Hi Prakash and Onclav2000,
Thanks for your answers. I still having some problem in solving my problem. I have sent the structure of the file am dealing with and the code I have so far come up with using Onclov2000 REGEX that captures only the first line in the file.
The structure of the text file is as follows:
FT CDS complement(7216..17805)
FT /locus_tag="TP01_0003"
FT /codon_start=1
FT /protein_id="XP_765530.1"
FT /db_xref="GI:71031777"
FT /db_xref="GeneID:3502673"
FT gene complement(<7216..>17805)
FT /locus_tag="TP01_0003"
FT /db_xref="GeneID:3502673"
FT mRNA complement(<7216..>17805)
FT /locus_tag="TP01_0003"
FT /product="hypothetical telomeric SfiI fragment 20 protein
FT 3"
FT /transcript_id="XM_760437.1"
FT /db_xref="GI:71031776"
FT /db_xref="GeneID:3502673"
FT CDS complement(join(18028..18116,19351..20668))
FT /locus_tag="TP01_0004"
FT /note="go_function: nutrient reservoir activity [goid
FT 0045735]"
FT /codon_start=1
FT /protein_id="XP_765531.1"
FT /db_xref="GI:71031779"
FT /db_xref="GeneID:3503550"
FT gene complement(<18028..>20668)
FT /locus_tag="TP01_0004"
FT /db_xref="GeneID:3503550"
FT mRNA complement(join(<18028..18116,19351..>20668))
FT /locus_tag="TP01_0004"
FT /product="hypothetical protein"
FT /transcript_id="XM_760438.1"
FT /db_xref="GI:71031778"
FT /db_xref="GeneID:3503550"
FT CDS complement(20951..21967)
FT /locus_tag="TP01_0005"
FT /codon_start=1
FT /protein_id="XP_765532.1"
FT /db_xref="GI:71031781"
FT /db_xref="GeneID:3503551"
FT gene complement(<20951..>21967)
FT /locus_tag="TP01_0005"
FT /db_xref="GeneID:3503551"
FT mRNA complement(<20951..>21967)
FT /locus_tag="TP01_0005"
FT /product="hypothetical protein"
FT /transcript_id="XM_760439.1"
FT /db_xref="GI:71031780"
FT /db_xref="GeneID:3503551"
This is my code
#!/usr/bin/perl
$file = 'Muguga.embl ';
open (F, $file) || die ("Could not open $file!");
while ($line = <F>)
{
($field1,$field2,$field3,$field4) = split( "\t" , $line);
print "$field1 $field2 $field3 $field4 \n";
my $string = (FT CDS complement(join(18028..18116,19351..20668))); # string to be searched
if ($string = ~ m/^FT \s+ CDS \s+ complement\(join\([0-9]+\)\)$/)
#search for the first line highlighted in bold
{
print 'match'
} else{
print 'no match';
}
}
close (F);
My wish is to able to search for the lines that are in bold and print them out.
I will be grateful if you are able to help my code though am still a perl newbie.
Thanks.
First things first, looking at your code, you're only searching on the string you provide
my $string = my $string = (FT CDS complement(join(18028..18116,19351..20668))); # string to be searched
So obviously you will only see that one and print it out....Try it with the input data,
Second, from what i'm understanding of your code, you're splitting each line up, so finding the data you want won't happen unless you look at the whole line, unless you modify the regex, and only look at the last field (for example).
So I would recommend changing to this (for the appropriate stuff):
while ($line = <F>)
{
print $line\n";
if (
$line = ~ m/^FT \s+ CDS \s+ complement\(join\([0-9]+\)\)$/)
#search for the first line highlighted in bold
{
print 'match'
} else{
print 'no match';
}
#insert additional regex's here
}
close (F);
Third, Once you've done that....try writing a regex for the second line you're trying to get, if you have problems post it and i'll gladly take a look at your regex and make some suggestions....
Fourth, I would recommend putting a counter in, and when you print the "match" you print the Line number as well (makes troubleshooting easier)
Fifth...wow I talk alot...sorry....anyways. You can turn that one regex into something that will match each line you're looking for, but IMHO it'll make for a messy looking regex, but you can do it, then there are variables that the regex will return so if you stick the right things into parentheses you can extract them, but again, I'm for a cleaner easier to follow code so I would break up each particular line into each regex...unless they are REALLY similar but they really don't look like it.
Onaclov.
Unsolved 
