Hello! I want my temp file to be overwritten every time I use it, but instead it keeps appending my data to it. How do I go about emptying it out?

forever thanks

 #!/usr/bin/perl5.8.8

use strict;
use warnings;

tempProteinFamFileCreator();

sub tempProteinFamFileCreator
{
print "Enter file to process\t";
my $count = <>; #captures input from STNDIN and finds the file associa
+ted with that number
chomp $count;

my $TEMPfa; #file handle to temp file which stores a protein family
my $infile = $count."_ProFam"; #iterates through all the protein famil
+y files with the count variable
open (my $INFILE,"<", $infile);
open ($TEMPfa,">","temp"); #opens temp file    

while(<$INFILE>)
{
    #putting a single protein family into a temp file and processing i
+t with two more subroutines
    if ($_ =~/^##UniRef90_([\w\d]+) Protein Family/)
    {
    close ($TEMPfa);
    MuscleHMMERsearch();
    TableParser();
    open ($TEMPfa,">","temp"); #opens temp file        
    }

    if ($_ =~/^>UniRef90_[\w\d]+\.UniRef100_[\w\d]+/) 
    { 
    chomp $_;
    print $TEMPfa "$_\n";
    }
    
    if ($_ =~/^[\w\d]+/) 
    {
    print $TEMPfa $_;
    }

    if ($_ =~/^>File/) #indicates end of file
    {
    close ($TEMPfa); 
    MuscleHMMERsearch();
    TableParser();
    }

}
close ($INFILE); #closes the infile handle
}

sub MuscleHMMERsearch
{
    #checking if the temp file has data or is empty
    if ($_ =~/^>(UniRef90_[\w\d]+)\.UniRef100_[\w\d]+/)
    {
    # MUSCLE creating a multiple alignment file
    my $Fprot = "temp"; #temp file is sent to MUSCLE
    my $maFprot = $1."_ProFam.afa";
    my $cmd = "/home/vcg/Documents/Trial/muscle -in $Fprot -out $maFpr
+ot";
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};
    #system (rm /chongle/jeri/bin/temp.fa);

    # HMMER creating a profile HMM from a multiple alignment file
    my $hmm_Fprot = $1."_ProFam.hmm";
    $cmd = "/home/vcg/Documents/Trial/hmmbuild --informat afa $hmm_Fpr
+ot $maFprot";
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};
    #system (rm /chongle/jeri/bin/$maFprot);

    # Searching the sequence database with hmmsearch
    my $results = $1."_PFhmmResults.out"; 
    $cmd = "/home/vcg/Documents/Trial/hmmsearch --tblout HMMtable.tbl 
+--cpu 1 -E .001 $hmm_Fprot uniref100.fasta"; #HMMtable is not being b
+uilt #Is only one family going through and only outputting one empty 
+file?
    print $cmd. "\n";
    system ($cmd);
    if ($?) {die "command $cmd failed\n"};
    #system (rm /chongle/jeri/bin/$hmm_Fprot);
    }
            else {print "File is empty\n";} 
}

sub TableParser
{
open (my $TABLE,"<","table.tbl");
open (my $OUTFILE,">","FamDATA");

print $OUTFILE "target name\tE-value\tscore\n";

while(<$TABLE>) #space delimited file
{
    if ($_=~/^#/){next;}
    
    my @data = split(" ", $_);

    if ($_=~/^UniRef100/)
    {
    my $TargetName = $data[0];
    my $E_value = $data[4];
    my $BitScore = $data[5];
    print $OUTFILE "$TargetName\t$E_value\t$BitScore\n";
    }    
}
close ($TABLE);
close ($OUTFILE);
}
[download]

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.