Closed:How to edit large txt file and how to find commons
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18 months ago
dimitrischat ▴ 140

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?

sequencing assembly • 88 views