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Need code for my problem

Myseq*.tsv file is a output file. I need file in this format, this is matrix form

DUplex_subset is a input file.

For example:

>hsa-miR-576-3p ENST00000379407

Forward: Score: 149.000000 Q:2 to 18 R:2388 to 2409 Align Len (16) (75.00%) (87.50%) Energy:[url removed, login to view]

(mRNA) Ref: 5' aagcaTAATTCTTACATATCTg 3'

:|||| || ||:||||

(miRNA) Query: 3' cuaagGUUAAAAAGGUGUAGAa 5'

Here Query is miRNA and Ref are mRNA. Extract only capital letter alignment is seed region and the lowercase alphabet is non-seed region.

I need to extract each alignment of seed only and put it in matrix form and give number to each as like in output file

Output:

Note: extract only which is in bold letters in each column:

miRNA mRNA R Pos1 Pos2 Pos3 Pos4 Pos5 Pos6 Pos7

hsa-miR-576-3p ENST00000379407 2388 to 2409 TA GC TA AU TU AG AG

Give the number to each alignment pairing:

Watson and Crick(GC, AU)-- 4

mismatch--- -1

GU ------ 1

Other mismatches ------ 0

Gap -------- -2

i sent my practice code also

Skills: Perl, Python

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