAMs $BAMs $BEDs; do cd $y; rm *; cd ~/Deinos/; done

#predict genes in Deino species using ICM model based on Drad's CDSs
for x in `ls $genomes`; do glimmer3 $genomes/$x $glimmer/ICMs/Drad_CDS.icm $predicts/$x.glimmer; done

#Extract CDSs using these predictions
for x in `ls $genomes`; do extract $genomes/$x $predicts/$x.glimmer.predict > $CDSs/$x.CDSs.fa; done

#Align predicted genes to Drad genome to create SAM file
for x in `ls $CDSs`; do bwa bwasw -f $SAMs/$x.sam ~/Deinos/BWA_INDEXES/Drad/Drad_full_genome.fa $CDSs/$x; done

#Convert to BAM
for x in `ls $SAMs`; do samtools view -b -S -o $BAMs/$x.bam $SAMs/$x; done

#Sort BAM
for x in `ls $BAMs`; do samtools sort $BAMs/$x $BAMs/$x.sorted; echo $x 'sorted'; done

#Create BED file
for x in `ls $BAMs | grep sorted`; do bamToBed -i $BAMs/$x > $BEDs/$x.bed; echo 'bed file created for ' $x; done

#echo done
echo "SUCCESS!!!! (hopefully) - see for yourself:"

echo "These are the word counts for the files in the BEDs directory:"
for x in `ls $BEDs`; do cd $BEDs; wc $x; done