window size

Question

[devhimd]

if i have a fasta sequence and i want to trim the sequences based on the window size having Cys at the center and if the window size is less than the residue number i want it to fill it with some alphabet

>sp|P39688|FYN_MOUSE Tyrosine-protein kinase Fyn OS=Mus musculus OX=10090 GN=Fyn PE=1 SV=4
MGCVQCKDKEAAKLTEERDGSLNQSSGYRYGTDPTPQHYPSFGVTSIPNYNNFHAAGGQGLTVFGGVNSSSHTGTLRTRGGTGVTLFVALYDYEARTEDDLSFHKGEKFQILNSSEGDWWEARSLTTGETGYIPSNYVAPVDSIQAEEWYFGKLGRKDAERQLLSFGNPRGTFLIRESETTKGAYSLSIRDWDDMKGDHVKHYKIRKLDNGGYYITTRAQFETLQQLVQHYSERAAGLCCRLVVPCHKGMPRLTDLSVKTKDVWEIPRESLQLIKRLGNGQFGEVWMGTWNGNTKVAIKTLKPGTMSPESFLEEAQIMKKLKHDKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKDGEGRALKLPNLVDMAAQVAAGMAYIERMNYIHRDLRSANILVGNGLICKIADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELVTKGRVPYPGMNNREVLEQVERGYRMPCPQDCPISLHELMIHCWKKDPEERPTFEYLQGFLEDYFTATEPQYQPGENL

Cys_Residue = 3
window size = 2 

[Joe]

I don't really understand the objective?

You want to find all cysteines at the centre of an amino acid triplet, and replace it with some random letter? Why?

[devhimd]

I have an FASTA sequence with Cys residue no = 16 and window size = 5. I want to print if the residue number is less than the Cys residue print with some other alphabet

start = res number + window end = res number - window

start = 16+5 = 21 = sequence : 16,17,18,19,20,21 end = 16-5 = 11 = sequence: 11, 12, 13, 14, 15, 16

total sequence = 11,12,13,14,15,16,17,18,19,20,21

start = res number + window end = res number - window

start = 2+5 = 7 = sequence : 2,3,4,5,6,7 end = 2-5 = -3 = sequence : -3,-2,-1,0,1,2

total sequence = XXXXACFGHLP

write a python script

[Friederike]

1. That sounds a lot like taken straight from a class assignment.
2. It's not clear what you need.
3. It's not clear what type of effort you made and what the specific issue is that you're running into.

Unless you address these aspects, we will have to close this post.