Rey Ortiz Bautista, Roman Fresquez, Max Zupfer

BioinformaticsProject.Answer

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+#Creating the Muscle for hspGenes
+cd ~/Private/bioinformaticsProject/ref_sequences | cat hsp70gene_*.fasta >> hspgenes.txt | ~/Private/Biocomputing2022/tools/muscle -in hspgenes.txt -out hspGenesmuscle.txt
+#HmmBuild for hspGenes
+~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.hsp hspGenesmuscle.txt
+#Copy hmmbuild.hsp  to Proteome Directory
+cp hmmbuild.hsp ../proteomes
+#Move to Proteomes Directory to Run for loop
+~/Private/bioinformaticsProject/proteomes
+#HmmSearch for hspGenes For Loop
+for file in proteome_*.fasta
+do
+	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmm.hspSearch${file} hmmbuild.hsp $file
+done
+
+
+
+#Creating the Muscle for the mcrAgenes
+cd ~/Private/bioinformaticsProject/ref_sequences | cat mcrAgene_*.fasta >> mcrAgene.txt | ~/Private/Biocomputing2022/tools/muscle -in mcrAgene.txt -out mcrAmuscle.txt
+#HmmBuild for mcrAgenes
+~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.mcrA mcrAmuscle.txt
+#Copy hmmbuild.mcrA to Proteomes Directory
+cp hmmbuild.mcrA ../proteomes
+#Move to Proteomes Directory to Run For Loop
+~/Private/bioinformaticsProject/proteomes
+#HmmSearch for mcrA gene For Loop
+for file in proteome_*.fasta
+do
+	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmmSearch.mcrA${file} hmmbuild.mcrA $file
+done
+

BioinformaticsProjectAnswer.sh

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+#Final Table Name: finaltable.txt 
+#Final Proteome Candidates: proteomecandidates.txt
+#Assumption that our file system looks the same as the Graduate Student
+#Usage: bash BioinformaticsProjectAnswer.sh
+#Creating the Muscle for hspGenes
+cd ~/Private/bioinformaticsProject/ref_sequences | cat hsp70gene_*.fasta >> hspgenes.txt | ~/Private/Biocomputing2022/tools/muscle -in hspgenes.txt -out hspGenesmuscle.txt
+#HmmBuild for hspGenes
+~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.hsp hspGenesmuscle.txt
+#Copy hmmbuild.hsp  to Proteome Directory
+cp hmmbuild.hsp ../proteomes
+#Move to Proteomes Directory to Run for loop
+~/Private/bioinformaticsProject/proteomes
+
+
+#Creating the Muscle for the mcrAgenes
+cd ~/Private/bioinformaticsProject/ref_sequences | cat mcrAgene_*.fasta >> mcrAgene.txt | ~/Private/Biocomputing2022/tools/muscle -in mcrAgene.txt -out mcrAmuscle.txt
+#HmmBuild for mcrAgenes
+~/Private/Biocomputing2022/tools/hmmbuild hmmbuild.mcrA mcrAmuscle.txt
+#Copy hmmbuild.mcrA to Proteomes Directory
+cp hmmbuild.mcrA ../proteomes
+#Move to Proteomes Directory to Run For Loop
+~/Private/bioinformaticsProject/proteomes
+
+#Make Final File
+echo proteome name, mcrAgenes, hsp70genes >> final.txt
+
+#HmmSearch for Loop for both Hsp70 and mcrA
+for file in proteome_*.fasta
+do 
+#HmmSearch for hspgenes
+	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmm.hspSearch${file} hmmbuild.hsp $file
+#HmmSearch for mcrAgenes
+	~/Private/Biocomputing2022/tools/hmmsearch --tblout hmmSearch.mcrA${file} hmmbuild.mcrA $file
+#Define Proteome Variable
+	proteome=$(echo $file)
+#Define mcrA Variable
+	mcrAmatches=$(cat hmmSearch.mcrA${file} | grep -v "#" | wc -l)
+#Define hsp70 Variable
+	hsp70matches=$(cat hmm.hspSearch${file} | grep -v "#" | wc -l)
+#Put Loop Results in a text file
+	echo "$proteome,$mcrAmatches,$hsp70matches" >> final.txt
+#Finish For Loop
+done
+
+#Remove .fasta from proteome names to Complete Final Table
+cat final.txt | tr "." "," | cut -d , -f 1,3,4 >> finaltable.txt
+
+#Make File With pH resistant methanogens
+echo Top 15 candidate pH-resistant methanogens >> pH.txt
+#See if mcrA is present, sort by hsp70 genes and  give top 15 results
+cat finaltable.txt | grep -E ,[1-2], | sort -t, -k3 -r | head -n 15 >> pH.txt
+#Give name of final 15 Proteomes
+cat pH.txt | cut -d , -f 1 >> proteomecandidates.txt
+

finaltable.txt

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+proteome_01,0,4
+proteome_02,0,1
+proteome_03,1,3
+proteome_04,0,4
+proteome_05,1,2
+proteome_06,0,0
+proteome_07,1,2
+proteome_08,0,5
+proteome_09,0,1
+proteome_10,0,3
+proteome_11,0,6
+proteome_12,0,6
+proteome_13,0,3
+proteome_14,0,1
+proteome_15,1,1
+proteome_16,1,1
+proteome_17,0,3
+proteome_18,0,8
+proteome_19,2,1
+proteome_20,0,3
+proteome_21,0,5
+proteome_22,0,9
+proteome_23,2,2
+proteome_24,1,2
+proteome_25,0,5
+proteome_26,0,1
+proteome_27,0,1
+proteome_28,0,1
+proteome_29,1,0
+proteome_30,0,1
+proteome_31,0,7
+proteome_32,0,4
+proteome_33,0,0
+proteome_34,0,1
+proteome_35,0,1
+proteome_36,0,3
+proteome_37,0,1
+proteome_38,1,1
+proteome_39,1,1
+proteome_40,0,1
+proteome_41,0,1
+proteome_42,1,3
+proteome_43,0,3
+proteome_44,1,1
+proteome_45,1,3
+proteome_46,0,1
+proteome_47,0,1
+proteome_48,1,1
+proteome_49,0,3
+proteome_50,1,3

pHcandidates.txt

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+proteome_50
+proteome_45
+proteome_42
+proteome_03
+proteome_24
+proteome_23
+proteome_07
+proteome_05
+proteome_48
+proteome_44
+proteome_39
+proteome_38
+proteome_19
+proteome_16
+proteome_15

proteomes/finaltable.txt

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+proteome_01,0,4
+proteome_02,0,1
+proteome_03,1,3
+proteome_04,0,4
+proteome_05,1,2
+proteome_06,0,0
+proteome_07,1,2
+proteome_08,0,5
+proteome_09,0,1
+proteome_10,0,3
+proteome_11,0,6
+proteome_12,0,6
+proteome_13,0,3
+proteome_14,0,1
+proteome_15,1,1
+proteome_16,1,1
+proteome_17,0,3
+proteome_18,0,8
+proteome_19,2,1
+proteome_20,0,3
+proteome_21,0,5
+proteome_22,0,9
+proteome_23,2,2
+proteome_24,1,2
+proteome_25,0,5
+proteome_26,0,1
+proteome_27,0,1
+proteome_28,0,1
+proteome_29,1,0
+proteome_30,0,1
+proteome_31,0,7
+proteome_32,0,4
+proteome_33,0,0
+proteome_34,0,1
+proteome_35,0,1
+proteome_36,0,3
+proteome_37,0,1
+proteome_38,1,1
+proteome_39,1,1
+proteome_40,0,1
+proteome_41,0,1
+proteome_42,1,3
+proteome_43,0,3
+proteome_44,1,1
+proteome_45,1,3
+proteome_46,0,1
+proteome_47,0,1
+proteome_48,1,1
+proteome_49,0,3
+proteome_50,1,3

proteomes/pHcandidates.txt

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+proteome_50
+proteome_45
+proteome_42
+proteome_03
+proteome_24
+proteome_23
+proteome_07
+proteome_05
+proteome_48
+proteome_44
+proteome_39
+proteome_38
+proteome_19
+proteome_16
+proteome_15