Remove a substring from lines starting with a specific character

November 28, 2022

I am trying to change long names in rows starting with >, so that I only keep the part till Stage_V_sporulation_protein...:

>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI_SpoIVAD_sporulation_protein_AEB_OS=Alkalihalobacillus_lehensis_G1_OX=1246626_GN=BleG1_2089_PE=4_SV=1
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG

I am doing a loop:

cat file.txt | while read line; do 
  if [[ $line = \>* ]] ; then
    cut -d_ -f1-4 $line; 
  fi; 
done

but in addresses files but not rows in the file (I get cut: >>tr_A0A024P1W8_A0A024P1W8_9BACI_Stage_V_sporulation_protein_AE_OS=Halobacillus_karajensis_OX=195088_GN=BN983_00096_PE=4_SV=1: No such file or directory).

My desired output is:

>tr_A0A024P1W8_A0A024P1W8_9BACI        
MTFLWAFLVGGGICVIGQILLDVFKLTPAHVMSSFVVAGAVLDAFDLYDNLIRFAGGGATVPITSFGHSLLHGAMEQADEHGVIGVAIGIFELTSAGIASAILFGFIVAVIFKPKG
>tr_A0A060LWV2_A0A060LWV2_9BACI        
MIFLWAFLVGGVICVIGQLLMDVVKLTPAHTMSTLVVSGAVLAGFGLYEPLVDFAGAGATVPITSFGNSLVQGAMEEANQVGLIGIITGIFEITSAGISAAIIFGFIAALIFKPKG

How do I change actual rows?

>Solution :

With the current state of the question, it seems easiest to do:

awk '/^>/ {print $1,$2,$3,$4; next}1' FS=_ OFS=_ file.txt

Lines that match the > at the beginning of the line get only the first four fields printed, separated by _ (the value of OFS). Lines that do not match are printing unchanged.