Therese Reisch, Tara Neufell, Kevin Buck bash project - Bioinformatics #3
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added 8 commits
October 12, 2022 11:03
qtran4
reviewed
Oct 21, 2022
| for index in {01..22} | ||
| do cat ref_sequences/hsp70gene_$index.fasta >> ref_sequences/hsp70master.fasta | ||
| done | ||
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qtran4
reviewed
Oct 21, 2022
| #aligning reference files using muscle tool | ||
| ~/Private/biocomputing2022/tools/muscle -in ref_sequences/mcrAmaster.fasta -out ref_sequences/mcrAmaster.aligned | ||
| ~/Private/biocomputing2022/tools/muscle -in ref_sequences/hsp70master.fasta -out ref_sequences/hsp70master.aligned | ||
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qtran4
reviewed
Oct 21, 2022
| #build hidden markov model with hmmer tool | ||
| ~/Private/biocomputing2022/tools/hmmbuild ref_sequences/mcrAmaster.build ref_sequences/mcrAmaster.aligned | ||
| ~/Private/biocomputing2022/tools/hmmbuild ref_sequences/hsp70master.build ref_sequences/hsp70master.aligned | ||
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qtran4
reviewed
Oct 21, 2022
| for index in {01..50} | ||
| do ~/Private/biocomputing2022/tools/hmmsearch --tblout proteomes/proteome$index.hsp70search ref_sequences/hsp70master.build proteomes/proteome_$index.fasta | ||
| done | ||
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qtran4
reviewed
Oct 21, 2022
| hsp70count=$(grep -v -c "#" proteomes/proteome$index.hsp70search) | ||
| echo "proteome_$index, $mcrAcount, $hsp70count" >> proteomecounttable.txt | ||
| done | ||
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qtran4
reviewed
Oct 21, 2022
| touch recommendationslist.txt | ||
| echo proteome_name, mcrA_count, hsp70_count >> recommendationslist.txt | ||
| cat proteomecounttable.txt | grep -E ", [1|2]," | sort -t , -k 3 -n -r >> recommendationslist.txt | ||
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-header comments, including usage line [1 point]
-general commenting of code throughout script [1 point]
-code efficiency [1 points]
=> 1 point was taken off since you don't need the for loop for lines 7-14
You can also make a for loop for hmm search for both Hsp and mcrA, as well as outputting the table form in just one for loop.
qtran4
reviewed
Oct 21, 2022
| @@ -0,0 +1,51 @@ | |||
| proteome_name, mcrA_count, hsp70_count | |||
| proteome_01, 0, 4 | |||
| proteome_02, 0, 1 | |||
qtran4
reviewed
Oct 21, 2022
| proteome_14, 0, 1 | ||
| proteome_15, 1, 1 | ||
| proteome_16, 1, 1 | ||
| proteome_17, 0, 4 |
qtran4
reviewed
Oct 21, 2022
| proteome_37, 0, 1 | ||
| proteome_38, 1, 1 | ||
| proteome_39, 1, 1 | ||
| proteome_40, 0, 1 |
qtran4
reviewed
Oct 21, 2022
| proteome_43, 0, 3 | ||
| proteome_44, 1, 1 | ||
| proteome_45, 1, 3 | ||
| proteome_46, 0, 1 |
qtran4
reviewed
Oct 21, 2022
qtran4
reviewed
Oct 31, 2022
| for index in {01..22} | ||
| do cat ref_sequences/hsp70gene_$index.fasta >> ref_sequences/hsp70master.fasta | ||
| done | ||
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We just need one line for this
cat ref_sequences/mcrAgene_* > ref_sequences/ref_mcrAgenes.fasta
same for hsp70
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