Burton_Doherty submission

Exercise11_files/Problem1/Problem1.sh

@@ -0,0 +1,41 @@
+#create a list of the ref sequences to input these names into muscle
+for file in *.ref
+do
+	echo $file | cut -d '.' -f1 >> ref_filenames.txt
+done
+
+#create a list of the fasta sequences to input these names into hmmsearch
+for file in *.fasta
+do
+	echo $file | cut -d '.' -f1 >> fasta_filenames.txt
+done
+
+#for loop starts by looping through the ref files list of 3 (sigma, transporter, sporecoat)
+for file in $(cat ref_filenames.txt)
+do
+echo $file
+#muscle alignment for the reference file in question
+muscle -in ${file}.ref -out ${file}.align
+#hmmbuild from the muscle alignment to create .hmm file
+hmmbuild ${file}.hmm ${file}.align
+#nested for loop (inside the above for loop) to loop through each organism for
+#the hmm references created for each sequence feature of interest (the hmm refs that
+#were created in the above for loop
+for fasta in $(cat fasta_filenames.txt)
+do
+#create hmmsearch output in the format of refsequence_organism.hits with
+#inputs refsequence.hmm and organism.fasta
+hmmsearch --tblout ${file}_${fasta}.hits ${file}.hmm ${fasta}.fasta
+#display the results of the hmm serach, remove lines with #, and print columns of interest
+#sed to change space delimiters to commas. Write to temp.txt file
+cat ${file}_${fasta}.hits | grep -v "#" | awk '{print $1, $3, $6}' | sed "s/ /,/g" > temp.txt
+#loop through each line(match within the orgamism for the sequence) in temp.txt
+for line in $(cat temp.txt)
+do
+#write to a new line in results.txt file in the format:
+#organism,reference hammer search name (refsequence.hmm),three colums of info from above
+echo "${fasta},${file}.hmm",$line >> results.txt
+done
+rm temp.txt
+done
+done

Exercise11_files/Problem1/results.txt

@@ -0,0 +1,104 @@
+Arthrobacter,sigma.hmm,tr|A0A0P7HFJ4|A0A0P7HFJ4_9MICC,sigma,78.3
+Arthrobacter,sigma.hmm,tr|A0A0P7FPV6|A0A0P7FPV6_9MICC,sigma,72.0
+Arthrobacter,sigma.hmm,tr|A0A0P7GDV0|A0A0P7GDV0_9MICC,sigma,55.2
+Arthrobacter,sigma.hmm,tr|A0A0P7FY19|A0A0P7FY19_9MICC,sigma,53.3
+Arthrobacter,sigma.hmm,tr|A0A0P7HEI0|A0A0P7HEI0_9MICC,sigma,50.0
+Arthrobacter,sigma.hmm,tr|A0A0P7GE65|A0A0P7GE65_9MICC,sigma,46.4
+Arthrobacter,sigma.hmm,tr|A0A0P7HL11|A0A0P7HL11_9MICC,sigma,42.5
+Arthrobacter,sigma.hmm,tr|A0A0P7FHT1|A0A0P7FHT1_9MICC,sigma,40.8
+Arthrobacter,sigma.hmm,tr|A0A0N8HX11|A0A0N8HX11_9MICC,sigma,40.8
+Arthrobacter,sigma.hmm,tr|A0A0P7GAX7|A0A0P7GAX7_9MICC,sigma,22.9
+Bacillus,sigma.hmm,tr|A6CNQ6|A6CNQ6_9BACI,sigma,83.6
+Bacillus,sigma.hmm,tr|A6CSJ0|A6CSJ0_9BACI,sigma,78.1
+Bacillus,sigma.hmm,tr|A6CJY3|A6CJY3_9BACI,sigma,75.3
+Bacillus,sigma.hmm,tr|A6CU12|A6CU12_9BACI,sigma,69.6
+Bacillus,sigma.hmm,tr|A6CJR5|A6CJR5_9BACI,sigma,65.9
+Bacillus,sigma.hmm,tr|A6CHU4|A6CHU4_9BACI,sigma,64.1
+Bacillus,sigma.hmm,tr|A6CMX3|A6CMX3_9BACI,sigma,63.2
+Bacillus,sigma.hmm,tr|A6CS17|A6CS17_9BACI,sigma,62.8
+Bacillus,sigma.hmm,tr|A6CU10|A6CU10_9BACI,sigma,62.3
+Bacillus,sigma.hmm,tr|A6CJX5|A6CJX5_9BACI,sigma,59.8
+Bacillus,sigma.hmm,tr|A6CSN9|A6CSN9_9BACI,sigma,58.3
+Bacillus,sigma.hmm,tr|A6CTI9|A6CTI9_9BACI,sigma,57.7
+Bacillus,sigma.hmm,tr|A6CPD2|A6CPD2_9BACI,sigma,57.7
+Bacillus,sigma.hmm,tr|A6CIS3|A6CIS3_9BACI,sigma,57.3
+Bacillus,sigma.hmm,tr|A6CII5|A6CII5_9BACI,sigma,56.5
+Bacillus,sigma.hmm,tr|A6CI15|A6CI15_9BACI,sigma,56.3
+Bacillus,sigma.hmm,tr|A6CU83|A6CU83_9BACI,sigma,55.0
+Bacillus,sigma.hmm,tr|A6CI19|A6CI19_9BACI,sigma,51.8
+Bacillus,sigma.hmm,tr|A6CQB8|A6CQB8_9BACI,sigma,50.3
+Bacillus,sigma.hmm,tr|A6CK70|A6CK70_9BACI,sigma,47.1
+Bacillus,sigma.hmm,tr|A6CIW8|A6CIW8_9BACI,sigma,42.5
+Bacillus,sigma.hmm,tr|A6CIF2|A6CIF2_9BACI,sigma,41.1
+Bacillus,sigma.hmm,tr|A6CM50|A6CM50_9BACI,sigma,35.4
+Bacillus,sigma.hmm,tr|A6CL73|A6CL73_9BACI,sigma,33.6
+Clostridium,sigma.hmm,tr|R7MFB1|R7MFB1_9CLOT,sigma,79.7
+Clostridium,sigma.hmm,tr|R7MJY2|R7MJY2_9CLOT,sigma,79.0
+Clostridium,sigma.hmm,tr|R7MGY2|R7MGY2_9CLOT,sigma,70.7
+Clostridium,sigma.hmm,tr|R7MFJ3|R7MFJ3_9CLOT,sigma,48.3
+Clostridium,sigma.hmm,tr|R7MFY1|R7MFY1_9CLOT,sigma,46.9
+Clostridium,sigma.hmm,tr|R7MAD7|R7MAD7_9CLOT,sigma,44.6
+Clostridium,sigma.hmm,tr|R7MHN3|R7MHN3_9CLOT,sigma,40.4
+Clostridium,sigma.hmm,tr|R7MCS9|R7MCS9_9CLOT,sigma,39.9
+Flavobacterium,sigma.hmm,tr|A0A1S1J8W1|A0A1S1J8W1_9FLAO,sigma,61.9
+Flavobacterium,sigma.hmm,tr|A0A1S1J0A5|A0A1S1J0A5_9FLAO,sigma,61.8
+Flavobacterium,sigma.hmm,tr|A0A1S1J9H9|A0A1S1J9H9_9FLAO,sigma,61.4
+Flavobacterium,sigma.hmm,tr|A0A1S1JAH2|A0A1S1JAH2_9FLAO,sigma,61.2
+Flavobacterium,sigma.hmm,tr|A0A1S1J7G0|A0A1S1J7G0_9FLAO,sigma,57.5
+Flavobacterium,sigma.hmm,tr|A0A1S1J0Z8|A0A1S1J0Z8_9FLAO,sigma,56.6
+Flavobacterium,sigma.hmm,tr|A0A1S1JF58|A0A1S1JF58_9FLAO,sigma,54.3
+Flavobacterium,sigma.hmm,tr|A0A1S1JAU9|A0A1S1JAU9_9FLAO,sigma,52.5
+Flavobacterium,sigma.hmm,tr|A0A1S1JAK2|A0A1S1JAK2_9FLAO,sigma,48.2
+Flavobacterium,sigma.hmm,tr|A0A1S1J180|A0A1S1J180_9FLAO,sigma,47.8
+Flavobacterium,sigma.hmm,tr|A0A1S1J4G5|A0A1S1J4G5_9FLAO,sigma,46.1
+Flavobacterium,sigma.hmm,tr|A0A1S1J5F7|A0A1S1J5F7_9FLAO,sigma,45.8
+Flavobacterium,sigma.hmm,tr|A0A1S1J7E0|A0A1S1J7E0_9FLAO,sigma,45.1
+Flavobacterium,sigma.hmm,tr|A0A1S1J430|A0A1S1J430_9FLAO,sigma,42.6
+Flavobacterium,sigma.hmm,tr|A0A1S1J2T6|A0A1S1J2T6_9FLAO,sigma,42.3
+Flavobacterium,sigma.hmm,tr|A0A1S1JDD3|A0A1S1JDD3_9FLAO,sigma,38.2
+Flavobacterium,sigma.hmm,tr|A0A1S1J6K9|A0A1S1J6K9_9FLAO,sigma,37.7
+Flavobacterium,sigma.hmm,tr|A0A1S1J9G5|A0A1S1J9G5_9FLAO,sigma,36.5
+Flavobacterium,sigma.hmm,tr|A0A1S1J5L5|A0A1S1J5L5_9FLAO,sigma,35.8
+Flavobacterium,sigma.hmm,tr|A0A1S1J6X1|A0A1S1J6X1_9FLAO,sigma,31.1
+Flavobacterium,sigma.hmm,tr|A0A1S1JCL3|A0A1S1JCL3_9FLAO,sigma,30.5
+Flavobacterium,sigma.hmm,tr|A0A1S1J6M2|A0A1S1J6M2_9FLAO,sigma,22.2
+Flavobacterium,sigma.hmm,tr|A0A1S1J022|A0A1S1J022_9FLAO,sigma,21.0
+Flavobacterium,sigma.hmm,tr|A0A1S1J312|A0A1S1J312_9FLAO,sigma,18.1
+Limnohabitans,sigma.hmm,tr|A0A0P0LD52|A0A0P0LD52_9BURK,sigma,74.9
+Limnohabitans,sigma.hmm,tr|A0A0P0LKP5|A0A0P0LKP5_9BURK,sigma,60.9
+Limnohabitans,sigma.hmm,tr|A0A0P0M8A4|A0A0P0M8A4_9BURK,sigma,58.7
+Limnohabitans,sigma.hmm,tr|A0A0P0MBT4|A0A0P0MBT4_9BURK,sigma,49.5
+Limnohabitans,sigma.hmm,tr|A0A0P0M9M9|A0A0P0M9M9_9BURK,sigma,47.6
+Limnohabitans,sigma.hmm,tr|A0A0P0MA37|A0A0P0MA37_9BURK,sigma,46.7
+Limnohabitans,sigma.hmm,tr|A0A0P0M9Z4|A0A0P0M9Z4_9BURK,sigma,21.2
+Rhizobium,sigma.hmm,tr|A0A1Q9ANZ6|A0A1Q9ANZ6_9RHIZ,sigma,75.3
+Rhizobium,sigma.hmm,tr|A0A1Q9ANQ8|A0A1Q9ANQ8_9RHIZ,sigma,75.1
+Rhizobium,sigma.hmm,tr|A0A1Q9AL94|A0A1Q9AL94_9RHIZ,sigma,65.5
+Rhizobium,sigma.hmm,tr|A0A1Q9ALF0|A0A1Q9ALF0_9RHIZ,sigma,61.3
+Rhizobium,sigma.hmm,tr|A0A1Q9AF84|A0A1Q9AF84_9RHIZ,sigma,61.2
+Rhizobium,sigma.hmm,tr|A0A1Q9AII6|A0A1Q9AII6_9RHIZ,sigma,59.6
+Rhizobium,sigma.hmm,tr|A0A1Q9ACE9|A0A1Q9ACE9_9RHIZ,sigma,56.9
+Rhizobium,sigma.hmm,tr|A0A1Q9AIU3|A0A1Q9AIU3_9RHIZ,sigma,55.8
+Rhizobium,sigma.hmm,tr|A0A1Q9AEH2|A0A1Q9AEH2_9RHIZ,sigma,54.1
+Rhizobium,sigma.hmm,tr|A0A1Q9ANU6|A0A1Q9ANU6_9RHIZ,sigma,44.9
+Rhizobium,sigma.hmm,tr|A0A1Q9AQ99|A0A1Q9AQ99_9RHIZ,sigma,43.5
+Rhizobium,sigma.hmm,tr|A0A1Q9AQ73|A0A1Q9AQ73_9RHIZ,sigma,43.4
+Rhizobium,sigma.hmm,tr|A0A1Q9ADJ9|A0A1Q9ADJ9_9RHIZ,sigma,32.2
+Rhizobium,sigma.hmm,tr|A0A1Q9APD8|A0A1Q9APD8_9RHIZ,sigma,24.5
+Roseobacter,sigma.hmm,tr|B7RH33|B7RH33_9RHOB,sigma,75.3
+Roseobacter,sigma.hmm,tr|B7RGX5|B7RGX5_9RHOB,sigma,64.7
+Roseobacter,sigma.hmm,tr|B7RH17|B7RH17_9RHOB,sigma,63.8
+Roseobacter,sigma.hmm,tr|B7RI57|B7RI57_9RHOB,sigma,62.7
+Roseobacter,sigma.hmm,tr|B7RJL9|B7RJL9_9RHOB,sigma,62.7
+Roseobacter,sigma.hmm,tr|B7RH51|B7RH51_9RHOB,sigma,56.6
+Roseobacter,sigma.hmm,tr|B7RSA6|B7RSA6_9RHOB,sigma,49.2
+Verrucomicrobia,sigma.hmm,tr|A0A1W9LF71|A0A1W9LF71_9BACT,sigma,75.1
+Verrucomicrobia,sigma.hmm,tr|A0A1W9LBX6|A0A1W9LBX6_9BACT,sigma,68.4
+Verrucomicrobia,sigma.hmm,tr|A0A1W9LH48|A0A1W9LH48_9BACT,sigma,61.3
+Verrucomicrobia,sigma.hmm,tr|A0A1W9LHW5|A0A1W9LHW5_9BACT,sigma,49.8
+Verrucomicrobia,sigma.hmm,tr|A0A1W9LA94|A0A1W9LA94_9BACT,sigma,48.6
+Bacillus,sporecoat.hmm,tr|A6BZD2|A6CT85_9BACI,sporecoat,118.6
+Bacillus,transporter.hmm,tr|A6CMF6|A6CMF6_9BACI,transporter,24.9
+Flavobacterium,transporter.hmm,tr|A0A1S1J3R7|A0A1S1J3R7_9FLAO,transporter,33.9
+Limnohabitans,transporter.hmm,tr|A0A0P0M9B4|A0A0P0M9B4_9BURK,transporter,34.2
+Roseobacter,transporter.hmm,tr|B7RKP8|B7RKP8_9RHOB,transporter,10.3

Exercise11_files/Problem2/problem2.py

@@ -0,0 +1,31 @@
+
+import re
+
+motifsortin=open("motifsort.fasta","r")
+motif1out=open("motif1.fasta","w")
+motif2out=open("motif2.fasta","w")
+nomotifout=open("nomotif.fasta","w")
+
+motif1= r'AKKPRVZE'
+motif2= r'AAQWWRNYGG'
+
+tempid_m1=[]
+tempid_m2=[]
+tempid_no=[]
+tempseq_m1=[]
+tempseq_m2=[]
+tempseq_no=[]
+
+
+for line in motifsortin:
+    line = line.strip()
+    if ">" in line:
+        seqid = line
+    elif re.search(motif1, line):
+        motif1out.write(seqid + "\n" +line + "\n")
+    elif re.search(motif2, line):
+        motif2out.write(seqid + "\n" +line + "\n")
+    else:
+        nomotifout.write(seqid + "\n" +line + "\n")
+
+