How to edit large txt file and how to find commons
Hello all. I got a large text file with sequence names(only names) like this:
>TRINITY_DN7758_c0_g1_i11_len_752_path_[8_0-295_10_296-520_12_521-751]
and i would like to find a command in terminal to change the the above names in that text file to this:
>TRINITY_DN7758_c0_g1_i11 len=752
So, i would have a text file with only sequence names like the above(the edited one). I want to subtract from a fasta file that contains these sequence names+amino acid sequence, in order to keep only the ones that are in the text file.
>TRINITY_DN7758_c0_g1_i11 len=752 path=[8:0-295 10:296-520 12:521-751]
CTGTGAAATGGAGGAATATGCGGTTAAGAAAGGAAAACCATGCTACATAAATTCTC.........
Which commands could i use in terminal in oder to do that?
Thanks in advance!
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Does the lines you need all follow the same pattern ? Could you show more lines and the expected result ?
Could you make it clearer ? I am not sure to understand what you need here.
Hello dimitrischat!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13043/how-to-edit-large-txt-file-and-how-to-find-commons
This is typically not recommended as it runs the risk of annoying people in both communities.
and thats prohibited?
In short, generally yes.
It is typically discouraged and definitely not recommended.
So, if someone is in stackexchange it automatically means he is also in biostars? ( i deleted my post in stackexchange so you can relax)
Not automatically, but a lot of people overlap. It is just courteous (to both communities) not to post in both. If some time passes and you don't get an answer, then it can be acceptable, but not immediately.
It's not prohibited, but it's disrespectful. We are all volunteers trying to help, but it's a finite resource. By making people in both communities "work" for you we are "wasting" more time than necessary.
can someone please delete this post also. i deleted in stack, i cant delete it here