Programming exercise tutorial

The following is the stepwise procedure that to be used in working on the programming exercise shared.

Getting started

Creating neccessary directories and required files

1. Create your project directory and name it Project_dengue making sure it has the necessary subdirectories needed for any bioinformatics project

    mkdir -p Project_dengue/{raw_data/{compressed},processed_data,scripts}

2. To put the downloaded zip file into the compressed subdirectory inthe raw data and unzipping.

• First move into compressed directory by

    cd Project_dengue/raw_data/compressed/

• Then copy the file using cp command as bellow

    cp /mnt/c/Users/micro/Desktop/Msc/lisso/dengue.zip .

• Exctract it by the unzip command which can be installed by sudo apt install unzip when not installed.
• Use unzip with -d option when specificing the output directory.

    unzip dengue.zip -d /home/genomics/Project_dengue/raw_data/

Exercise

Qn1: How manyfiles are in the zipped file?

Use unzip command with -l option to get a summary of the zipped file without extracting it.

    unzip -l dengue.zip

Output

Archive:  ./dengue.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
     2795  2024-11-19 09:23   dengueseq1.fasta
     8006  2024-11-19 09:23   dengueseq2.fasta
     6476  2024-11-19 09:24   dengueseq3.fasta
     7844  2024-11-19 09:24   dengueseq4.fasta
    10936  2024-11-19 09:20   dengueseq5.fasta
---------                     -------
    36057                     5 files

Qn2: How manylines are in each file?

Use wc with -l to count lines only in each file with .fasta extension in the raw_data directory where extracted files were placed.

    wc -l *.fasta

Output

  42 dengueseq1.fasta
  115 dengueseq2.fasta
   94 dengueseq3.fasta
  113 dengueseq4.fasta
  157 dengueseq5.fasta
  521 total

Qn3: How manylines are in all the files combined?

Use the cat to combined all files and pipe | the output to count all lines combined by wc -l

    cat *.fasta | wc -l

Output

521

Qn4: Mergethe files into one file and name it dengue_merged.fasta

Use cat command and redirect output to new the name.

    cat *.fasta > dengue_merged.fasta

Qn5: How manyheaders does the new file have?

Use grep command with flag -c

    grep -c ">" dengue_merged.fasta

Output

5

Qn5: How many sequences does the new file have?

Use grep command with flag -c

    grep -c ">" dengue_merged.fasta

Output

5

Qn6: Extract the headers, and put them in a new file called dengue_headers.txt

Use grep command and redirect the of output to a new folder. You can use cat to view contents of the new file dengue_headers.txt

    grep ">" dengue_merged.fasta > dengue_headers.txt

Qn7:a Extract only the names of the viruses, and create a new file called viruses.txt

Use both awk to search for columns and pipe output to sed to remove identfires.

    awk -F '[>,]' '{print $2}' dengue_headers.txt | sed 's/^[^ ]* //' > viruses.txt

Qn7:b Extract only the unique identifiers and create a new file called identifiers.txt

Use the awk command to sort columns

    awk -F '>' '{print $2}' dengue_headers.txt | awk '{print $1}' > identifiers.txt

Qn8: Create a file for only the sequences. Name it dengue_seq.txt

Use grep -v to invert the output or sed with d option to to delete all headers.

    grep -v '^>' dengue_merged.fasta > dengue_seq.txt

or

   sed '/^>/d' <dengue_merged.fasta > dengue_seq.txt

Qn9: Replace the values in dengue_seq.txt with small letters

Use the tr command to translate from upper to lower case.

    tr '[:upper:]' '[:lower:]' < dengue_seq.txt > dengue_seq_lowercase.txt

Done 🖊️