You will write a Python program that finds all the ORFs in a genomic sequence.
A genomic sequence has 6 reading frames, corresponding to the six possible ways of translating the sequence into three-letter codons. Frame 1 treats each group of three bases as a codon, starting from the first base. Frame 2 starts at the second base, and frame 3 starts at the third base. Frames 4, 5 and 6 are defined in a similar way, but refer to the opposite strand, which is the reverse complement of the first strand.
Specifications:
Write a Python program called orfs to find all the open reading frames (ORFs) in the input sequence.
INPUT: The program will take in as input a file, which will contain any number of DNA sequences in the FASTA format: – A line beginning with a “>” is the header line for the next sequence – All lines after the header contain sequence data. – There will be any number of sequences per file. – Sequences may be split over many lines. – Sequence data may be upper or lower case. – Sequence data may contain white space, which should be ignored.
Ask the user for the minimum ORF to search for. The default is 50, which means your program should print out all ORFs with at least 50 bases.
OUTPUT:
Print your output in FASTA format, with one header line for each ORF, followed by the DNA in the ORF. The header should be the same as the header in the input file, followed by a bar “|” followed by FRAME = POS = LEN = , where is the frame number (1-6)
is the genomic position of the start of the ORF (left end is base 1) is the length of the ORF (in bases) If N = 4, 5 or 6, then P should be a negative number that indicates the position of the start of the ORF from the right end of the sequence. The DNA in the ORF should be printed out with a space between each codon, and no more than 15 codons per line.
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