Elias_Issa-Project1

candidates.txt

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+proteome_03
+proteome_42
+proteome_45
+proteome_50

projectScript.sh

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+#Compiles all the individual hsp70 and mcrA sequences into one file 
+cat ref_sequences/hsp70*.fasta > hsp70seq.fasta
+cat ref_sequences/mcrA*.fasta > mcrAseq.fasta
+
+#Uses combined seq files to form alignments using muscle
+~/Private/Biocomputing2022/Tools/muscle -in hsp70seq.fasta -out hsp70align.afa
+~/Private/Biocomputing2022/Tools/muscle -in mcrAseq.fasta -out mcrAalign.afa
+
+#Uses alignments to build a profile with hmmbuild 
+~/Private/Biocomputing2022/Tools/hmmbuild hsp70profile.hmm hsp70align.afa
+~/Private/Biocomputing2022/Tools/hmmbuild mcrAprofile.hmm mcrAalign.afa
+
+#Sets headings for summary file and creates or overwrites summary csv file
+echo proteome, hsp70_matches, mcrA_matches > summary.csv
+
+#loops through all proteomes in proteomes file
+for file in proteomes/*
+do
+
+#Represents the name of the current proteosome and modifies formatting 
+a=$(echo $file | sed 's/.fasta//' | sed -e 's/proteomes.//')
+
+#Searches the hsp70 profile in current proteome and gets match number
+b=$(~/Private/Biocomputing2022/Tools/hmmsearch hsp70profile.hmm $file | grep 'Domain search space' | cut -d ' ' -f 20) 
+
+#Searches for mcrA profile in current proteome and gets match number
+c=$(~/Private/Biocomputing2022/Tools/hmmsearch mcrAprofile.hmm $file | grep 'Domain search space' | cut -d ' ' -f 20)
+
+#Appends proteome name and hsp70 and mcrA matches to summary file
+echo $a, $b, $c >> summary.csv
+done 
+
+#Removes heading of summary file as well as proteomes with no matches 
+#Sorts by number of hsp70 matches (highest to lowest), gets top four matches (each with 3 hsp70) and saves proteome names to candidate file
+cat summary.csv | sed '1d' | sed -e '/, 0/d'| sort -k2,2nr | head -n 4 | cut -d, -f 1 > candidates.txt
+
+