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# File : warmup.py

def lines_starts_with(f, s):

____"""Return a list containing the lines of the given open file that start with

____the given str. Exclude leading and trailing whitespace.

____

____Arguments:

____- `32313133353236313431303231363533e58685e5aeb931333238646361f`: the file

____- `s`: str at the beginning of the line

____"""

____result = []

____for line in f:

________if line.startswith(s):

____________result.append(line.strip())

____return result

def file_to_dictionary(f, s):

____"""Given an open file that contains a unique string followed by a given

____string delimiter and more text on each line, return a dictionary that

____contains an entry for each line in the file: the unique string as the key

____and the rest of the text as the value (excluding the delimiter, and leading

____and trailing whitespace).

____

____Arguments:

____- `f`: the file

____- `s`: the delimiter str

____"""

____result = {}

____for line in f:

________k, _, v = line.partition(s)

________result[k.strip()] = v.strip()

____return result

def merge_dictionaries(d1, d2):

____"""Return a dictionary that is the result of merging the two given

____dictionaries. In the new dictionary, the values should be lists. If a key is

____in both of the given dictionaries, the value in the new dictionary should

____contain both of the values from the given dictionaries, even if they are the

____same.

____merge_dictionaries({ 1 : 'a', 2 : 9, -8 : 'w'}, {2 : 7, 'x' : 3, 1 : 'a'})

____should return {1 : ['a', 'a'], 2 : [9, 7], -8 : ['w'], 'x' : [3]}

____Arguments:

____- `d1`, 'd2': dicts to be merged

____"""

____result = {}

____for key in d1:

________if key in d2:

____________result[key] = [d1[key], d2[key]]

________else:

____________result[key] = [d1[key]]

____for key in d2:

________if not key in result:

____________result[key] = [d2[key]]

____return result

-----------------------------------------------------

# File fasta.py

from warmup import *

def count_sequences(f):

____"""Return the number of FASTA sequences in the given open file. Each

____sequence begins with a single line that starts with >.

____

____Arguments:

____- `f`: the file

____"""

____return len(lines_starts_with(f, '>'))

def get_sequence_list(f):

____"""Return a nested list where each element is a 2-element list containing a

____FASTA header and a FASTA sequence from the given open file (both strs).

____

____Arguments:

____- `f`: the file

____"""

____result = []

____current_key = ''

____current_data = ''

____for line in f:

________if line.startswith('>'):

____________if current_data:

________________result.append([current_key, current_data])

________________current_data = ''

____________current_key = line.strip()

________else:

____________current_data+= line.strip()

____result.append([current_key, current_data])

____return result

____

def merge_files(f1, f2):

____"""Return a nested list containing every unique FASTA header and sequence

____pair from the two open input files. Each element of the list to be returned

____is a 2-element list containing a FASTA header and a FASTA sequence.

____

____Arguments:

____- `f1`, 'f2': The File

____"""

____seq = get_sequence_list(f1) + get_sequence_list(f2)

____seq = list( set(seq) )

____return seq

def get_codons(s):

____"""Return a list of strings containing the codons in the given DNA sequence.

____

____Arguments:

____- `s`: DNA sequence, divied by 3

____"""

____return [s[3*i : 3*(i+1)] for i in xrange(len(s)/3)]

def get_amino_name_dict(f):

____"""Return a dictionary constructed from the given open file, where the keys

____are amino acid codes and the values are the amino acid names.

____

____Arguments:

____- `f`: the file, like amino_names.txt

____"""

____return file_to_dictionary(f, ' ')

def get_codon_amino_dict(f):

____"""Return a dictionary where the keys are codons and the values are amino

____acid codes from the given open file.

____

____Arguments:

____- `f`: the file, like codon_aminos.txt

____"""

____return file_to_dictionary(f, ':')

def translate(s, d):

____"""Return the given DNA sequence (the str parameter) translated into its

____amino acid codes, according to the given dictionary where the keys are

____codons and the values are amino acid codes. You may assume that the length

____of the string is divisible by 3.

____

____Arguments:

____- `s`: given DNA sequence

____- `d`: given dictionary

____"""

____codons = get_codons(s)

____result = []

____for i in codes:

________result.append(d[i])

____return result

def codon_to_name(s, d1, d2):

____"""Return the name of the amino acid for the given codon (the str

____parameter).

____

____Arguments:

____- `s`: given codon

____- `d1`: codons for keys and amino acid codes for values

____- `d2`: amino acid codes for keys and name for values

____"""

____return d2[d1[s]]

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