OK, here is something to horrify the unix programmers. here i am trying to analyze the datafile "fake", i am trying to do a couple of things

take the lines between matrix and end.
remove first line
remove last line

then i used your awk expression to duplicate all remaining line

then wcount up all of the lines and stick that somewhere

then grep and wc to count the occurrences of each of a number of expressions

then stick the line counts in front of the datafiles.

then remove all of the junk files...

here is another question

if i want to write

./myscript INPUTFILE

how do I code that into the script. here i just put the name of the file into the script. this is probably an easy one...i am just new to this! i don't even know the names of what to search for.

Here is the code: I would love any feedback.
And below that is a datafile

code:

awk '/matrix/,/;end;/' INPUTFILE > ZZoutput
sed '$d' ZZoutput > ZZoutfile
sed '1d' ZZoutfile > ZZoutfile1
awk '
/_X/ || /_Y/ { print; next; }
{ print; print; }
' ZZoutfile1 > ZZ_number_of_taxa
grep 'Gg' ZZ_number_of_taxa > ZAGg
wc -l ZAGg > ZQGg
grep 'Hs' ZZ_number_of_taxa > ZAHs
wc -l ZAHs > ZQHs
grep 'Panp' ZZ_number_of_taxa > ZAPanp
wc -l ZAPanp > ZQPanp
grep 'Ptro' ZZ_number_of_taxa > ZAPtro
wc -l ZAPtro > ZQPtro
grep 'Pts' ZZ_number_of_taxa > ZAPts
wc -l ZAPts > ZQPts
grep 'Ptv' ZZ_number_of_taxa > ZAPtv
wc -l ZAPtv > ZQPtv
wc -l ZZ_number_of_taxa > ZZlinecount
cat ZZlinecount ZQ* ZZ_number_of_taxa > dataset
rm ZZ*
rm ZA*
rm ZQ*





datafile:

junk stuff
matrix
Gg447874 CTTGAACATT
Gg447875 CTTGAACATT
Hs287867 CTTGAACATT
Hs287868 CTTGAACATT
Hs287869 CTTGAACATT
Hs287870 CTTGAACATT
Hs287871 CTTGAACATT
Hs287872 CTTGAACATT
;end;

---------- Post updated at 08:54 PM ---------- Previous update was at 08:53 PM ----------

whoops i meant to analyze the datafile
"INPUTFILE" at the beginning.
you probably knew what i meant.

thanks again for any advice

best

mikey