Consider nucleotide sequences that contain the possible characters: 'A', 'C', 'G', 'T', and the end-of-sequence character: 'ε'.
Implement a command-line program that accepts a nucleotide stream on stdin, scans the stream for any sequence matching a specified target nucleotide, and writes each match to stdout along with its surrounding context. The program should end when encountering the end-of-sequence character or the end of the stream.
More specifically: given a nucleotide stream S, a target sequence T, and two integers x and y; for each T in S: print the x preceding nucleotides, the sequence matching T, and the y succeeding nucleotides.
An example command line
echo "ACACGTCAε" | matchseq -T:ACGT -x:1 -y:2
would yield
C ACGT CA
where C is the x=1 preceding nucleotide, ACGT is the nucleotide sequence matching T, and CA is the y=2 succeeding nucleotides.
Be aware that:
- x may be unspecified, which indicates that no preceding nucleotides should be printed. Likewise, y may be unspecified, which indicates that no succeeding nucleotides should be printed. However, a non-empty value for T is required.
- If the stream contains fewer than x nucleotides before T, or fewer than y nucleotides after T, print as many as there actually are.
- The end-of-sequence value 'ε' will not appear in T.
- Targets may overlap in the sequence S, and each should be treated as a distinct occurrence with its own surrounding context.
- Streams are potentially unlimited, so be sure to consider the case where the size of S exceeds a system's memory.
echo "AAGTACGTGCAGTGAGTAGTAGACCTGACGTAGACCGATATAAGTAGCTAε" | matchseq -T:AGTA -x:5 -y:7
should print the following lines:
A AGTA CGTGCAG
CAGTG AGTA GTAGACC
TGAGT AGTA GACCTGA
ATATA AGTA GCTA
Notice that the 2nd and 3rd lines display overlapping targets and that the 1st and 4th show fewer than x and y elements of context, respectively.