from Bio import SeqIO

# highly or mildly hydrophobic or hydrophilic residues 
mildphob=['A','M','C','F']
highphob=['L','V','I']
mildphil=['G','S','T','W','P','Y']
highphil=['D','E','H','K','N','Q','R']

def hphob(aa):  # return a score for a given amino acid based on its hydrophobicity
    score = 0   # this is the default, in case you can't find the amino acid
    if aa in mildphob:   # True if aa matches any member of the list mildphob
        score = 2
    elif aa in highphob:    
        score = 4
    elif aa in mildphil:
        score = -1
    elif aa in highphil:
        score = -4
    return score

# score a sliding window of length L for hydrophobicity
#
def evalseq(seqname, inputseq, winlen):

# your code goes here






    
 
L = 21   # window size
for seq_record in SeqIO.parse("tmcombined.fasta", "fasta"):
    name=seq_record.id
    result=evalseq(name,seq_record.seq,L)    # return list: [bestscore, position]
    score=result[0]
    pos=result[1]
    print "%s: \t\tmax is %d at position %d" % (name, score, pos)