awk - counting the number of residues in a file -



awk - counting the number of residues in a file -

i have file follows. count number of each character.

>1dmla mtdspggvapaspvedasdaslgqpeegapcqvvlqgaelngilqafaplrtslldsllvmgdrgilihntifgeqvflp lehsqfsryrwrgptaaflslvdqkrsllsvfranqypdlrrvelaitgqapfrtlvqriwtttsdgeavelasetlmkr eltsfvvlvpqgtpdvqlrltrpqltkvlnatgadsatpttfelgvngkfsvfttstcvtfaareegvssststqvqils naltkagqaaanaktvygenthrtfsvvvddcsmravlrrlqvgggtlkfflttpvpslcvtatgpnavsavfllkpqk >1dmlb ddvaarlraagfgavgagataeetrrmlhrafdtla >2bhdc mtdspggvapaspvedasdaslgqpeegapcqvvlqgaelngilqafaplrtslldsllvmgdrgilihntifgeqvflp lehsqfsryrwrgptaaflslvdqkrsllsvfranqypdlrrvelaitgqapfrtlvqriwtttsdgeavelasetlmkr eltsfvvlvpqgtpdvqlrltrpqltkvlnatgadsatpttfelgvngkfsvfttstcvtfaareegvssststqvqils

i tried next code.

awk '/^>/ { res=substr($0, 2); } /^[^>]/ { print res " - " length($0); }' <file

the output of above code is

1dmla - 80 1dmla - 80 1dmla - 80 1dmla - 79 1dmlb - 36 2bhdc - 80 2bhdc - 80 2bhdc - 80

my desired output is

1dmla - 319 1dmlb - 36 2bhdc - 240

how alter above code getting desired output?

here's 1 way using awk:

awk '/^>/ && r { print r, "-", s; r=s="" } /^>/ { r = substr($0, 2); next } { s += length } end { print r, "-", s }' file

results:

1dmla - 319 1dmlb - 36 2bhdc - 240

awk

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