Updated script

bioinformaticsProject/biocomp_projectupdated.sh

@@ -0,0 +1,120 @@
+#usage: To determine candidates based on hsp70 (more than two copies) and mcrA (one copy). Looking for organisms with both.
+# Absolute Path to ref_sequences: Private/Biocomputing_Project/bioinformaticsProject/ref_sequences/
+#Direct path to muscle tool: ~/Private/bin/muscle. Absolute path to hmmbuild:  ~/Private/bin/hmmbuild
+#Direct path to proteomes cd Private/Biocomputing_Project/bioinformaticsProject/proteomes/
+# Direct path to hmm search ~/Private/bin/hmmsearch 
+
+#access ref files, starting in the home directory 
+#cd ref_sequences 
+
+cd $1
+
+#to combine the raw hsp70 files into one fasta that we will hmm
+
+cat hsp70g* | grep -v fasta > hsp70.fasta
+
+#to combine the raw mcrAgene files into one fasta that we will hmm
+
+cat mcrAgene_* | grep -v fasta > mcrA.fasta
+
+#muscling the compiled hsp70
+
+$2 -in hsp70.fasta -out hsp70.hmm
+
+#muscling the compiled mcrA
+
+$2  -in mcrA.fasta -out mcrAgene.hmm
+
+#Build a profile HMM from muscle output for hsp70
+
+$3  hsp70results hsp70.hmm 
+
+#Build a profile HMM from muscle output for mcrA
+
+$3  mcrAresults mcrA/gene.hmm 
+
+#Compile proteomes to use as file to search using hmmsearch
+
+mv ./mcrAresults $4 
+
+mv ./hsp70results $4
+
+#Move to proteome directory from ref_sequences
+
+cd $4
+
+#hmmsearch hsp70
+
+for file in proteome*
+do
+echo | $5  --tblout hsp70search$file  hsp70results  $file
+done
+
+#Sorting hsp based on proteome
+
+for file in hsp70searchproteome_*
+do
+grep "# Target\|WP" $file > newcomposite2$file
+done
+
+#Finding amount of hsp in each proteome
+
+for file in newcomposite2hsp70searchproteome_*
+do
+echo
+wc -l $file >> CompiledWChsp70
+done
+
+
+#hmmsearch mcrA
+
+for file in proteome*
+do
+echo | $5  --tblout mcrAsearch$file  mcrAresults  $file
+done
+
+#Sorting mcrA  based on proteome
+
+for file in mcrAsearchproteome_*
+do
+grep "# Target\|WP" $file > newcomposite1$file
+done
+
+#Finding amount of mcrA in each proteome 
+
+for file in newcomposite1mcrAsearchproteome_*
+do
+echo
+wc -l $file >> CompiledWCmcrA
+done
+
+#Renaming the mcrA gene copy results into the format of number of copies of hsp70
+
+sed 's/newcomposite2hsp70searchproteome/proteome/' CompiledWChsp70 > abbreviatedhsp70
+
+#Listing all the hsp70 candidates. Need at least two copied of the gene.
+#1 line has the title, so we need at least 3 lines in each search
+
+grep -E  "[3-9] "  abbreviatedhsp70 > completehsp70
+
+#Renaming the mcrA gene copy results into the format of number of copies and th$
+
+sed 's/newcomposite1mcrAsearchproteome/proteome/' CompiledWCmcrA > abbreviatedmcrA
+
+#Listing all mcrA candidates into file "completemcrA". Just needs 1 copy.     
+#Therefore, select all proteomes with more than	1 line,	indicating presence
+#of the	gene
+
+grep -v 1 abbreviatedmcrA | sort -n > completemcrA
+
+#Combine both complete searches	into a compilation of candidates
+
+cat completehsp70 completemcrA >> candidatesofficial
+
+#Successful candidates
+
+cat candidatesofficial | sort -k 2 | cut -d " " -f 2| uniq -d
+
+#Successful candidates were found to be	3,5,7,23,24,42,45,50
+
+

bioinformaticsProject/proteomes/CompiledWChsp70

@@ -0,0 +1,50 @@
+5 newcomposite2hsp70searchproteome_01.fasta
+3 newcomposite2hsp70searchproteome_02.fasta
+4 newcomposite2hsp70searchproteome_03.fasta
+5 newcomposite2hsp70searchproteome_04.fasta
+3 newcomposite2hsp70searchproteome_05.fasta
+1 newcomposite2hsp70searchproteome_06.fasta
+3 newcomposite2hsp70searchproteome_07.fasta
+6 newcomposite2hsp70searchproteome_08.fasta
+2 newcomposite2hsp70searchproteome_09.fasta
+4 newcomposite2hsp70searchproteome_10.fasta
+7 newcomposite2hsp70searchproteome_11.fasta
+7 newcomposite2hsp70searchproteome_12.fasta
+4 newcomposite2hsp70searchproteome_13.fasta
+3 newcomposite2hsp70searchproteome_14.fasta
+2 newcomposite2hsp70searchproteome_15.fasta
+2 newcomposite2hsp70searchproteome_16.fasta
+5 newcomposite2hsp70searchproteome_17.fasta
+9 newcomposite2hsp70searchproteome_18.fasta
+2 newcomposite2hsp70searchproteome_19.fasta
+4 newcomposite2hsp70searchproteome_20.fasta
+1 newcomposite2hsp70searchproteome_21.fasta
+1 newcomposite2hsp70searchproteome_22.fasta
+3 newcomposite2hsp70searchproteome_23.fasta
+3 newcomposite2hsp70searchproteome_24.fasta
+1 newcomposite2hsp70searchproteome_25.fasta
+2 newcomposite2hsp70searchproteome_26.fasta
+2 newcomposite2hsp70searchproteome_27.fasta
+2 newcomposite2hsp70searchproteome_28.fasta
+1 newcomposite2hsp70searchproteome_29.fasta
+2 newcomposite2hsp70searchproteome_30.fasta
+8 newcomposite2hsp70searchproteome_31.fasta
+5 newcomposite2hsp70searchproteome_32.fasta
+1 newcomposite2hsp70searchproteome_33.fasta
+3 newcomposite2hsp70searchproteome_34.fasta
+2 newcomposite2hsp70searchproteome_35.fasta
+4 newcomposite2hsp70searchproteome_36.fasta
+2 newcomposite2hsp70searchproteome_37.fasta
+2 newcomposite2hsp70searchproteome_38.fasta
+2 newcomposite2hsp70searchproteome_39.fasta
+3 newcomposite2hsp70searchproteome_40.fasta
+2 newcomposite2hsp70searchproteome_41.fasta
+4 newcomposite2hsp70searchproteome_42.fasta
+4 newcomposite2hsp70searchproteome_43.fasta
+2 newcomposite2hsp70searchproteome_44.fasta
+4 newcomposite2hsp70searchproteome_45.fasta
+3 newcomposite2hsp70searchproteome_46.fasta
+2 newcomposite2hsp70searchproteome_47.fasta
+2 newcomposite2hsp70searchproteome_48.fasta
+4 newcomposite2hsp70searchproteome_49.fasta
+4 newcomposite2hsp70searchproteome_50.fasta

bioinformaticsProject/proteomes/CompiledWCmcrA

@@ -0,0 +1,50 @@
+1 newcomposite1mcrAsearchproteome_01.fasta
+1 newcomposite1mcrAsearchproteome_02.fasta
+2 newcomposite1mcrAsearchproteome_03.fasta
+1 newcomposite1mcrAsearchproteome_04.fasta
+2 newcomposite1mcrAsearchproteome_05.fasta
+1 newcomposite1mcrAsearchproteome_06.fasta
+2 newcomposite1mcrAsearchproteome_07.fasta
+1 newcomposite1mcrAsearchproteome_08.fasta
+1 newcomposite1mcrAsearchproteome_09.fasta
+1 newcomposite1mcrAsearchproteome_10.fasta
+1 newcomposite1mcrAsearchproteome_11.fasta
+1 newcomposite1mcrAsearchproteome_12.fasta
+1 newcomposite1mcrAsearchproteome_13.fasta
+1 newcomposite1mcrAsearchproteome_14.fasta
+2 newcomposite1mcrAsearchproteome_15.fasta
+2 newcomposite1mcrAsearchproteome_16.fasta
+1 newcomposite1mcrAsearchproteome_17.fasta
+1 newcomposite1mcrAsearchproteome_18.fasta
+3 newcomposite1mcrAsearchproteome_19.fasta
+1 newcomposite1mcrAsearchproteome_20.fasta
+1 newcomposite1mcrAsearchproteome_21.fasta
+1 newcomposite1mcrAsearchproteome_22.fasta
+3 newcomposite1mcrAsearchproteome_23.fasta
+2 newcomposite1mcrAsearchproteome_24.fasta
+1 newcomposite1mcrAsearchproteome_25.fasta
+1 newcomposite1mcrAsearchproteome_26.fasta
+1 newcomposite1mcrAsearchproteome_27.fasta
+1 newcomposite1mcrAsearchproteome_28.fasta
+2 newcomposite1mcrAsearchproteome_29.fasta
+1 newcomposite1mcrAsearchproteome_30.fasta
+1 newcomposite1mcrAsearchproteome_31.fasta
+1 newcomposite1mcrAsearchproteome_32.fasta
+1 newcomposite1mcrAsearchproteome_33.fasta
+1 newcomposite1mcrAsearchproteome_34.fasta
+1 newcomposite1mcrAsearchproteome_35.fasta
+1 newcomposite1mcrAsearchproteome_36.fasta
+1 newcomposite1mcrAsearchproteome_37.fasta
+2 newcomposite1mcrAsearchproteome_38.fasta
+2 newcomposite1mcrAsearchproteome_39.fasta
+1 newcomposite1mcrAsearchproteome_40.fasta
+1 newcomposite1mcrAsearchproteome_41.fasta
+2 newcomposite1mcrAsearchproteome_42.fasta
+1 newcomposite1mcrAsearchproteome_43.fasta
+2 newcomposite1mcrAsearchproteome_44.fasta
+2 newcomposite1mcrAsearchproteome_45.fasta
+1 newcomposite1mcrAsearchproteome_46.fasta
+1 newcomposite1mcrAsearchproteome_47.fasta
+2 newcomposite1mcrAsearchproteome_48.fasta
+1 newcomposite1mcrAsearchproteome_49.fasta
+2 newcomposite1mcrAsearchproteome_50.fasta

bioinformaticsProject/proteomes/abbreviatedhsp70

@@ -0,0 +1,50 @@
+5 proteome_01.fasta
+3 proteome_02.fasta
+4 proteome_03.fasta
+5 proteome_04.fasta
+3 proteome_05.fasta
+1 proteome_06.fasta
+3 proteome_07.fasta
+6 proteome_08.fasta
+2 proteome_09.fasta
+4 proteome_10.fasta
+7 proteome_11.fasta
+7 proteome_12.fasta
+4 proteome_13.fasta
+3 proteome_14.fasta
+2 proteome_15.fasta
+2 proteome_16.fasta
+5 proteome_17.fasta
+9 proteome_18.fasta
+2 proteome_19.fasta
+4 proteome_20.fasta
+1 proteome_21.fasta
+1 proteome_22.fasta
+3 proteome_23.fasta
+3 proteome_24.fasta
+1 proteome_25.fasta
+2 proteome_26.fasta
+2 proteome_27.fasta
+2 proteome_28.fasta
+1 proteome_29.fasta
+2 proteome_30.fasta
+8 proteome_31.fasta
+5 proteome_32.fasta
+1 proteome_33.fasta
+3 proteome_34.fasta
+2 proteome_35.fasta
+4 proteome_36.fasta
+2 proteome_37.fasta
+2 proteome_38.fasta
+2 proteome_39.fasta
+3 proteome_40.fasta
+2 proteome_41.fasta
+4 proteome_42.fasta
+4 proteome_43.fasta
+2 proteome_44.fasta
+4 proteome_45.fasta
+3 proteome_46.fasta
+2 proteome_47.fasta
+2 proteome_48.fasta
+4 proteome_49.fasta
+4 proteome_50.fasta

bioinformaticsProject/proteomes/abbreviatedmcrA

@@ -0,0 +1,50 @@
+1 proteome_01.fasta
+1 proteome_02.fasta
+2 proteome_03.fasta
+1 proteome_04.fasta
+2 proteome_05.fasta
+1 proteome_06.fasta
+2 proteome_07.fasta
+1 proteome_08.fasta
+1 proteome_09.fasta
+1 proteome_10.fasta
+1 proteome_11.fasta
+1 proteome_12.fasta
+1 proteome_13.fasta
+1 proteome_14.fasta
+2 proteome_15.fasta
+2 proteome_16.fasta
+1 proteome_17.fasta
+1 proteome_18.fasta
+3 proteome_19.fasta
+1 proteome_20.fasta
+1 proteome_21.fasta
+1 proteome_22.fasta
+3 proteome_23.fasta
+2 proteome_24.fasta
+1 proteome_25.fasta
+1 proteome_26.fasta
+1 proteome_27.fasta
+1 proteome_28.fasta
+2 proteome_29.fasta
+1 proteome_30.fasta
+1 proteome_31.fasta
+1 proteome_32.fasta
+1 proteome_33.fasta
+1 proteome_34.fasta
+1 proteome_35.fasta
+1 proteome_36.fasta
+1 proteome_37.fasta
+2 proteome_38.fasta
+2 proteome_39.fasta
+1 proteome_40.fasta
+1 proteome_41.fasta
+2 proteome_42.fasta
+1 proteome_43.fasta
+2 proteome_44.fasta
+2 proteome_45.fasta
+1 proteome_46.fasta
+1 proteome_47.fasta
+2 proteome_48.fasta
+1 proteome_49.fasta
+2 proteome_50.fasta

bioinformaticsProject/proteomes/candidatesofficial

@@ -0,0 +1,41 @@
+5 proteome_01.fasta
+3 proteome_02.fasta
+4 proteome_03.fasta
+5 proteome_04.fasta
+3 proteome_05.fasta
+3 proteome_07.fasta
+6 proteome_08.fasta
+4 proteome_10.fasta
+7 proteome_11.fasta
+7 proteome_12.fasta
+4 proteome_13.fasta
+3 proteome_14.fasta
+5 proteome_17.fasta
+9 proteome_18.fasta
+4 proteome_20.fasta
+3 proteome_23.fasta
+3 proteome_24.fasta
+8 proteome_31.fasta
+5 proteome_32.fasta
+3 proteome_34.fasta
+4 proteome_36.fasta
+3 proteome_40.fasta
+4 proteome_42.fasta
+4 proteome_43.fasta
+4 proteome_45.fasta
+3 proteome_46.fasta
+4 proteome_49.fasta
+4 proteome_50.fasta
+2 proteome_03.fasta
+2 proteome_05.fasta
+2 proteome_07.fasta
+2 proteome_24.fasta
+2 proteome_29.fasta
+2 proteome_38.fasta
+2 proteome_39.fasta
+2 proteome_42.fasta
+2 proteome_44.fasta
+2 proteome_45.fasta
+2 proteome_48.fasta
+2 proteome_50.fasta
+3 proteome_23.fasta

bioinformaticsProject/proteomes/completehsp70

@@ -0,0 +1,28 @@
+5 proteome_01.fasta
+3 proteome_02.fasta
+4 proteome_03.fasta
+5 proteome_04.fasta
+3 proteome_05.fasta
+3 proteome_07.fasta
+6 proteome_08.fasta
+4 proteome_10.fasta
+7 proteome_11.fasta
+7 proteome_12.fasta
+4 proteome_13.fasta
+3 proteome_14.fasta
+5 proteome_17.fasta
+9 proteome_18.fasta
+4 proteome_20.fasta
+3 proteome_23.fasta
+3 proteome_24.fasta
+8 proteome_31.fasta
+5 proteome_32.fasta
+3 proteome_34.fasta
+4 proteome_36.fasta
+3 proteome_40.fasta
+4 proteome_42.fasta
+4 proteome_43.fasta
+4 proteome_45.fasta
+3 proteome_46.fasta
+4 proteome_49.fasta
+4 proteome_50.fasta