Below is a set of tasks and questions that will require all the skills you have gained from the advanced linux part practical.
You can check my solutions by clicking the expandable boxes. These are not the definitive solution but only examples of solutions. If your method works and you understand why then you have carried it out correctly.
13.1 Advanced tasks
Task 1
Copy the directory ~/Linux/advanced_practice to ~/Linux/advanced_practice_exercise
With one command move all the fastq files into the directory fastq
mv*.fastq fastq/
Task 5
With one command move all the txt files, excluding metadata.txt and samples.txt, into the directory txt
mv sample_*txt txt/
Task 6
Create a file in the fastq directory called patient_1_corrected.fastq and put all the corrected fastq data for patient_1 into the file. You can look at the metadat.txt file to see which samples belong to patient_1.
For all the corrected fastq files find the sequences that start with a stop codon in the forward orientation (i.e. TAG, TAA or TGA). Print out to screen the sample name and sequence info separated by a “:” only (e.g. sample_10_AAGT:TAAGAGAACAATGAACAGATATTAATAATTTTGCCGCTTTTCTGCGGGAT)
Get the fastq headers of sequences with homopolymers made of As with a length of 5 or greater for the uncorrected fastq files for samples 3,4,5,13,14 and 15 with one command.
Superlative! Those were definetly difficult tasks so great going getting through them all. That is all the practice and challenges done, there is some information on other languages and the appendix you can continue onto.