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)
