Instruction to run test data:

1. In the terminal, navigate to the “testData” directory.

2. make installation_test file executable with the following command:
“sudo chmod 755 installation_test”

3. run installation_test file with the following command:
“./installation_test”



You will see the following output show up in the terminal if your installation is successful.


“Python command: AASRA-index.py  -i index.fa -l CCCCCCCCCC -r GGGGGGGGGG -s index.saf

Input index is a fasta file. Anchor sequence is:
5':CCCCCCCCCC, 3':GGGGGGGGGG

Generating anchored index.
Index anchored successfully.

Generating index.saf.
SAF file generated successfully.

Start building bowtie2 index
Bowtie2 command: bowtie2-build -q -f anchored_index.fa, anchored_index.fa

python input command: AASRA.py -i sample.fa -l CCCCC -r GGGGG -b anchored_index.fa

Input sample is a fasta file. Anchor sequence is:
5':CCCCC, 3':GGGGG
Generating anchored sample.
Sample anchored successfully.

Entering alignment phase.
bowtie2 input command: bowtie2 --norc -N 1 -L 16 -i S,0,0.2 -f -p 4 -x anchored_index.fa -U anchored_sample.fa -S anchored_sample.fa.sam
6 reads; of these:
  6 (100.00%) were unpaired; of these:
    0 (0.00%) aligned 0 times
    6 (100.00%) aligned exactly 1 time
    0 (0.00%) aligned >1 times
100.00% overall alignment rate”