looping through a big file containing a set of files.

[aboxylica]

what i exactly should do is that. for every sequence(from the list of file) and every matrix(that is also a list of matrices in file form) i should calculate the scores.
the output should be in in the form of sequence header(this is the heading that follows the> symbol in the file),position of the sequence read",log value
for eg:
matrix1:
>ref1
01,2.0012
02,3.0047
.
.
.
>ref2
01,3.0047
02,8.0067
matrix 2
>ref1
01,2.0012
02,3.0047
.
.
.
>ref2
01,3.0047
02,8.0067

so ..on

the problem is for every sequence in the sequence file and for every position in the file, i am going to calculate the log value.is it clear now?

[bvdet]

Then I suppose the window-size changes for each matrix... It was just some thoughts on the task, because I am into genetics as well... Thanks for the clarification :), I overlooked that.

Thank you for your comments and suggestions. I hope we have helped the OP find a solution.

[aboxylica]

sorry i am not sure if i got what u meant. but i have posted how exactly my o/p should be.so tell me accordingly

[elbin]

the problem is for every sequence in the sequence file and for every position in the file, i am going to calculate the log value.is it clear now?

The partial sequence for which you are calculating the log has the length of the matrix, doesn't it? So you need to combine the code from this thread and the matrix thread, so you have both the sequences and matrices, and the scoring, and then run it over all matrices and over all sequences.

[aboxylica]

After that for each sequence in the file .for every A,T,G,C I am going to calculate the values,like i give specific scores for each alphabet,then calculate the divide the score of the martix divided by the score of this(at each position) take a log for this. and give the o/p in the form i mentioned.
q=len(d)
print q
seqq=""

value={"A":0.3, "T":0.3,"C":0.2 ,"G":0.2}
for i in range(q-16):
part=d[i:i+16]
seqq=part
res=1
score=1
for j in range(16):
key=seqq[j]
res=res*datadic t1[key]["%02d"%(j+1 )]
print res
for key in seqq:
score=score * value[key]
log_ratio=log10 (res/score)
print i,log_ratio

[aboxylica]

The partial sequence for which you are calculating the log has the length of the matrix, doesn't it? So you need to combine the code from this thread and the matrix thread, so you have both the sequences and matrices, and the scoring, and then run it over all matrices and over all sequences.

but my matrix file is something like this. i am not gonna be specific about the datasets it is a huge file.like this.(this ia a part)
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
//
//
NA BEAF-32
PO A C G T
01 16.78 0.91 0.00 3.45
02 0.62 0.92 11.18 8.41
03 0.07 20.94 0.00 0.14
04 0.45 0.47 19.97 0.25
05 11.06 2.12 4.95 3.01
06 0.90 0.00 9.47 10.77
07 12.46 3.27 0.00 5.41
08 0.45 6.88 13.48 0.33
09 0.10 1.02 0.00 20.03
10 9.15 1.11 5.14 5.75
11 2.37 0.29 0.00 18.48
12 0.00 8.76 8.01 4.37
13 0.42 8.63 11.09 1.00
14 7.27 1.53 12.08 0.26
15 1.82 0.05 3.23 16.04
//
//
NA BEAF-32A
PO A C G T
01 1.00 0.00 0.24 1.30
02 0.93 0.00 1.53 0.08
03 1.53 0.00 1.00 0.00
04 1.53 1.00 0.00 0.00
05 0.00 0.00 2.54 0.00
06 0.00 1.69 0.77 0.08
07 0.00 0.00 2.46 0.08
08 0.00 0.64 1.30 0.60
09 0.00 0.08 2.46 0.00
10 0.00 1.05 0.00 1.49
11 0.24 0.00 2.30 0.00
12 0.08 0.11 0.00 2.35
13 0.24 0.00 2.30 0.00
14 0.00 0.93 0.00 1.61
15 0.00 0.00 2.54 0.00
16 0.08 1.53 0.00 0.93
//
//
NA BEAF-32B
PO A C G T
01 0.00 7.91 0.00 0.00
02 0.00 0.00 7.91 0.00
03 7.91 0.00 0.00 0.00
04 0.00 0.00 0.00 7.91
05 7.91 0.00 0.00 0.00
06 0.00 1.67 3.51 2.73
07 0.00 0.00 0.00 7.91
08 3.49 0.16 0.00 4.27
09 0.00 0.00 0.00 7.91
10 0.00 5.11 0.91 1.89
11 0.00 4.31 3.60 0.00
12 0.16 7.64 0.00 0.11
13 7.00 0.00 0.91 0.00
14 0.00 6.18 0.00 1.73
15 4.27 2.80 0.00 0.84
16 1.84 5.11 0.84 0.11
//
//
NA Cf2-II
PO A C G T
01 0.00 0.00 0.43 12.03
02 0.00 10.74 0.00 1.72
03 6.27 0.00 6.19 0.00
04 0.00 11.76 0.00 0.70
05 0.78 0.00 11.25 0.43
06 0.00 0.00 0.00 12.46
07 11.91 0.00 0.12 0.43
08 6.27 0.00 0.00 6.19
09 11.56 0.12 0.78 0.00
10 5.88 0.00 0.00 6.58
11 8.86 0.00 3.60 0.00
12 5.77 0.12 0.00 6.58
13 0.00 6.27 6.19 0.00
14 0.00 12.46 0.00 0.00
15 6.69 0.00 5.77 0.00
16 3.52 0.00 8.94 0.00
//
//
NA Deaf1
PO A C G T
01 5.42 5.98 1.71 0.42
02 7.31 4.33 0.25 1.64
03 12.16 1.24 0.13 0.00
04 13.04 0.13 0.00 0.36
05 7.25 1.66 4.62 0.00
06 0.37 1.29 11.76 0.11
07 0.00 13.47 0.00 0.05
08 0.75 1.71 11.07 0.00
09 11.53 0.13 0.05 1.81
10 0.37 0.00 0.00 13.16
11 0.00 12.82 0.00 0.71
12 0.00 0.00 12.84 0.68
13 8.00 0.25 4.24 1.04
14 0.00 6.03 0.00 7.50
15 0.42 0.13 4.38 8.60
16 0.05 0.98 7.93 4.57
//
//
NA Dfd
PO A C G T
01 0.50 1.66 0.07 68.40
02 52.59 9.34 8.31 0.39
03 69.57 0.66 0.00 0.40
04 2.22 0.14 0.41 67.86
05 0.44 0.18 23.53 46.49
06 36.75 5.44 26.74 1.70
07 16.27 4.86 18.49 31.01
08 8.79 3.43 17.07 41.35
09 1.40 3.62 29.62 36.00
10 1.89 20.88 10.86 37.00
11 30.75 25.66 13.32 0.91
//
//
NA Dref
PO A C G T
01 1.28 2.13 14.78 18.90
02 5.33 12.15 12.68 6.92
03 4.99 8.72 21.15 2.22
04 10.42 6.71 18.00 1.95
05 22.25 0.51 10.62 3.70
06 15.72 3.00 0.00 18.36
07 26.44 3.26 4.01 3.38
08 10.33 5.61 9.50 11.64
09 8.67 18.41 0.18 9.83
10 2.83 0.84 0.24 33.17
11 35.50 0.91 0.60 0.08
12 0.35 0.08 1.05 35.60
13 0.22 34.76 0.79 1.31
14 4.00 0.88 31.28 0.93
15 23.50 6.09 0.33 7.16
16 4.83 1.79 1.77 28.69
//
//
NA E-spl-
PO A C G T
01 0.26 16.93 0.00 0.00
02 16.31 0.88 0.00 0.00
03 0.00 11.13 0.00 6.05
04 0.00 0.00 10.52 6.67
05 8.95 2.38 0.00 5.86
06 0.21 0.07 16.91 0.00
07 8.38 8.81 0.00 0.00
08 0.00 17.07 0.12 0.00
09 17.13 0.05 0.00 0.00
10 0.81 13.88 2.38 0.12
11 8.89 0.00 8.22 0.07
12 8.08 0.07 2.31 6.72
13 0.21 2.38 14.60 0.00
14 0.00 8.45 8.74 0.00
15 11.34 0.00 0.00 5.85
16 0.00 0.00 2.58 14.60
//
//
NA Eip74EF
PO A C G T
01 26.64 2.84 3.15 0.66
02 28.55 3.74 0.18 0.82
03 13.77 1.02 15.46 3.05
04 5.12 14.05 4.35 9.78
05 14.07 17.06 1.63 0.52
06 31.86 0.47 0.07 0.89
07 15.27 1.33 14.82 1.88
08 9.00 10.66 5.19 8.44
09 16.44 0.08 3.58 13.18
10 8.17 0.00 14.74 10.38
11 7.69 7.01 16.85 1.75
12 13.60 6.89 2.36 10.44
13 2.20 0.34 26.98 3.77
14 4.30 0.43 2.94 25.63
15 4.05 2.54 3.78 22.93
//
//
NA HLHm5
PO A C G T
01 6.96 4.69 0.00 0.00
02 0.00 3.00 0.00 8.65
03 0.00 6.96 4.69 0.00
04 0.00 11.65 0.00 0.00
05 4.69 0.00 0.00 6.96
06 0.00 0.00 0.00 11.65
07 0.00 0.00 6.96 4.69
08 0.00 0.00 0.00 11.65
09 0.00 0.00 11.65 0.00
10 4.69 0.00 6.96 0.00
11 0.00 11.65 0.00 0.00
12 4.69 0.00 0.00 6.96
13 0.00 11.65 0.00 0.00
14 0.00 0.00 11.65 0.00
15 0.00 0.00 0.00 11.65
16 0.00 0.00 11.65 0.00
//
//
NA His2B
PO A C G T
01 0.41 0.61 0.53 21.43
02 0.00 0.00 0.00 22.97
03 22.97 0.00 0.00 0.00
04 0.00 22.97 0.00 0.00
05 0.00 22.97 0.00 0.00
06 0.00 0.00 0.00 22.97
07 22.97 0.00 0.00 0.00
08 22.97 0.00 0.00 0.00
//
//

[aboxylica]

i donno how to incorporate the length of the sequence each time.its gonna change.this is a part of my sequence file:
>CG9571_O-E|Drosophila melanogaster|CG 9571|FBgn003108 6|X:19926374..1 9927133
CCAGTCCACCGGCCG CCGATCTATTTATAC GAGAGGAAGAGGCTG AACTCGAGGATTACC CGTGTATCCTGGGAC GCG
GATTAGCGATCCATT CCCCTTTTAATCGCC GCGCAAACAGATTCA TGAAAGCCTTCGGAT TCATTCATTGATCCA CAT
CTACGGGAACGGGAG TCGCAAACGTTTTCG GATTAGCGCTGGACT AGCGGTTTCTAAATT GGATTATTTCTACCT GAC
CCTGGAGCCATCGTC CTCGTCCTCCGTCCC TTAGCGCCTCCTGCA TGGATGTCGTTTTTG GGTTTCATACCTTTT CAC
ACTGGAAAAATACGG AATTTGTTGTAAGCC CTTTCAAGACGAATG GGATTTAGCTTCGGA TGTCAACGTCACCAT AAT
CATATTAGGAATATT TCTACTCAATTGCAA TATTGGTACTTTTCT GACTGTAAACGCGAT GATAATTACAAATAT GCC
TAATTTGCTGTCTTT ATAATCAAATGGAGT TCTTTATATTTCCAA AATATTGAAATTCCG ATTCCCTAGAAAATA ATA
CGTTTTTCTGTTATT AATAAAAAACCAATA GGAAAGTTCTCAAAA ATTACTCTGTTGTAT TTGATCATTTCTTTT CCG
GTATAATCTTTTATT TTAAGCATTCCCATG TGAATAAATTTCAGA CTAATGTATTAATAA GATGTCGTGTTTTTC CAC
TTACAAATTTCTCAT ACAGCTGGATATATA CTACGAGTACTATAC ACATGCTCTGGG
>Cp36_DRR|Droso phila melanogaster|Cp 36|FBgn0000359| X:8323349..8324 136
AGTCGACCAGCACGA GATCTCACCTACCTT CTTTATAAGCGGGGT CTCTAGAAGCTAAAT CCATGTCCACGTCAA ACC
AAAGACTTGCGGTCT CCAGACCATTGAGTT CTATAAATGGGACTG AGCCACACCATACAC CACACACCACACATA CAC
ACACGCCAACACATT ACACACAACACGAAC TACACAAACACTGAG ATTAAGGAAATTATT AAAAAAAATAATAAA ATT
AATACAAAAAAAATA TATATATATACAAAA ATTTGTTGTGTTTGA ATTGAATTAAGAGCT TATCAAGAAAAAAAT TTC
AGTGACTCATAATAC ACTACTCTACAAGTT TAAATTGAATCAACA ATTTAACTTTCATTG CTCAGGTTTTTAGTA ACA
ATGTTTATATAAGTT TAGGTATAACAAATG ATTTAAATATAAGAT ACTGTATTTCACATT GAGACGAAACAATCC ACC
GAAAATCATAAAATA TAAGAATGTTGCATT TTATTTTTAAAAATA AAGATGCCTTTTAAG AGGAATAACTTAAAT GTC
TTTAATACCTTTGAA TTTAATTATATGGCT AATAAACACAAACTT AAAGCTTAAAACTGC ATCGAATTGAATGCG GTT
ATAAATGTACTTATA TATCTAATATAATCT GCTAATATGGTTTAC ATGGTATATCTTTCT CGGAAATTTTTACAA AAA
TTATCTATTCATATA TCTCGAGCGTAAGAT ATTTATCAGTTTATA GATAACATCTTTAAA TTTGGGTGATTAAAA AAA
AACATTG
>Cp36_PRR|Droso phila melanogaster|Cp 36|FBgn0000359| X:8324430..8324 513
TCTAGAGATCTGGGC ACGATGGCGAGACAA AGATGCGGCGCAAAA TCGGAAATGGAGATG GATCACGTAGCCGGC CAT
GGCGG
>Him_distal|Dro sophila melanogaster|Hi m|FBgn0030900|X :18039896..1804 3470
GGTTTTCTGCGATGG CTTCCGCGCCAGCTG AAGTATCTGATTTGC TGCCTTGTTTTTGTT GATATTTCTGCGAAG GGA
CTTGTGCTTTTCAAA TGGCCTTTTTTTGGG ATTACGGCAAGGGCG CGTTTCCCACGCTCG ATCCCCACTTACCAT TGG
TGCACGCGATTGCGG CAAGCTGCTGAGGCA AGCTATTAAACGCCA CACTGGGCCGGGGGG CGGTACCGGTGGGCG TGG
CAGGGGAGTCGACAC ATGTTGTGTGCCAGA GAACTTTGCTCCGAT CCCCAGATCATCAAA TAGTTGTCGCTGTCT GCT
CGTGCGCAAATTGCA ATACTTTGCATACCC TTACTGCAGGGTATC TGAGCTTGGACTTTA AATAAGGGGGTATAA CAT
AGCTTATACTCTCTA TCTCTGTTATAAAGT CAATTTTCCTTAGAT CTTTAGTACAGTGGG TAGTTAAGGAGACAT AAC
TTCCAAAAAAAAAAA CTATAAAATTGCAAT AATTTATGCAAAATA TGTATTTTATTGAAT GGGATGAATAATTTA CCT
TATACGACTGTAAAA CATTTCTAACGATTA AATGCACTTCTAAAA GTTTTCCCACAAGTA GGTGAGCTATTATGC TAA
GCGTTCCATGACTTG GAATCTAAGATCTTG TTTTGATCTTCGCTG ATCTTTGAGAACTCG GGGATTACTTACACA TTT
CTGGGCAGGCACAAG TGGGCCGAGGCAGTG TAGATTCATCACGTT TTCACTCAACACACG CAGCTCATTAACAGC CCC
GCTGACAACTTGTCA GGACTTCCCCCTCGT GAATCCCCCTGCTAC GCAACCCCCATTCCC CGCCCATTCCAACAC TTC
CCGCCGGGAGCGTGG GAAATTATGCGTGTT GGTGGGACGTCGGGC GGTGAAAATTGGCGC GCTCTTCGGGGGGCC ACA
CCGCGTGGCATTGAC AACTCTTCCACATTT CGCGCCCAACGATGC GTTGGCATCAGTGGG TCACAGGGATTACGG CTG
GCTGGGATTCCAGAG CCAGATCTTTTTCAG CCAAAACTTTCAGCT TTCGAAGACCTCAAG CGATAGGAGAGTGTC GGA
AGTCCAGAAATAGAC GCGTAGCACATAAAT TATGGATCGTATCGA GTATCGATTAGCCCG GGACAAGCGAAGCGA TAG
GGAGACATATTTTTA TTACCCTCTCGGGGA CCTGCACTTGTTGGC TTCGCTTCTATGAAA GATCCCTCTACCATA TCA
CGTATGTGGGCTCCC CCAATCGAACCGAGT TGTGGGAAATGTTTT CCCAGGCCAACAGCT AATTGTCACTCCAAG GGT
TGTCCCCGCAGCCCA GACGACAGATAAGCG GGCAAGTGAAGCCCA GCGATCTGAGTCAAG TGAAGGGCTTCAATT TCT
TTCCCGAGTGGAACT GGGATATCGAAATTA CATTTGTAACAGACG TTTTAGTCCGCAATC CTCAGCTAATGGGAC TTA
CGAACATATATTCAT CTGAAATTCAAGAAC ATGCGCACTTAAAGA GCAGGGAAGTCGCAC ACGCGCAAGTCAGGC GCT
CAAAAAGGGATCTTC GGAGGTACAGTGGGC AAAAGACTGTAAATA AATAATATAAATAAA ATAATATTTAGCTCT ATG
TGTTTATATAATCTA CAAAGTAGTTAACAA AAAATATAAAATGGA TATAAAAATACATCT TATATATCCCTATAA TAA
GAAATAAATAATAAT TTTAGTAAATTAATT TTGTTACACAAAGTA CCTGTATTATTACCT CTTTTTTGTTGGTTG GTT
CTTTTTTGATGTGGC CCCACTGTGCTCTCT TATCAGTGCGACAAT CAGGCATTGCCTTTC CCCATCGGGGGATTC TAA
TTCCGTGGACGATGG GCCGAAACGCCTATA AAGTCGCTCATTAAA AATGTTTAATTATGG CCCATCTTGCATCTT GCA
CCGATGTGGATGGGG TTTGTCGGCAATGAT TTACATTATAAAAAT GCCCGTTATCTGAGC ATTTTGTACGCTCCA CTC
CCTCTTCCCCCCTCC AAAAAAAAAAAAAAC AGATATGTATATTCC CCGAGATATTCCCAA GCGGCCAAAAATAGA CGC
AAATTGTAACGCACT TGAAGTGCACTCTGA AACATCTTGAAGTCC AAATAAAATAGCAGA GAGACCCACAATAAT ATA
CGTTGATATACACAT GTATATATGTATGTA TGTACATAAAGGGCC AGGAGCAGGAACGTT AGGCATGCGGTGGTA CGA
GCACCGTGGTGCGAG CGAGAGCGCTGTGCT GCCTGAGGGAGAGGT AGCGAGTGGGTTGCA TTGCGCACACAGAAC ATG
TGAATGCAGAGTTCA AGTGCATGCCGTGAC ACAGACACGCACACA CACACACGCACACAC AGATGAGTAGCCGCT GCA
AAGTGTTTTTTCCCA GGCGCTATTTATAAT ATGCATCCCGTCGCC GATCCGATCCGATCC AATCCAATCCGATTG GAT
CCCATCTTGCGGCAC TACGATTATGACGCT CGACACGATGATGCA TTCGCAGAGTTTCCC GATCGCAGAGTACCC TGT
ACTCGAGTAGTTTTT AGATGCAGTATTATT AAGTAGAAAATTGTA ACCGTATAATATTCC ATTATATTAAATATT TTT
ATAGCACTAAAGAAA TAAAAGCCCATTTTA TAATTTATATTACAA AAATACTTAACCATA GAAACTTATGATATG ATA
CCAATATTTAAGTTC CAAAAAATGTAGAAC ATTTTTAAGTATATA CTCGAAAATATTAAT TTTCAAAATTGATAT TCA
AGAGATATTATAAAA AGATCCCCATTCTAA ATATCTAACATCATG CCATGCTTTCTAATG AGTATAGTATACCCC TGC
TACCCTGTCAATCCG CAAAACAGGCGCCGA AACATGCGGTTTCTC GCAGCAGACTGCCAC GGGAAAAATTCGGTT CGA
GATTTGGGAATGGAT GTATGACGGAGCAGA AGGAGCAGGACCCGG ATTTCGGATTTCGGA ATGGATATGGAAATG AAG
ATGGAAATGGGACTT TGACTGCGCGACGGC CACATGCGCCGCTGG CGATGCCGCTGGATG TTGCATGTGGCAGCG GTC
GGTGCAGCAGCGAAA GTGTTGCAGCTGTAT GAGAGGGTCTATTTT TGGGGCGATTGTGCG GCGCTGGTGCTGCCA CAT
GTGTTCTGTGTTGGG CTGCTAAAAGGCATT GTAATGAGAGCAGAA AATAGAATTGACTCC ACTTGAGCAATGTCC CAT
AAAGCGGGAGTTTCG AGTTTGGCGCGCAAT GTGCCGCACCAGCAA ACGAACAAAAGAAAA AAAAAAAAAAAAAAC ACA
GCCAGTAACACATGG GCCCACGAGTTATGT TTTATTTTTAATCCC ACAAAGAGTCGATCT CCAAAACAAACCCGC AGA
GAGCACATATAAAGA GACTCGGTGGACGAG TGGTTCGAAACAGTC TTCCGCCGCAGCTCG ACGCGCTCGCATATC GGG
AATATATAGATCGGA GATATCGCAGGACCC ACAGCAGAGCAGAGC CGCAGAGCCACCAAC CTCG
>Him_proximal|D rosophila melanogaster|Hi m|FBgn0030900|X :18041232..1804 3470
GCCCAGACGACAGAT AAGCGGGCAAGTGAA GCCCAGCGATCTGAG TCAAGTGAAGGGCTT CAATTTCTTTCCCGA GTG
GAACTGGGATATCGA AATTACATTTGTAAC AGACGTTTTAGTCCG CAATCCTCAGCTAAT GGGACTTACGAACAT ATA
TTCATCTGAAATTCA AGAACATGCGCACTT AAAGAGCAGGGAAGT CGCACACGCGCAAGT CAGGCGCTCAAAAAG GGA
TCTTCGGAGGTACAG TGGGCAAAAGACTGT AAATAAATAATATAA ATAAAATAATATTTA GCTCTATGTGTTTAT ATA
ATCTACAAAGTAGTT AACAAAAAATATAAA ATGGATATAAAAATA CATCTTATATATCCC TATAATAAGAAATAA ATA
ATAATTTTAGTAAAT TAATTTTGTTACACA AAGTACCTGTATTAT TACCTCTTTTTTGTT GGTTGGTTCTTTTTT GAT
GTGGCCCCACTGTGC TCTCTTATCAGTGCG ACAATCAGGCATTGC CTTTCCCCATCGGGG GATTCTAATTCCGTG GAC
GATGGGCCGAAACGC CTATAAAGTCGCTCA TTAAAAATGTTTAAT TATGGCCCATCTTGC ATCTTGCACCGATGT GGA
TGGGGTTTGTCGGCA ATGATTTACATTATA AAAATGCCCGTTATC TGAGCATTTTGTACG CTCCACTCCCTCTTC CCC
CCTCCAAAAAAAAAA AAAACAGATATGTAT ATTCCCCGAGATATT CCCAAGCGGCCAAAA ATAGACGCAAATTGT AAC
GCACTTGAAGTGCAC TCTGAAACATCTTGA AGTCCAAATAAAATA GCAGAGAGACCCACA ATAATATACGTTGAT ATA
CACATGTATATATGT ATGTATGTACATAAA GGGCCAGGAGCAGGA ACGTTAGGCATGCGG TGGTACGAGCACCGT GGT
GCGAGCGAGAGCGCT GTGCTGCCTGAGGGA GAGGTAGCGAGTGGG TTGCATTGCGCACAC AGAACATGTGAATGC AGA
GTTCAAGTGCATGCC GTGACACAGACACGC ACACACACACACGCA CACACAGATGAGTAG CCGCTGCAAAGTGTT TTT
TCCCAGGCGCTATTT ATAATATGCATCCCG TCGCCGATCCGATCC GATCCAATCCAATCC GATTGGATCCCATCT TGC
GGCACTACGATTATG ACGCTCGACACGATG ATGCATTCGCAGAGT TTCCCGATCGCAGAG TACCCTGTACTCGAG TAG
TTTTTAGATGCAGTA TTATTAAGTAGAAAA TTGTAACCGTATAAT ATTCCATTATATTAA ATATTTTTATAGCAC TAA
AGAAATAAAAGCCCA TTTTATAATTTATAT TACAAAAATACTTAA CCATAGAAACTTATG ATATGATACCAATAT TTA
AGTTCCAAAAAATGT AGAACATTTTTAAGT ATATACTCGAAAATA TTAATTTTCAAAATT GATATTCAAGAGATA TTA
TAAAAAGATCCCCAT TCTAAATATCTAACA TCATGCCATGCTTTC TAATGAGTATAGTAT ACCCCTGCTACCCTG TCA
ATCCGCAAAACAGGC GCCGAAACATGCGGT TTCTCGCAGCAGACT GCCACGGGAAAAATT CGGTTCGAGATTTGG GAA
TGGATGTATGACGGA GCAGAAGGAGCAGGA CCCGGATTTCGGATT TCGGAATGGATATGG AAATGAAGATGGAAA TGG
GACTTTGACTGCGCG ACGGCCACATGCGCC GCTGGCGATGCCGCT GGATGTTGCATGTGG CAGCGGTCGGTGCAG CAG
CGAAAGTGTTGCAGC TGTATGAGAGGGTCT ATTTTTGGGGCGATT GTGCGGCGCTGGTGC TGCCACATGTGTTCT GTG
TTGGGCTGCTAAAAG GCATTGTAATGAGAG CAGAAAATAGAATTG ACTCCACTTGAGCAA TGTCCCATAAAGCGG GAG
TTTCGAGTTTGGCGC GCAATGTGCCGCACC AGCAAACGAACAAAA GAAAAAAAAAAAAAA AAAACACAGCCAGTA ACA
CATGGGCCCACGAGT TATGTTTTATTTTTA ATCCCACAAAGAGTC GATCTCCAAAACAAA CCCGCAGAGAGCACA TAT
AAAGAGACTCGGTGG ACGAGTGGTTCGAAA CAGTCTTCCGCCGCA GCTCGACGCGCTCGC ATATCGGGAATATAT AGA
TCGGAGATATCGCAG GACCCACAGCAGAGC AGAGCCGCAGAGCCA CCAACCTCG
>Obp18a_prom|Dr osophila melanogaster|Ob p18a|FBgn003098 5|X:18969778..1 8972746
ATGGCGAAAATCTGT TTCCCAACTAACAAT GAGCGCATCATCACA GCTCTATATATATAA CCCATCGATTTGCTA ATT
CAGCTCAAAAGTAGA CAGGAGATTTTAATT AAATAATTGGATGCT ACTTTACATTCGCCA CACACCAACAAATAA AGT
CTATAATTGAAATTT TAAGCGCAGTTCCCG ATTATGAGCTACACG TATGTCGTATGCGCA ATATCTGCATTACAA TTG
CCAATAGTAAATTAC CAACTTGGTTTTCTT CATATTTATTAAGAT AGAAAACATACAATT TTTGGCTTTTACACT CCA
AGCATCTCTGAAGTT TAAACAAAAAACATA TGTGTAGCCTATCTA CTGTATTGGACTTTA TTCGTATATTTTATA TGG
TTCATTAATATAGGT ATAAATACAAATTAT ATTCACGCTTTGCGA TTTGCAGCGAATATC ACATCTTATACACGA TGT
AAAAAAAAAAAAAAT ATTTCGTCATGTTTT TAGGTTGGCCGCAGG CAGTGCTCACTGTAC CGCCACAATGTTTAT CGT
TTTGCATTTTTTTTT TCTTTGTTTTCTTGC GGTTTCCCCTAATTA TCTTTAGTATAAACT TAGTCTACTGTCTTT TTT
GGTAAGTATTTTCGT GATGGGCTCGTCTAT GCGAATTCCCATTTC CAATGAATAAATAAA GTAATTAGAACATTA AAA
TTAGCAATAAAACAC GTACATTTAAAGCTG ACAACAAAAAAAAAA AGTATTCTTATGTTA AACTGTAGTATGTGC CTA
TGCAATATTAAGAAC AATTAAATAAAATAG CATATTAACTTATGG CAGCACTTTGTTGCT ATGTTTATGTTTATG TTT
ATGCACGCAGTTAGG CCAGGGCGGATGTAA CATGATCACCCACTC GAAGGCAAAAAGTAT AAGTGCATGGTCAGC ATT
CACACGCCGACCAAA TACATATTACATACG TACATACATATCTCG CTCTCCCGATAAGCC TAGATATATAAGATA TAC
ATAAGAACGCCGCTC CGCTGCTGGCGTACC CGGCAGCGCAGCTAC GCGGATTAGCCTAAG TCCAAATATATTAAA AAC
TGTAAAATCAGAGAG ACTCTGTAGACGTTG AGCTGACAGAACCAT TTCTGCCTACTCTAA AATCAAAAGAAGAAA TTG
AATAAATATATGTCA GCCCGACGGCTGCCT TCAACTTAAAACGGA CTTGTGTTCTGAATT GGAGTTCATCATTAC ATG
GCGACCGTGACAGTC GTCCAACGCTGGACG AATTGACCAAAGCTG GTGAAAACAAAGGAA CAAAGGAACACTGGA CTG
GAAGAAGACTGGACT AATTAAATGGAACTG CAAAAACCAAGGAAA AATCTGAGTGAGTAG AGTTCTATTGAGTAT GGG
CAAACACCGTGGCGG TTTGAAAACTAAGCT GAATAAACGTATAGC CCACGTAAGGTGGCT AATATACGGTCAGCA AAC
GCCACCGGTTTGGTC GAAAGCTCTAAAGCT ACATGCAGAGCTAGA CCACTTGTTGCAATA TCAGCAAGAATTAAA GAC
CCATAAGCTCGAGAA AACTCACTCAGATAA TATTAAAAATATACC CACAATTAATGAAGT TCCAAAATACCAGGC ATG
TCCAGCACCAGCACC AGCATTAACAAAACC AAAGAAGTCCTGCCC CCCTGGCTGCGAAGG AATCTGGAGTCCCCA CTG
CCTGGGGACTTGTGA GCGACCATCGACGTC TTCAGCGGCGAAGAA ATAGACAGCAGCGAG GGAGTGTCAGCGTGC CAC
CCCCGGCGACGCCCA GCTGACACCTGATGA GCATCATCAACAGCA GAATATAATAATAAA TATATATAAATATAA AGT
AAATATAAAATATAT ATAGATAAGAAAAAT TGTAAGAAATATTGT AAAACGGAGCATATA CTATTATGCCCTGTT AAC
CCAATATGGCCCGTG AAGCCATAGCTAGAA TCAGGCAGGCAACAA TGTAAAATACAATTT TTTTTTACTCTTGCG AAC
ATTGAAAGATTTTAT AAATAGATAATTCCA AACATAAATGTCTAT AGAGACAAATGAAAT AAGTAAAACTGAAAA TAA
AAGTATATACAAAGG AAATTTTCTATTCTA TTCTCCAAAATATAA AATTAGTATACCCAA AATGGGTCTAATAGA CAC
TAAAACTGTGGACTC TACAGCCAATGTAAT AAATAAAGTAGAAGT CCAAAATGCAGACTT GTTCTGGATAACCAT AAT
ACTAATTGTAATTGC ATTAATTATGGTATC CAATGCATTAATAAA AATATACAAACTGCA TAACAAGTGTCTTAA GAA
ACGATACCGTAGCAC TGCTAACGGTATAGA TAATATTTAAGGAAG ATCTTTAATAAAGTC AATTATGAATGAAAA TAT
GAGAAAAATTATATG AAAAAAAAAAAATAA TAAATAAAAAAAAAA ATATAAAACGTAATA TTGAATTTATCTACG TTA
AAAAAAAAAATATAT ACAAATGAATAAATT TGAAGTTATGAGTAT ACCACAGCATGGACT GGGAAAAGCTTGTTG ATC
AGATAAAAGATCAAA ATGAAAATTTCAGAA AATCCTATAAGTGCT TAACGCAAAACAGAT CAACACAAGCTGTAA CAA
TCAATAGGAATGCCC AAGTCTTGGTAAATA GTTATAATGAAATCA GAGAGTTGATCCAAC AAAATAGAAAGAATT TGG
AACGCAAACAGTGTG CTAAGGCTTTGAACC TACTGGTGACATTAA GAGAAAAATTAATAT TTATAAAAAATAAAT TCA
GTCTCCAGATAGAAA TTCCAACCATAGTAA ACACCCCACTAAGAA TAAATTTGAATGAAG ACAGCACTAACTCTG ACG
AGGAAGATAGGACTA TAGTCAAGGAAGACA TTAAAGAGGAAGATC TTCACGATCTAACTA TACCAGCAAAATTAA TGC
TGAA

[bvdet]

what i exactly should do is that. for every sequence(from the list of file) and every matrix(that is also a list of matrices in file form) i should calculate the scores.
the output should be in in the form of sequence header(this is the heading that follows the> symbol in the file),position of the sequence read",log value
for eg:
matrix1:
>ref1
01,2.0012
02,3.0047
.
.
.
>ref2
01,3.0047
02,8.0067
matrix 2
>ref1
01,2.0012
02,3.0047
.
.
.
>ref2
01,3.0047
02,8.0067

so ..on

the problem is for every sequence in the sequence file and for every position in the file, i am going to calculate the log value.is it clear now?

Not to me. I can't seem to follow the logic in your code:[code=Python]
def readfasta():
file1= open("chr011.py ",'r')
file_content=fi le1.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(lin e)-1):
seq+=line[i]
else:
for i in range(0,len(lin e)-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*datadic t1[key]["%02d"%(j+1 )]
#print res
for key in seqq:
score=score * value[key]
#print score,"******** ***********",re s
log_ratio=log10 (res/score)
print i,log_ratio[/code]I have modified function parseData() to include the header:[code=Python]def parseData(fn, dataset=1, key='>'):
'''
Read a formatted data file of alpha sequences
Return a list of sequences
The first element in the list is the header
'''
# initialize output list
dataList = []

# open file for reading
f = open(fn)

# skip to required data set
for _ in range(dataset):
try:
s = f.next()
while not s.startswith(ke y):
s = f.next()
except StopIteration, e:
print 'We have reached the end of the file!'
f.close()
return False

# initialize output list
dataList = [s,]

for line in f:
if not line.startswith (key):
dataList.append (line.strip())
else:
break

f.close()
return dataList

dataSeq = parseData(fnSeq , dataset)
print dataSeq[0][/code]Output:
>>> >Cp36_PRR|Droso phila melanogaster|Cp 36|FBgn0000359| X:8324430..8324 513

I have given you the code to parse the matrix data and sequence data so it can easily be manipulated. I don't understand the log calculation you want. Maybe someone smarter than me can figure it out.

[elbin]

for i in range(q-16):
    part=d[i:i+16]
    seqq=part
    res=1
    score=1
    for j in range(16):
        key=seqq[j]
        res=res*datadict1[key]["%02d"%(j+1)]

This means that you take for granted that the subsequence you are examining is 16 characters long, and the matrix you are using is 16 lines too. But they are not all 16 lines. So you need to change this part to

len(datadict['A'])

for example.
And what do you mean by "integrate the length of the sequence"?

To bvdet: For the log see http://www.thescripts.com/forum/thread672978.html

[aboxylica]

yes, sixteen is not fixed its gonna varry all through.these aspects confuse me.:(
as to how my code should be
and what i should exactly do is that
>seq1
atattatatat
>seq2
atatattatatata
>seq3
attattatatatata t
...so on..
weightmat1
po
values
weightmat2
values
weightmat3
values
Now
i am actually calculating the log odds ratio(u must be knowing since you are into this)
i calculate for each position the log value..
am i clear now??
you told me previously how to do it for one seq and one weight matrix..now there are multiple matrices and multiple sequences i have to calculate the logodds ratio for each position
am i clear?
waiting for ur reply
cheers

[elbin]

I think you already have all the needed code for this task, please make an effort and combine it, and you will get the result.

[aboxylica]

okay il try that.but i don seem to be confident though.but il try.
thanks!

[bvdet]

See if this is what you need:[code=Python]if __name__ == '__main__':

value={"A":0.3, "T":0.3,"C":0.2 ,"G":0.2}

fnArray = 'arraydata.txt'
fnSeq = 'seqdata.txt'
dataset = 3
dataArray = parseArray(fnAr ray, dataset)
dataSeq = parseData(fnSeq , dataset)

seq = ''.join(dataSeq[1:])
subKeys = dataArray['A'].keys()
subKeys.sort()

i,j = divmod(len(seq) , len(subKeys))
keys = subKeys*i + subKeys[:j]

print dataSeq[0],
outList = ['%s[%s]*%s = %0.4f' % (s, keys[i], s, dataArray[s][keys[i]]*value[s]) for i, s in enumerate(seq)]
print '\n'.join(outLi st)
print sum([float(s.split(' =')[1]) for s in outList])[/code]Output:

>>> >Cp36_PRR|Drosophila melanogaster|Cp36|FBgn0000359|X:8324430..8324513
T[01]*T = 0.0131
C[02]*C = 0.0015
T[03]*T = 0.0019
A[04]*A = 0.0017
G[05]*G = 0.0014
A[06]*A = 0.2515
G[07]*G = 0.0969
A[01]*A = 0.0624
T[02]*T = 0.0014
C[03]*C = 0.0755
T[04]*T = 0.2952
G[05]*G = 0.0014
G[06]*G = 0.0022
G[07]*G = 0.0969
C[01]*C = 0.0093
A[02]*A = 0.0016
C[03]*C = 0.0755
G[04]*G = 0.0010
A[05]*A = 0.0014
T[06]*T = 0.0424
G[07]*G = 0.0969
G[01]*G = 0.1403
C[02]*C = 0.0015
G[03]*G = 0.0011
A[04]*A = 0.0017
G[05]*G = 0.0014
A[06]*A = 0.2515
C[07]*C = 0.0054
A[01]*A = 0.0624
A[02]*A = 0.0016
A[03]*A = 0.1832
G[04]*G = 0.0010
A[05]*A = 0.0014
T[06]*T = 0.0424
G[07]*G = 0.0969
C[01]*C = 0.0093
G[02]*G = 0.1965
G[03]*G = 0.0011
C[04]*C = 0.0011
G[05]*G = 0.0014
C[06]*C = 0.0019
A[07]*A = 0.1154
A[01]*A = 0.0624
A[02]*A = 0.0016
A[03]*A = 0.1832
T[04]*T = 0.2952
C[05]*C = 0.0128
G[06]*G = 0.0022
G[07]*G = 0.0969
A[01]*A = 0.0624
A[02]*A = 0.0016
A[03]*A = 0.1832
T[04]*T = 0.2952
G[05]*G = 0.0014
G[06]*G = 0.0022
A[07]*A = 0.1154
G[01]*G = 0.1403
A[02]*A = 0.0016
T[03]*T = 0.0019
G[04]*G = 0.0010
G[05]*G = 0.0014
A[06]*A = 0.2515
T[07]*T = 0.0310
C[01]*C = 0.0093
A[02]*A = 0.0016
C[03]*C = 0.0755
G[04]*G = 0.0010
T[05]*T = 0.2773
A[06]*A = 0.2515
G[07]*G = 0.0969
C[01]*C = 0.0093
C[02]*C = 0.0015
G[03]*G = 0.0011
G[04]*G = 0.0010
C[05]*C = 0.0128
C[06]*C = 0.0019
A[07]*A = 0.1154
T[01]*T = 0.0131
G[02]*G = 0.1965
G[03]*G = 0.0011
C[04]*C = 0.0011
G[05]*G = 0.0014
G[06]*G = 0.0022
5.0655
>>> seq
'TCTAGAGATCTGGGCACGATGGCGAGACAAAGATGCGGCGCAAAATCGGAAATGGAGATGGATCACGTAGCCGGCCATGGCGG'

[aboxylica]

okay.one thing I am doubtful about what does dataset refer to??
and in the last code the calculation u sent me. is it something like
A[01]*A which means your multiplying the normalised value of A at position one and dividing it by the standard A value??so please tell me. and which statement of the code does that??
what I should ba doing is
if i have a sequence like
>header
ATTTATTATATATAT ATTATTATAATTAAA TAT
and using the matrix
calculate A[01]*T[02]*T[03]*.............. ...divided by standard values which is
A=0.3,T=0.3.
C=0.2,G=0.2
so it should be done like A[01]*T[02]*T[03]*.............. .../0.3*0.3*0.3.... ........
for the sequence
then take a log for this value.Then move to the next window of the sequence
TTTATTATATATATA TTATTATAATTAAAT AT(I am just leaving the A) calculate the same way with T in the first position.
I have to do this way for all the sequences.

[aboxylica]

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 random_seq(nchars,insertat,astring):
    seq=""
    for i in range(nchars):
      if i== insertat:
          seq+=astring
      ch=random.choice(("ATGC"))
      seq+=ch
    print seq
    return seq
 
thestring="CGTCAAGTTCAAGTGCAAAA"
count=50-len(thestring)
p=random_seq(count,15,thestring)
file=open("temp.txt",'w')
file.write(str(p))
file.close()
 


 
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

This is the code that works and calculates for a single sequence and a single matrix(containi ng 16 positions) I want to do it for many sequences and many matrices.I guess am clearer now.I have given how my sequences and matrices look like.I just need to generalize it.am i clearer now
waiting for ur reply
cheers!