looping through a big file containing a set of files.

[aboxylica]

hey!
I have a program that takes two input files(one in the matrix form) and one in the sequence form.Now my problem is that i have to give the matrix file(containing many matrices) and sequence file containing many sequences and calculate the same log score as I did for one matrix file and one sequence file.
how it should exactly work is that. for every sequence it should calculate log values for all the weight matrices,then go to the second sequence and calculate all the log values using the matrices.
my matrix file is huge containing so many matrices. a part of it is here.

//
NA Abd-B
PO A C G T
01 10.19 0.00 10.65 6.24
02 5.79 0.67 10.50 10.11
03 4.50 0.00 0.00 22.57
04 0.00 0.00 0.00 27.08
05 0.00 0.00 0.00 27.08
06 0.00 0.00 0.00 27.08
07 27.08 0.00 0.00 0.00
08 0.00 2.83 0.00 24.25
09 0.00 0.00 24.45 2.62
10 19.33 0.00 4.34 3.41
11 0.31 12.28 3.39 11.09
//
//
NA Adf1
PO A C G T
01 0.71 0.08 26.02 1.55
02 3.03 23.00 1.24 1.09
03 0.26 10.50 3.29 14.31
04 0.00 0.06 28.23 0.07
05 0.12 27.27 0.06 0.91
06 1.44 20.36 0.37 6.19
07 5.35 0.28 21.49 1.24
08 7.81 16.10 3.81 0.63
09 0.51 17.77 0.45 9.63
10 0.00 0.14 28.21 0.00
11 0.00 25.69 0.20 2.46
12 0.48 9.98 0.07 17.82
13 1.27 0.00 27.01 0.07
14 15.59 7.98 2.92 1.87
15 4.28 22.37 0.00 1.70
16 0.18 0.77 22.70 4.70
//
//
NA Aef1
PO A C G T
01 0.00 0.06 12.49 0.00
02 3.80 0.17 0.00 8.57
03 0.87 0.06 0.00 11.62
04 0.06 9.76 2.32 0.41
05 9.82 0.00 2.73 0.00
06 9.76 0.00 0.00 2.78
07 3.80 0.31 0.00 8.43
08 0.00 0.00 0.00 12.54
09 0.00 6.53 5.85 0.17
10 0.00 12.38 0.17 0.00
11 2.73 1.02 8.80 0.00
12 5.85 0.00 6.70 0.00
13 1.02 5.96 0.00 5.57
14 0.00 5.16 4.66 2.73
15 1.03 7.55 3.97 0.00
16 4.82 5.00 2.73 0.00
//
//
NA Antp
PO A C G T
01 5.52 14.49 27.56 0.49
02 8.17 14.02 11.42 14.47
03 18.18 27.29 1.31 1.29
04 40.26 5.66 1.83 0.32
05 19.05 12.67 0.43 15.91
06 9.94 0.07 0.20 37.86
07 26.63 15.17 0.00 6.27
08 47.45 0.06 0.00 0.56
09 0.81 0.48 0.00 46.79
10 26.46 19.05 1.81 0.75
11 48.07 0.00 0.00 0.00
12 30.51 0.00 0.00 17.56
13 43.45 0.00 0.00 4.62
14 30.06 5.98 0.00 12.03
15 0.38 0.64 0.00 47.05
16 22.14 0.29 7.15 18.49
//
//

the sequence file is here( I mean this is also a part of my file)the actual file starts from "CC" the line before is just heading which we omit and this file is containg two sequences.
>CG9571_O-E|Drosophila melanogaster|CG9571|FBgn0031086|X:19926374..199271 33
CCAGTCCACCGGCCGCCGATCTATTTATACGAGAGGAAGAGGCTGAACTC GAGGATTACCCGTGTATCCTGGGACGCG
GATTAGCGATCCATTCCCCTTTTAATCGCCGCGCAAACAGATTCATGAAA GCCTTCGGATTCATTCATTGATCCACAT
CTACGGGAACGGGAGTCGCAAACGTTTTCGGATTAGCGCTGGACTAGCGG TTTCTAAATTGGATTATTTCTACCTGAC
CCTGGAGCCATCGTCCTCGTCCTCC
>Cp36_DRR|Drosophila melanogaster|Cp36|FBgn0000359|X:8323349..8324136
AGTCGACCAGCACGAGATCTCACCTACCTTCTTTATAAGCGGGGTCTCTA GAAGCTAAATCCATGTCCACGTCAAACC
AAAGACTTGCGGTCTCCAGACCATTGAGTTCTATAAATGGGACTGAGCCA CACCATACACCACACACCACACATACAC
ACACGCCAACACATTACACACAACACGAACTACACAAACACTGAGATTAA GGAAATTATTAAAAAAAATAATAAAATT
AATACAAAAAAAATATATATATATA
this is my code which works(prints the log value for one sequence and one matrix)

from math import *
import random
f=open("deeps1.txt","r")
line=f.next()
while not line.startswith('PO'):
    line=f.next()
 
headerlist=line.strip().split()[1:]
linelist=[]
 
 
line=f.next().strip()
while not line.startswith('/'):
    if line != '':
        linelist.append(line.strip().split())
    line=f.next().strip()
 
keys=[i[0] for i in linelist]
values=[[float(s) for s in item] for item in [j[1:] for j in linelist]]
 
array={}
linedict=dict(zip(keys,values))
keys = linedict.keys()
keys.sort()
for key in keys:
    array=[key,linedict[key]]
 
datadict={}
datadict1={}
for i,item in enumerate(headerlist):
    datadict[item]={}
    for key_ in linedict:
        datadict[item][key_]=linedict[key_][i]
 
 
for keymain in datadict:
    for keysub in datadict[keymain]:
        datadict[keymain][keysub]+=1.0
 
datadict1=datadict.copy()
for keysub in datadict:
    for keysub in datadict[keymain]:
        datadict1[keymain][keysub]=datadict[keymain][keysub]/(sum(values[int(keysub)-1])+4)
 
 
 
def readfasta():
    file1= open("chr011.py",'r')
    file_content=file1.readlines()
    first=1
    list1=""    
    for line in file_content:
        if line[0]==">":
            if first==0:
                print "***********"
                list1+=sequence
                print "***********"
            else:
                first=0
                sequence=""
                seq=""
                for i in range(0,len(line)-1):
                    seq+=line[i]
        else:
                for i in range(0,len(line)-1):
            sequence+=line[i]  
    list1+=sequence
    return list1
 
 
 
p=readfasta()
 
 
 
 
 
res=1
part=""
q=len(p)
seqq=""
 
value={"A":0.3,"T":0.3,"C":0.2,"G":0.2}
for i in range(q-16):
    part=p[i:i+16]
    seqq=part
    res=1
    score=1
    for j in range(16):
        key=seqq[j]
        res=res*datadict1[key]["%02d"%(j+1)]
        #print res
    for key in seqq:
        score=score * value[key]
    #print score,"*******************",res
    log_ratio=log10(res/score)
    print i,log_ratio
 

what changes should i make and how?/
waiting for your reply,
cheers!

[aboxylica]

i want to print the header only if it satifies the following condition:
how do i do it??

return 'Sequence Header: %s\n%s' % (dataSeq[0], outStr)if (log10(num/denList[i]))>=2
 

[bvdet]

i want to print the header only if it satifies the following condition:
how do i do it??

return 'Sequence Header: %s\n%s' % (dataSeq[0], outStr)if (log10(num/denList[i]))>=2
 

def compileData(fnArray, fnSeq, arraySet=1, seqSet=1):
    # sequence factor dictionary
    value={"A":0.3,"T":0.3,"C":0.2,"G":0.2}
 
    dataArray = parseArray(fnArray, arraySet)
    if dataArray:
        dataSeq = parseData(fnSeq, seqSet)
        if not dataSeq:
            return False
    else:
        return None
 
    # This is the complete sequence  
    seq = ''.join(dataSeq[1:])
    # These are the subkeys of dataArray - '01', '02', '03',.............
    subKeys = dataArray['A'].keys()
    subKeys.sort()
 
    # Calculate num/den for each slice of sequence
    # Each sequence slice length = length of subKeys
    # Example:
    # seq = 'ATCGATA'
    # subKeys length = 3
    # 'ATC', 'TCG', 'CGA', 'GAT', 'ATA'
    numList = []
    denList = []
    seqList = []
    for i in range(len(seq) - len(subKeys) + 1):
        subseq = seq[0:len(subKeys)]
        seqList.append(subseq)
        num, den = 1, 1
        for j, s in enumerate(subseq):
            num *= dataArray[s][subKeys[j]]
            den *= value[s]
        numList.append(num)
        denList.append(den)
        seq = seq[1:]
 
    resultList = []
    seqList1 = []
 
    for i, num in enumerate(numList):
        result = log10(num/denList[i])
        # limit output to results greater than 1
        if result > 2:
            # print 'Seq = %s Result = %0.12f' % (seqList[i], result)
            resultList.append(result)
            seqList1.append(seqList[i])
 
    outStr = '\n'.join(['Sequence = %s Calculation = %0.12f' % \
                        (seqList1[i], res) for i, res in enumerate(resultList)])
    return 'Array set # = %d\nSequence set # = %d\nSequence Header: %s\n%s' % \
           (arraySet, seqSet, dataSeq[0], outStr)

[aboxylica]

i am getting an error and still many sequence headers whose values are less than 2 are printed!
but i want the headers only for those value is more than 2
Traceback (most recent call last):
File "C:\Python25\this_final_1.py", line 165, in <module>
calcdata=compileData(fnArray,fnSeq,arraySet,seqSet )
File "C:\Python25\this_final_1.py", line 137, in compileD
seqList1.append(seqList[i])
IndexError: list index out of range

[bvdet]

I am baffled. The code works fine for me, and limits the output to values over 2. Add print statements to check the status of seqList and the calculation results.