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@@ -8,6 +8,50 @@ |
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class Sequence(object):
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+ # 1
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+ tdict_standard = {
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+ 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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+ 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'I', 'ATC':'I', 'ATT':'I',
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+ 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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+ 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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+ 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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+ 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'*', 'TAA':'*'
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+ }
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+
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+ start_standard = ['ATG', 'TTG', 'CTG']
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+
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+ standard_stop = ['TAA', 'TAG', 'TGA']
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+
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+ # 2
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+ tdict_vertebrate_mitochondrial = {
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+ 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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+ 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'M', 'ATC':'I', 'ATT':'I',
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+ 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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+ 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'*', 'AGG':'*', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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+ 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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+ 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'W', 'TAA':'*'
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+ }
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+
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+ # 3
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+ tdict_yeast_mitochondrial = {
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+ 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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+ 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'M', 'ATC':'I', 'ATT':'I',
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+ 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'T', 'CTC':'T', 'CTG':'T', 'CTT':'T', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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+ 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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+ 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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+ 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'W', 'TAA':'*'
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+ }
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+
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+ # 11
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+ tdict_bacterial_archaeal_plant_plastid = {
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+ 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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+ 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'I', 'ATC':'I', 'ATT':'I',
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+ 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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+ 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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+ 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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+ 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'*', 'TAA':'*'
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+ }
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+
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def __init__(self, name, seq):
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if Sequence.validate_name_string(name):
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self.name = name
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@@ -30,47 +74,7 @@ def validate_seq(self): |
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'''
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validates general seqence not specified for DNA or others.
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'''
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- # pattern to find not allowed chars.
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- pattern = re.compile('[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]')
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- if pattern.search(self.seq):
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- if re.search('(\d+)', self.seq):
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- seq_array = self.seq.split('\n')
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- new_array = [] # array to store new sequence
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- for r in seq_array:
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- r = r.lstrip() # removing ' ' from beginings and ends
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- nr = r.split(' ') # split to array to catch all blocks aaaaaaaaaa aaaaaaaaaa
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- new_array.append(nr)
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-
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- end_of_seq_array = len(seq_array)
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- # if min. two lines calculate expected line length
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- if end_of_seq_array > 1:
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- line_length = int(new_array[1][0])-int(new_array[0][0])
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-
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- # validate ecah block (between " ") of sequence ()
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- i = 0
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- while i < end_of_seq_array:
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- if not re.search('(\d+)', new_array[i][0]):
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- return 7 # line doesn't starts with digit
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- if not (len(new_array[i])-1)*10 == line_length and i != (end_of_seq_array-1):
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- return 0 # bad line length
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- for a, r in enumerate(new_array[i][1:]): # skip first elem which is digit
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- if len(r) != 10: # block not eq 10
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- if len(r) < 10: # if less it can be ok if last elem of last line
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- if(i == end_of_seq_array - 1):
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- if a != len(new_array[i]) - 2: # if last -2 because enumerate is from first elem not 0 elem.
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- return 0 # not last elem of last line
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- else:
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- return 0 # not last line
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- else:
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- return 0 # block not eq 10
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- if pattern.search(r):
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- return 0
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- i += 1
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- else:
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- return 0 # digit is not first char
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- # return pattern.search(self.seq) but nan error code returned before
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- return 1
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- return 1 # valid
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+ return Sequence.generic_validate(self.seq, '[^ACGNTUBDHKMRSVWY\-\nacgntubdhkmrsvwy]')
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@staticmethod
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def generic_validate(seq, domain):
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@@ -199,7 +203,6 @@ def cut(self, length, step): |
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def cut_name(self, length, start = 0):
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self.name = self.name[start:length]
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- print self.name
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def leave_name_after_marker(self, mark, length = 0, keep_marker = 1):
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m = re.search(re.escape(mark), self.name)
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@@ -305,7 +308,6 @@ def translate2protein_in_range_generic(seq, start, stop, tdict): |
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while i+3 <= stop_pos:
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ret += Sequence.translate(seq[i:i+3], tdict)
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if re.match(p_stop, seq[i:i+3]):
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- #print 'exiting on: '+seq[i:i+3]
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i = i+3
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break
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else:
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@@ -322,14 +324,6 @@ def translate2protein_in_range_generic(seq, start, stop, tdict): |
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return [frame1, frame2, frame3]
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def translate2protein_in_range(self, start, stop, tdict):
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- tdict = {
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- 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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- 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'I', 'ATC':'I', 'ATT':'I',
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- 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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- 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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- 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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- 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'*', 'TAA':'*'
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- }
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f = Sequence.translate2protein_in_range_generic(self.seq, start, stop, tdict)
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r = Sequence.translate2protein_in_range_generic(self.reverse().seq, start, stop, tdict)
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@@ -353,14 +347,7 @@ def translate2protein_generic(seq, tdict): |
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return [('',f1,seq[-2:]),(seq[0:1],f2,seq[-1:]),(seq[0:2],f2,'')]
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def translate2protein(self, tdict):
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- tdict = {
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- 'GCA':'A','GCC':'A','GCG':'A','GCT':'A', 'TGC':'C','TGT':'C', 'GAC':'D', 'GAT':'D', 'GAA':'E', 'GAG':'E',
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- 'TTC':'F', 'TTT':'F', 'GGA':'G', 'GGC':'G', 'GGG':'G', 'GGT':'G', 'CAC':'H', 'CAT':'H', 'ATA':'I', 'ATC':'I', 'ATT':'I',
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- 'AAA':'K', 'AAG':'K', 'TTA':'L', 'TTG':'L', 'CTA':'L', 'CTC':'L', 'CTG':'L', 'CTT':'L', 'ATG':'M', 'AAC':'N', 'AAT':'N',
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- 'CCA':'P', 'CCC':'P', 'CCG':'P', 'CCT':'P', 'CAA':'Q', 'CAG':'Q', 'AGA':'R', 'AGG':'R', 'CGA':'R', 'CGC':'R', 'CGG':'R',
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- 'CGT':'R', 'AGC':'S', 'AGT':'S', 'TCA':'S', 'TCC':'S', 'TCG':'S', 'TCT':'S', 'ACA':'T', 'ACC':'T', 'ACG':'T', 'ACT':'T',
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- 'GTA':'V', 'GTC':'V', 'GTG':'V', 'GTT':'V', 'TGG':'W', 'TAC':'Y', 'TAT':'Y', 'TAG': '*', 'TGA':'*', 'TAA':'*'
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- }
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+
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f = Sequence.translate2protein_generic(self.seq, tdict)
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r = Sequence.translate2protein_generic(self.reverse().seq, tdict)
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return {'fwd':f, 'rev':r}
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blazejmarciniak
committed
0 comments on commit
a2b810b