Myseq*.tsv file is a output file. I need file in this format, this is matrix form
DUplex_subset is a input file.
Forward: Score: 149.000000 Q:2 to 18 R:2388 to 2409 Align Len (16) (75.00%) (87.50%) Energy:-9.900000
(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
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
GU ------ 1
Other mismatches ------ 0
Gap -------- -2
i sent my practice code also
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