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Extracting introns and the number of reads associated with them from a SAM file using base Python (no existing libraries used) Grade: A2

Input Required:

  1. Standard sam file.
  2. A comma-separated file with the gene_IDs, transcript_ID and genomic location of all the genes of whatever chromosome is aligned in the SAM file.

What the code does:

  1. Parses the sam file, and identifies whether each line in the file is a deletion, insertion, matches, splits or a JUNCTION(intron)
  2. For each junction identified, it counts how many reads are associated with it
  3. Next it checks if the junction is inside a gene from the list of genes from the second file.
  4. If the junction is inside a gene, it is marked as an intron, and it is outputted to a file that tells us the gene ID, the start and end of the intron, and the number of reads in that.