def findAllOrf(text, limit): # look for the file, and call the other functions
if ((len(sys.argv) < 2) or (len(sys.argv) > 3)):
print "Usage: python", sys.argv[0], "<filename> [<min ORF length>]"
else:
fileName = sys.argv[1]
if (len(sys.argv) > 2): # This should be an integer
try:
limit = int(sys.argv[2]) # Convert string to integer
except ValueError: # try-except catches errors
print "\n\tExpecting an integer to define min ORF length, found",
print sys.argv[2]
exit()
print "ORF must be at least", limit, "Base pairs long"
text = cs58FileUtil.readFastaFile(fileName)
process_all_reading_frames(text,limit)
longest_pal = "Longest Palindrome @ Position: ", pos, "Sequence:", longest_pal
return longest_pal
#This a recursive method I previously developed for checking
# palindromes of a single small string. I thought
# to use it to submit substrings to here and return true
# if indeed the substring is a palindrome
def isPalindrome(sub_seq, sub_comp):
sub_seq_length = len(sub_seq)
sub_comp_length = len(sub_comp)
# base case for recursion
if sub_seq_length <= 1 or sub_comp_length <= 1:
return True
#if first char equals last char, call method again
if sub_seq[0] == sub_comp[0]:
return isPalindrome(sub_seq[1:], sub_comp[1:])
# if this statement is reached, it cannot be a palindrome
return False
if (len(sys.argv) != 2):
print "Usage: python", sys.argv[0], "<filename>"
else:
fileName = sys.argv[1]
seq = cs58FileUtil.readFastaFile(fileName)
comp_seq = comp_strand(seq)
print find_palindromes(seq, comp_seq)
longest_pal = "Longest Palindrome @ Position: ", pos, "Sequence:", longest_pal
return longest_pal
#This a recursive method I previously developed for checking
# palindromes of a single small string. I thought
# to use it to submit substrings to here and return true
# if indeed the substring is a palindrome
def isPalindrome (sub_seq, sub_comp ):
sub_seq_length= len(sub_seq)
sub_comp_length= len(sub_comp)
# base case for recursion
if sub_seq_length<=1 or sub_comp_length <=1 :
return True
#if first char equals last char, call method again
if sub_seq[0] == sub_comp[0]:
return isPalindrome(sub_seq[1:], sub_comp[1:])
# if this statement is reached, it cannot be a palindrome
return False
if (len(sys.argv) !=2):
print "Usage: python", sys.argv[0], "<filename>"
else:
fileName =sys.argv[1]
seq = cs58FileUtil.readFastaFile(fileName)
comp_seq =comp_strand(seq)
print find_palindromes(seq, comp_seq)
this_snippet = seq[cursor:cursor+length_to_try]
reverse = reverseComplement(this_snippet)
if this_snippet == reverse: #if we get a palindrome, save it and move on to checking the next length
this_start = cursor + 1
best_so_far = [this_snippet, this_start]
length_to_try +=2
cursor = 0
else: #if not a palindrome, keep checking snippets of this length
cursor += 1
found_longest=True #If we make it here, no palindromes for that length so we're done
return best_so_far
if ((len(sys.argv) < 2) or (len(sys.argv) > 3)):
print "Usage: python", sys.argv[0], "<filename>"
else:
fileName = sys.argv[1]
if (len(sys.argv) > 2): # This should be an integer
try:
limit = int(sys.argv[2]) # Convert string to integer
except ValueError: # try-except catches errors
print sys.argv[2]
exit()
text = readFastaFile(fileName) #remove 'cs58FileUtil" because it was giving a not defined error
text = prepare(text)
print find_longest_palindrome (text)
profile.run("find_longest_palindrome(text)")
if this_result[winner] > 1:
biggest_repeat_length = attempting_length
biggest_repeat = winner
best_result = this_result
else:
not_stumped = False
attempting_length +=1
if (DEBUG):
return biggest_repeat_length, biggest_repeat, best_result
return biggest_repeat_length, biggest_repeat
if ((len(sys.argv) < 2) or (len(sys.argv) > 3)):
print "Usage: python", sys.argv[0], "<filename>"
else:
fileName = sys.argv[1]
if (len(sys.argv) > 2): # This should be an integer
try:
limit = int(sys.argv[2]) # Convert string to integer
except ValueError: # try-except catches errors
print "\n\tExpecting an integer to define min ORF length, found",
print sys.argv[2]
exit()
seq = readFastaFile(fileName)
seq = prepare(seq)
print "The biggest repeat in this sequence is: ",find_biggest_repeat(seq)
this_snippet = seq[cursor:cursor + length_to_try]
reverse = reverseComplement(this_snippet)
if this_snippet == reverse: #if we get a palindrome, try the next length
this_start = cursor + 1
best_so_far = [this_snippet, this_start]
length_to_try += 2
cursor = 0
else: #if not, continue to the end of the sequence to see if there is one
cursor += 1
found_longest = True #If we make it down this far, we've reached the end of the sequence for a length that doesn't have any hits
return best_so_far
if ((len(sys.argv) < 2) or (len(sys.argv) > 3)):
print "Usage: python", sys.argv[0], "<filename>"
else:
fileName = sys.argv[1]
if (len(sys.argv) > 2): # This should be an integer
try:
limit = int(sys.argv[2]) # Convert string to integer
except ValueError: # try-except catches errors
print "\n\tExpecting an integer to define min ORF length, found",
print sys.argv[2]
exit()
text = readFastaFile(
fileName
) #remove 'cs58FileUtil" because it was giving a not defined error
print find_longest_palindrome(text)