import re if __name__ == '__main__': #print(sys.argv) inFile = sys.stdin else: workDir = '/home/ashis/work/github/courses/JHU_Computational_Genomics/HW3' os.chdir(workDir) sys.path.append(os.path.abspath(os.getcwd())) inputFilePath = 'data/6_edit_alignment_1.txt' inFile = open(inputFilePath, 'r') import Fasta # read inputs proteins = Fasta.parse_fasta(inFile) inFile.close() protein1 = proteins[0] protein2 = proteins[1] sigma = 1 ## create scores and backtrack arrays len1 = len(protein1) len2 = len(protein2) scores = [[0]*(len2+1) for x in range(len1+1)] backtracks = [[-1]*(len2+1) for x in range(len1+1)] ## put first row and first column of scores and backtrack arrays for i in range(1,len1+1):
import re if __name__ == '__main__': #print(sys.argv) inFile = sys.stdin else: workDir = '/home/ashis/work/github/courses/JHU_Computational_Genomics/HW3' os.chdir(workDir) sys.path.append(os.path.abspath(os.getcwd())) inputFilePath = 'data/4_subsequence_1.txt' inFile = open(inputFilePath, 'r') import Fasta # read inputs dnas = Fasta.parse_fasta(inFile) inFile.close() s = dnas[0] t = dnas[1] subseqIndexes = [] si = -1 for ti in range(len(t)): tchar = t[ti] while 1: si += 1 if s[si] == tchar: subseqIndexes.append(si) break
codonMapFile = sys.argv[1] else: workDir = "/home/ashis/work/github/courses/JHU_Computational_Genomics/HW3" os.chdir(workDir) sys.path.append(os.path.abspath(os.getcwd())) inputFilePath = "data/rosalind_splc.txt" inFile = open(inputFilePath, "r") codonMapFile = "inputs/rna-codon.txt" import Dna import Rna import Fasta # read inputs lines = Fasta.parse_fasta(inFile) inFile.close() dna = lines[0] introns = lines[1:] # splice dna re_pattern = "|".join(introns) splicedDna = re.sub(re_pattern, "", dna, 0) sdna = Dna.Dna(splicedDna) # transcribe and translate rna = Rna.Rna(sdna.transcribe(), codonMapFile=codonMapFile) protein = rna.translate() print(protein)