calling all Perl experts

[paradise!]

Hey guys, so I'm brand new to perl. So i'm in quite a pickle, I have the code I need in FORTRAN, but I am trying to translate it into Perl.

parameter(ntm=10000,nspc=1000,particles=201,specie s=4)
integer cfg,nt,nxspc(nspc)
double precision tm,ran2
integer nconfg,nbin(ntm),nhist,ndev,ntspc1(ntm,nspc),flag1 ,flag2,flag3,flag4,flag5
integer ntspc2(ntm,nspc),ntspc3(ntm,nspc),ntspc4(ntm,nspc)
integer ntspc5(ntm,nspc),knt1,knt2,knt3,knt4,knt5
double precision histp,histm,avspc(nspc),sumspc(nspc)
double precision hist1(particles,species),TT1,chist1(nspc,nspc)
double precision hist2(particles,species),TT2,chist2(nspc,nspc)
double precision hist3(particles,species),TT3,chist3(nspc,nspc)
double precision hist4(particles,species),TT4,chist4(nspc,nspc)
double precision hist5(particles,species),TT5,chist5(nspc,nspc)


nconfg=4


do j=1,1000
avspc(j)=0.d0
enddo

do i=1,10000
do j=1,1000
ntspc1(i,j)=0
ntspc2(i,j)=0
ntspc3(i,j)=0
ntspc4(i,j)=0
ntspc5(i,j)=0
enddo
enddo


do i=1,1000
nxspc(i)=0
sumspc(i)=0.d0
do j=1,1000
chist1(i,j)=0.d0
chist2(i,j)=0.d0
chist3(i,j)=0.d0
chist4(i,j)=0.d0
chist5(i,j)=0.d0
enddo
enddo
do i=1,particles
do j=1,species
hist1(i,j)=0.d0
hist2(i,j)=0.d0
hist3(i,j)=0.d0
hist4(i,j)=0.d0
hist5(i,j)=0.d0
enddo
enddo

do cfg=1,nconfg
flag1=0
flag2=0
flag3=0
flag4=0
flag5=0


call system("$home\abdurehman1\BioNetGen\Perl2\BNG2.pl rxn1.txt
& > test.txt")

c call system("tac test>>test1")

cc # gives number of lines in the file test
call system("cat test | wc -l > inpl")
cc # gives number of columns in the file test
call system("cat test | tail -3 | head -1|awk '{print NF}'>inpc")


open(unit=10,file='inpl',status='old')
read(10,*)nt
close(10)

open(unit=11,file='inpc',status='old')
read(11,*)ncol
close(11)


c TT1=60.d0
c TT2=160.d0
c TT3=260.d0
c TT4=460.d0
c TT5=760.d0

TT1=60.d0
TT2=100.d0
TT3=200.d0
TT4=660.d0
TT5=2000.d0

open(unit=2,file='test',status='old')


do i=1,nt-1
read(2,*)tm,(nxspc(j),j=1,ncol-1)



if(flag1.eq.0) then
if(tm.ge.TT1)then
flag1=1

do j=1,ncol-1
hist1(nxspc(j)+1,j)= hist1(nxspc(j)+1,j)+1

enddo
endif
endif
if(flag2.eq.0) then
if(tm-TT2.ge.0)then
flag2=1

do j=1,ncol-1
hist2(nxspc(j)+1,j)= hist2(nxspc(j)+1,j)+1

enddo
endif
endif

if(flag3.eq.0) then
if(tm-TT3.ge.0)then
flag3=1

do j=1,ncol-1
hist3(nxspc(j)+1,j)=hist3(nxspc(j)+1,j)+1

enddo

endif
endif

if(flag4.eq.0) then
if(tm-TT4.ge.0)then
flag4=1

do j=1,ncol-1
hist4(nxspc(j)+1,j)=hist4(nxspc(j)+1,j)+1

enddo
endif
endif
if(flag5.eq.0) then
if(tm-TT5.ge.0)then
flag5=1

do j=1,ncol-1
hist5(nxspc(j)+1,j)=hist5(nxspc(j)+1,j)+1

enddo
endif
endif


enddo
close(2)
enddo


open(unit=31,status='unknown')
write(96,*)"# histogram at",TT1,"secs"
do i=1,201

write(96,'(1X,I4,28F15.5)')i-1,(hist1(i,j), j=1,ncol-1)

enddo

[paradise!]

I know in Perl I can skip like all of this defining and most of the initiliazing

#!/usr/bin/perl


#$runs=<>;
$runs=20; #comment


for($i=1;$i< $runs+1; $i++)
{


`BioNetGen\Perl2\BGN2.pl $me/rxn1.txt`;

`mv rxn_ssa.cdat test`;



@avspc ("j")

@ntspc1 ("i", "j")

@ntspc2 ("i", "j")

@ntspc3 ("i", "j")

@ntspc4 ("i", "j")

@ntspc5 ("i", "j")

@chist1 ("i","j")

@chist2 ("i","j")

@chist3 ("i","j")

@chist4 ("i","j")

@chist5 ("i","j")

@hist1 ("i", "j")

@hist2 ("i", "j")

@hist3 ("i", "j")

@hist4 ("i", "j")

@hist5 ("i", "j")


$flag1=0

$flag2=0

$flag3=0

$flag4=0

$flag5=0



`cat test | wc -l > inpl` #open test, read # of rows, print to inpl


`cat test | tail -3 | head -1|awk '{print NF}'>inpc` # read columns, print to inpc



open FILE, "inpl.txt"
$nt=<FILE>

[Nockm]

I'll do it but you'll have to paypal me $100 first for my time.

[paradise!]

I'll do it but you'll have to paypal me $100 first for my time.

not asking you to do it,

anyways, been googling past 2 hours, how do i read a text file, and only store the first column into an array.

i have:

open (filehandle, 'inpc')
while (<Filehandle> {
$ _=@array

should i just do a split? but i've seen splits done only on data inputted by the user, where there are like clearly different sets of values (ints and strings for instance)

in fortran i would do a do loop and just do read(unit, *)@array, @array2, but this is just implied syntax to make it read only the first value of the first row, and continue from there.
but asfkjasf i CANT GET IT.

edit: the whole thing must be done in Perl, all those saying call Fortran can just forget it!!!

[soup]

you serious?


this shit is way too easy, not going to tell you


good luck with your search

[Jason]

disclaimer: i am all sorts of rusty. haven't done a lick of coding in a good long while. never messed with perl very much.


do you know the width of each column? (width in terms of the number of characters) if so, you should be able to pull a substring out of the text file and push that into your array.

http://www.trilug.org/~chilcote/Perl/flatfiles.html - start reading under the "Flat File Sorting" heading.

[paradise!]

i actually figured it out, after some excruciating visual parsing of hundreds of google pages

push @columnTime,(split(/\s+/,$_))[0]

so this basically does the job haha, i read more about the split function and the column syntax and it worked out well.

and for the rest of the columns, just did a for loop and stored every i=1, i++ column into $columnRest, split(akfmklaf)[$i]

haven't really compiled in a while since i don't want my hopes and dreams to get murderized, but i will be doing it tonight, thanks for the help though jason, the push was it

[Rob Dougan]

Oh well, got here too late.