rosalind_GC_content.py

def GCcontent (seq):   #function takes a sequence and returns the %age of characters that are C's and G's
    DesiredBases=["C","G"]
    Length= len(seq)
    GCcounter = 0
    GCresult = 0
    for char in seq:  #loop through the string and tally the C's & G's
        if char in DesiredBases:
            GCcounter += 1  
    GCresult =  (100 * GCcounter/float(Length)) #cast the length as a float to preserve decimal

    return GCresult
    

def get_winner (list_of_seqs): 
    winner= []
    this_id= ''
    this_seq=''
    this_score=0    
    winning_id= ''
    winning_score=0
    
    for seq in list_of_seqs:
        this_id = seq[0]
        this_seq = seq[1]
        this_seq = this_seq.lstrip()
        this_score = GCcontent(this_seq)
        if this_score > winning_score:
            winning_score = this_score
            winning_id =this_id
    
    return winning_id, winning_score

def make_list_of_seqs(string):
    temp_list= string.split()   
    list_of_seqs = [] 
    num_of_pairs = len(temp_list)/2

    cursor=0
    while cursor < 2*num_of_pairs: 
        seq_ID = temp_list[cursor]
        seq_ID = seq_ID.lstrip('>')
        list_of_seqs.append([seq_ID, temp_list[cursor+1]])
        cursor += 2
    return list_of_seqs


big_string_to_check =  '>Rosalind_2471 TAAAGGATCGTAGCTACGCCCAAAGACTTGAGTTGTGTTTTGGCGACACACGGCTCCGCCCTGAACGATACGTGAAGATCGAATCTTTCCCAGGAACATAGAGTGGGATGAATAGAGGTAAGCTTGTGCTATCGTACCAGATATAGGCGGCTTGACTGGTTCATCGTTTTCTTGGTCTAAGGCCGGGGTTGAGGGTGCTGTACGTGCGACGTTCGTCAGCCCTTACTCGGTGTCTTTTTGGCGGAATTATCATGCGCACGATGAGACCCTCTTGGAAACATCTTCCCAAGATCCCTTAAAGACGGCTACGTGACAGTGTCCGTCCCTGGCCTTTGTAAAAATTACGACACGGTTTACTTGAGTTTTATCCTGGAAGGAGTTCTGCATGCCTGGAAGAGTCCCCCTACCGCTAATGACAATTCGGGACGACCTCGGGCATACGAGCCCGTACTACCCAAGTTTCGTCATATCTCTAAGGGCCTTATGTTGATACACAGAGGAAGGGTTTCTCCGCGTTCGAACCCGACTAGCCTAAAGGCGGGTGGTCTTCCGAAACTTAATAGCTGACAATACGCCCACCGATAGATGCTTCTGTTGTAAGGCGGGTCGGCCAGGTCGTAGTACGGGCTAGGTTGGGATATGTGTATCTGTGGACTATCTGACGGTGATAGTCTCCAATACGAATTCACTAACGACCGTGCTCGGGCTCCAAAGCGATCTAACATTTATCTATAGTGTTCTCACATTGAGCTGTTAGAAGGGTTTGTGCTTCAAAACCTAGTTTCCAGAAGAAAATCCGGTACCCAAACGATGCGGCAAAGCGTACATCAAGATCATCACTTCGAGAACAAGTTAACGATCGGTGAGAAATCTGATTAGAATGGGCGCAATGACGGCGTTAGTTCGTGGAGTCGGTGGAACGGACCATAAGACTGTACA >Rosalind_5788 CACGACCGTGTTGAGTAGACTTAACAGGGTAATTGGATCCCGGGAACACGTCAGAGAGGGTGAAACCTAGACACAGCACGGAAGCATCCCCTTGTTATAAGCCAGCGCTTCACACACCATAGTATTCACCGTGAGCATATTTACTGTAGCCTTTACTCCAGGAACTGATGGGGTAAGCCCTAAACGTCACATATTAACAGCCAGAATTCCACCACTACTTTCGAGTTCTTCAGAGTGTCCTATACTGCCTTCAGAGATCCACGTCATATCGATGGTTTACAATCGGCTAACTTTTCGTAGGATGGCTAACCCACCACGCGTCGCTGAGAGAGTGGGAAGGAGGATCCTCTTCGACCTCACGGCAGCGGAACCCAGACAGCGTGACCCGGATAGGCGTACCCCACCTCCCTCCTCGCTGGGGATGCTATCTCATTTCCGCTCGCTCACTAAGGTCGCTCCTACATCACTCACTAGACGTCTCCCGATACCATAGCTGAGGCACATAAGACTCGATACACTATAAATTTGGTGTCGTTAGCTTCAGACATGGGCTTTACAAATACAGACACTTGTCGAACCATTTGCAGGAGGGTAACGTACATCGCTTTCGCTGAGGACATTGGAGGACATCTGCCAATCGGACATGCCCAACGTGTAATGGGGGCATGCACATGAGTTCGTAGCGCGCAGCCACACATCGTTCAACCGCATGGGCTTTAAATCGTCACACATTCGACTCCGAGTGTGGCATGGCAGCGAGCACGGTTTTCGAGGCTGCACAAAGTGAAGATTGCTTATTCTCCTGATGATTCGT >Rosalind_4093 GTTAGCGTTGTAGGGATTGTGAGGGAGAAGCCCTCGGGGCTAGTATCTCCGTTTAAATTTACGTGCACCGTTTTTTCTTACGAGTCTATGCTCACCACCAACGGTCGAAGGCTCCACGTCTGCTGTGGACTTCCTAGCCTGTCAATGTTACAGAGGCCTAAGATGGCTGCGATCCAGAAACTACTGTGACGTCGATTTAGACCCCTAGGCGCCCCTTGTAGTCTAGTTGAAAAATTATTCGACTTCGCTAGATTGTCGTCGTTAAGAAGGAGGTAGAGGGATCGGGGGGCGGTGGTTGTGCTTACGAGTCGCATAGAGGCCTTGTCCTGCGGGATTTACGACTTCTAGCGTGCCAGGCAATAGAACGTAGGGTATCGGTTTACAAGAAAGGTCTATTGCTTACAAGCGGAACGCCTGTTCAAAAAGGTCAAGGAACCAGACAGGCACCTCTTCGAGGCTGTATCTAATCGTTGGTTCTCATAAAAACTTGTTAGGTACGCAAGGAGATCCAAGCGAAGGCAACATTTAAACAGAGGTTTCGGATTGAATCACGGACTAGATTGCCATGATTTGCGTTGGCGAGAAGGAATTAATATTCCGGTGTTACGTAGGATCATCGTGACCCAAGACAGCGCCCCATGGTCGGACTCATTCCGCCGCAGTGTTGTCCATCAGCTGTCTTGGACTCATGGCGTAAGATTATTTCTCTGCAAGCGCCAGTAAGAATAGCTCACTTTGAGACGGTCGTTTCGTGCGACGGATCTCCGGCGAGCCGCTTAGGAAATGGACATCTCCACCAACCGGAATATTAGGGACCAGCTCTCCTCGCCTTCTACGAGATACCAGGTCGGCGGTCTGAAAATTTATATGGACAGATAATGAGCTTTGCGGTCCAGCTGGCTTAGAAAATCGTCTTTCAAACCTAGTTAAGTCGACGTCTTCGCTTTCACAGAATTGACCATCC >Rosalind_4486 CATCCTGATGTATAAGAATTGGATGGCCACTATCTTTTACCGGTGTACAGAGCATCGTCAAGAACAGATTCCATCGGCTTAGTTCCCCGCCAACCTGAATTGAATCGTTCATTGTGCTATAACTTGACGCCCTACTGACTCCAATTACGATTCCACGCAAATTAAATCCCCATACACTTGTTAAGAGCTCATCAACCACATCCCAACAACCGCGACTACACTCTTTTAGCTGAATGAGGCATGCACCGAATGTCGGGACGATCCAGGGCCAGGGGATGTTTTGGCTAACGGTTAAACTGGGCAAGTAATCTGCATGGTTTAGCGCCCAACGACCAAGTTTTGTGTCTGTTACAATATGCAAGACCGTTCCCGCCTCTTCGAATAATCTATGCATGCCTGTGACCGCCTAATTAGAGCATGGTGAGTAGATACCGGGTGTTCTGCGTTAGTCTTCGCACGAGGAGAGCTCCGGCTCCCCTCACCGTCCAAATCCCGTACTTATTCTTTTAGCATTTCCGAGGTTATGACCGCCGATTTCTTCGCGCAGACCCATCCAGCAATATCGCGCAGGGGACCGAGCGATTATGGCGGTGTCCATGCGTTCACGAATCTGAGCAAGTGCGACCATACCGAGTACGCAGTCCGAAGCTTCTCTACTTAAATTTCTTCCACTAGGCTGGAGCCCAACCGACGTGTGCAACATCCTTCTGTGGCGCGCGGGTGTGTGTGTGAGTCGTGGGCTACCGTTACCCTCCCCTGCCAAGTTCCTAGGTCTGGAGCGTTAATTGGCTGATAGTAGCTGAAACAGAACTGGGGCTCCTGTA >Rosalind_6754 ATCAACAGACTGCACGCAATCGCGCTACATAGCCGGTCGGTTGCATATAACTGTCGGTTGGCTCTCGCAAGTGCCAGATCGGCACGGATGAAGCCCCCTCCGCGGGGTAGTTGCTCCACTTGTATCCTACCTACGAATAGACTCGATAATAGGGAATAGCGCCTTATACGACGAGGTTCTGTAGTCCACATGGTCCTGCTTCAGATACTCGCACTTCGCAAATTTGGGACCATGCTAGATGCTCGAAAAAGACATATGTCCCCCATGTCTGGTGCAGCTTTTATCAACGCACGATTTGCATTATAGCGGGGGCGGGGGTTTCCCCTAGCTAGTATTCTCCTCCACATGAGCCTTTTCGATGCAGTAGCCCCTTATATCCTCCATATAGGAGGCATCTCTCTCTGAAAGAGGAGGGTTAAATACTCCGGCCGCTTAGAGTCACCGTGCAATCGTTCAAATTGTAATTGCCTTGCAGCTGCGGTAGGTCGCTTTACTGCCTCTTCGTTACCCGTTCTTGGACCTGTCCCGCTATTGGAGCCAAGAAGGTCCTAACATCGAATGCCGAGACCCACTATCGGGCGTTGGTAGGCCGTACGTCCTCGATGTAATGTAACGACGAGTCTGCACTAAAGTGTGTCTTTTTTGATAGATAATAATGCACGTCCGAGGTACCCACCAACGGCAGGATCCACCACAGTCAAAAACTGTATCGAGCGCAGTGGTAAGCCATGTCACGACGAAATACCGTTAAGTTTCCATAACGTATGTTTAAACGTTCCGCTACCCCCTCTTTCCACCCTGCGTAAAATCCAGTCTGTGGGTACGTTTCGATTTCAGCGCCTCATACGGTGTCGTTATTTATCTCTCTAAGAAGGGCCTTCTGCGGGGTGGTAACAGTGGCTATACC >Rosalind_9760 TGACCGAGTGGAGGTTCCAGTCCTTCTAGTGCTACCCATCGATTGAGCATCATACCACTAATCAGGGTCGGGACCAGGCCCAAACTCGTTCGGCGGTCGTACTCCGGCAGCATCCAGTGGATCTAGAGAGAGACAGTCCGCTGATGCACGCACGGGTCCCCGGCCATCACATGAGAATCACGGACGCAGTCGATGGTGGGCTGCAAACCTCTGCGCCAGCTATCGTGTGCAGAGTTGTCGAACGTTCTGTGTCCAGTCTCCCGGCTAGTCTTGAATACAGATCTAACATTATATTCTAGCGGCCTTGGGCGGCACTATGAGCAGCGGCGCCACAGGTAAAATCCGGAATTAGGTGTCTCTGGAGTCTCATAACCTTTCTGAATGGGAATAACCTTGCGGTGGCGCGTGCCCTAACGGGAAACTGCCGACTGTGCTCTGCGTGAGGAAACCCCGTAGAAAGCTGCGAGGGATCTTCCCCTTGTGCCGTTGGTAGAGCTCGATTTTATCTAAGTAGACCGCAACTGGCATCCGCACAATAGACAACTCTCTTGAAGGCGTAGTTCCTGGGATAGACCAGTCTAGGATGCACGGCGTCCGACATGGAACCTGGACCGCGTGACCGGGAAGTCCCATAGCAGCCCTAGACAGACACACGAATCCAGACTAGTAGCCTCGTTGCTGTGCATTCTCGAGTACAGTCTGTCGGATAATATGCCAGCTGACATCTCCGATCCTAGCGCCGAACGGACCCAATTCAGGGGCTGGGAGCGATTAGCGGAAATATCTCCTCCACTCTGTGTCAAACCCGATCAAACAAGTATTCACGTGGCTACGTATGACTGAGTGACCATTACTTTGAAAATAACAACAATGGCTCACTTGATTATGGCCATTGTTATTAAGGTCGTGTTCTAAACCCTTCCTGTTTTATCGCTACTGAAACATC >Rosalind_8295 GATGTGCCTTTGTGACATACCTAATCTCGGCCTGACAATGCCGGGTCTCAAGAGAGGGACATTGGGATACCTTGCGCCCGTAAGTATAGGATACAAACGAGCACACAGCTAGCACTCCCTGCTAAAGCTACCGTAGTCAGGAAACACGAAAGCATACGCTTTGTTTAGCGAGGTGATGAAGTTTCGTAATTCGTGTAATCATGACCCGCATCTGCACGCTTATTGGGCGCACTAAAATGACGGCACAATGAAAGCAATTACAGTGTGAAACAGTCGGACATGCTAAAAGCGCAGTTGGTACATCTCGTCTTGCTGCTTAGTTGTGCCTCCAAATCAAGAGAATGCAGATCAGAAGTCCCGGGAAAGCAAAGGCCACAGCAAGTGCAACCGTGGCAACCGACCTACTTCAAGGTAGCGTTCTGTTTATGTGGCGGGAGAGGTGTTTTACGACTATTGTGCTATTCGGGTGCATTCGCTTTACTCTCACAAAGTAGTCGTCGGCAGAAGCCTGTAGCCCCTTTGCTAGAGCGATATCTCGATCGGAGACATAACCACATACACACGTGGATTAATAAAGAACGGTTCGCCAGCCTCTATGGGTTAGTACCATTTCGTTACTAGGCCCTGGCAAAAGGGACACTCACGATAGGCAAATTTCCGGGTGGTTTAGTCCATTCCGACGGCGCTGATCAAGCGGGCCAACCGTCGACACCTACACAGGTGGATGGCGTTAAAAGATGTCTTCGATGCAATTGACCTGCACATTTTGCACGAAGGCAACGTGAGACAAAACTCACACTCCGTTTCCCGGGGGGAAGCTGTGGGCCGCGTGACACGTGGGACAAGAGCATCTTTCCGTACGCCCAGGCATGTGCGAACCGCG >Rosalind_0051 ACTTTCACTGCTCTTAAACGTAGCTATTAGGTGTGACCTACCATCCCCACTCAATCGGCCTGTGAATTTGCCAGCGGCATTCCTGCCACGAGCAACTAAATATCCGGTGATACTCCACCACACAGGAGGCCGGAACACCGTTGTACAGGCACGTCCCCATGCTTACTAGAATGAGACTAGTCCTTTGTGAGGTAGTAGCGGTACGACTCCCAAGGCCTGCCATGTTACTATCAAACTGGGCCTTGCTCAGCATGTTCGTGGTTTCATGGTTTATAGGCACCACGTAAAATTCGACTACATCGGGTGGTCCCAGCCTGCTTATTCGGCGCGTTCGGGCGACCCGGAGATCACCCGGGTACTAGCGCCCCGTGATAGAGGCTGAGCTGCCATTTCGGGCCATCTCTGATGGTTGACTAAATTACGCCTTACTTGACTCGATCCAAAAGTAGGCACGGTGGTCGTGCTATGTTATAGAACGTATTAAGACTTTTGACCGTCATTGCTTCCAACTATGGGCGCCGACCCGGTATTCCGCCAAACTGTATAAGCAGCTCGCCCTGGCCCGGCTGAGCTAGTTAGGGCTGGCGTCTATCAACATTACGGCATACAGTCGACTCTGTGTTCTAACCAACTGTGGCGCCGAACAATCCTCTGACCCTGGCATTTGATACGTTTTTAATTTCAAATTCCCTATGACCAGCTTTCGCGATAAAAACCCTGTTTCCATCCTCGAGGATTAGACCGCGTGATAGGATCCAGAAACACCATTTTTCGCCATCTTGAGTTCTGCGTTATCGTGACTACCGATCACTCGATAACAAGTAC'

processed_list = make_list_of_seqs(big_string_to_check)

#print "processed_list is: ", processed_list
print get_winner(processed_list)