sample input file:

1: AT2G01060 myb family transcription factor [ Arabidopsis thaliana ] 
Function Evidence
transcription factor activity


Process Evidence
regulation of transcription


Component Evidence
nucleus IEA 

2: AT2G01140 fructose-bisphosphate aldolase, putative [ Arabidopsis thaliana ] 
KEGG pathway: Carbon fixation00710KEGG pathway: Fructose and mannose
metabolism00051KEGG pathway: Glycolysis / Gluconeogenesis00010KEGG pathway:
Pentose phosphate pathway00030

Function Evidence
fructose-bisphosphate aldolase activity


Process Evidence
pentose-phosphate shunt TAS 
response to oxidative stress


Component Evidence
chloroplast
mitochondrion
plastoglobule

3: AT2G01275 zinc finger (C3HC4-type RING finger) family protein [ Arabidopsis
Function Evidence
protein binding RCA 
zinc ion binding RCA 

4: AT2G01320 ABC transporter family protein [ Arabidopsis thaliana ] 
Process Evidence
ATPase activity, coupled to transmembrane movement of substances ISS 

##</code><code>##

AT2G01060 

myb family transcription factor

Unknown

transcription factor activity

regulation of transcription

nucleus IEA 

AT2G01140 

fructose-bisphosphate aldolase, putative 
 
Carbon fixation00710 Fructose and mannose metabolism00051 Glycolysis / Gluconeogenesis00010 Pentose phosphate pathway00030

fructose-bisphosphate aldolase activity

pentose-phosphate shunt TAS 
response to oxidative stress

chloroplast
mitochondrion
plastoglobule

AT2G01275 

zinc finger (C3HC4-type RING finger) family protein 

Unknown

protein binding RCA 
zinc ion binding RCA 

Unknown

Unknown

AT2G01320 

ABC transporter family protein 

Unknown

Unknown

ATPase activity, coupled to transmembrane movement of substances ISS 

Unknown

##</code><code>##

#!/usr/bin/perl   
# to modify cleangene
# an infile (to be read in)and an outfile (to write to)
# and both should be open
$infile = "clean.txt"; #output of batch entrez gene cleaned
open (IN, $infile) or die "can't open file: $!";

$outfile = "genetable.txt";
open (OUT, ">$outfile") or die "can't open file: $!";
# reading one line at a time using the FILE handle

while (<IN>) {
	if ($_ =~ /^(\d+:\s\w.+)/) { # disecting the first line into locus tag and name
	$name = $_;
	$name =~ s/(\[\sArabidopsis\sthaliana\s\])|(\[\sArabidopsis\s)|(\[)//;
	$name =~ s/^\d+:\s//;
	@array = split(/\s+/, $name);
	$locus_tag = @array[0];
	print OUT "$locus_tag\n \n";
	$name =~ s/^(AT\w+)|(\w+)//;
	$name =~ s/^\s//;
	print OUT "$name\n";
}
	next if /(^Function\sEvidence)|^(Process\sEvidence)|^(Component\sEvidence)|^(\d+:\s\w.+)/;
	
	if ($_ =~ /(KEGG\spathway:)|(\w+\d\d\d\d\d\s)/){ #removing "KEGG pathway" from the kegg description
		$kegg = $_,
		$kegg =~ s/^(KEGG\spathway:\s)//;
		$kegg =~ s/KEGG/ KEGG/g;
		$kegg =~ s/(KEGG\spathway:\s)//g;
		print OUT "$kegg";
}	
	else {print OUT $_;}
	
	
	
}