Entering edit mode
8.5 years ago
weissert
•
0
Hi,
I have trouble to reformat my current fasta file header. This is the header it need to be like:
>tRNA_name predicted_anti-codon_positions
This is my current header:
>chrA01_622419_622487_+_Sup_TTA_28.44
>chrA01_2528533_2528604_+_His_GTG_63.70
This is the fileformat I could extract the anti codon position from:
chrA01.trna1 (622419-622487) Length: 69 bp
Type: Sup Anticodon: TTA at 33-35 (622451-622453) Score: 28.44
Possible pseudogene: HMM Sc=-4.46 Sec struct Sc=32.90
* | * | * | * | * | * | *
Seq: AGATCTGTAaGCTCAAaaTGGTAGAGCTCTCGTTATGAGAGTtTGGTGGTTCGAATCCACCCAGATCTG
Str: >>>>>>>...>>>>.........<<<<.>>>.....<<<.....>>>>>.......<<<<<<<<<<<<.
chrA01.trna2 (2528533-2528604) Length: 72 bp
Type: His Anticodon: GTG at 34-36 (2528566-2528568) Score: 63.70
* | * | * | * | * | * | * |
Seq: GTGGCTGTAGTTTAGTGGTgAGAATTCCACGTTGTGGCCGTGGAGACCTGGGCTCGAATCCCAGCAGCCACA
Str: >>>>>>>..>>>>........<<<<.>>>>>.......<<<<<....>>>>>.......<<<<<<<<<<<<.
Any suggestions on how to solve this issue? Christian
Hello,
I am having trouble identifying which are the fields you need to extract. This is your current header:
and you want it to be like this:
Is the "chrA01" the tRNA name? and "2528533_2528604" the positions in the sequence? If so, is this what you want?:
Or am I wrong? I am unsure if I understood right
This is not an answer, it is a request for clarification. It belongs in a comment. I'm moving it to one now.
(Ups, sorry an thank you, I am new to this)
No worries. Take a look at these posts to get an idea of how stuff works here: https://www.biostars.org/t/how-to/
The original description is unclear and badly formatted. My guess is @weissert wants the headers to look like this:
To clarify my question. I have two files one is in fasta format the other one is the cove output of tRNAscanSE, indicating the secodnary structure of my tRNA and the position of the Anticodon.
I want my header like this: