Dear all,

could you please help me with grep.
I have pdb files where there is SEQ section like this:
SEQRES 30 A 413 TRP SER PRO VAL GLU MET MET GLY LYS GLN LEU
SEQRES 31 A 413 ARG VAL VAL LEU SER VAL SER SER GLY GLY GLN
SEQRES 32 A 413 VAL LEU LEU VAL LYS ASP LYS GLU
SEQRES 1 B 413 ARG ARG SER PRO PRO ALA ASP ALA ILE PRO LYS
SEQRES 2 B 413 LYS VAL LYS VAL SER HIS ARG SER HIS SER THR
SEQRES 3 B 413 GLY LEU VAL LEU THR LEU GLY GLN GLY ASP VAL
SEQRES 4 B 413 LEU GLY LEU GLY GLU ASN VAL MET GLU ARG LYS
SEQRES 5 B 413 ALA LEU VAL SER ILE PRO GLU ASP VAL VAL GLN
SEQRES 3 C 413 GLY LEU VAL LEU THR LEU GLY GLN GLY ASP VAL
SEQRES 4 C 413 LEU GLY LEU GLY GLU ASN VAL MET GLU ARG LYS
SEQRES 5 C 413 ALA LEU VAL SER ILE PRO GLU ASP VAL VAL GLN

i need to grep only SEQRES section with ID in 3rd column indecated in id_file:
AB

that is i need to grep line with 3rd comuln A and B.


while read file < pdb_file && read id < id_file
do

grep '\<SEQRES' ${file} | grep " ${id} " > ${file}_new

done

it seems that my double read doesn't work. and ${id} can be two or three symbols and i need to separate them because in each line there 3rd column there is only one symbol

any ideas?

learn to use awk instead

learn to use awk instead

1 members found this post helpful.

that is nice, but i read id_s from id_file and sometimes there is only one symbol and somtimes 2 or 3 or even 4. How to separate symbols in ${id}?

while read file < pdb_file && read id < id_file
do

awk '$1=="SEQRES" && $3 ?? ${id}' ${file}

done