Hello friends,

I am new to perl programming still I have to practice Regular expression and NCBI file handling but here I have a task to do I have done half cud anybody help doing the rest

File 1:

Candida glabrata CBS 138 chromosome D, complete genome - 1..651701
283 proteins
Location    Strand    Length    PID        Gene    Synonym        Code    COG Product
17042..17914    -    290    50285983    -    CAGL0D00154g    -    -               
23693..25075    +    460    50285985    -    CAGL0D00176g    -    -    
27559..28710    +    383    50285987    -    CAGL0D00198g    -    -    
29345..29914    +    189    50285989    -    CAGL0D00220g    -    -

So on 40 lines.....

File 2: Contains

>ref|NC_006027.1|:c17914-17042 hypothetical protein [Candida glabrata CBS 138]
ATGGAAACAGAACATCAGGCAGACAAAAATGCGGAATTGGGTTATGACAGTGGATCAACCGTTGCTCCCC
CCAATAAATATAGTACATTACGCTCTAGGTTCAATTTAGGACCTGACACTATGAGAAATCATGTTATTGC
CTTTTTTGGGGAGTTGGTTGGCACATTCATGTTTTTATGGTGTGCCTATGTTATTGCAAATATTGCAAAT

>ref|NC_006027.1|:23693-25075 hypothetical protein [Candida glabrata CBS 138]
ATGTCTTCTCAAGTTAACGAACCAGAATTTCAACAAGCTTACCACGAAGTTGTTTCCTCTTTGAAGGACT
CTTCTTTGTTCGAAAAGCACCCAAAATATGCTAAGGTTCTTCCAGTTGTCTCTGTCCCAGAGAGAATCAT

so on number of locations in file 1 is equal to no. of Seq in File 2..

here is what I have to do if the location of FILE 1 i.e "17042..17914" matches with the Header of the FILE 2 i.e "c17914-17042 match with either upper or the lower limit

then it should remove header of fasta of file 2 then insert">CAGL0D00154g" which is in synonym column of File 1 , location with the corresponding synonym

then my Output file should come as follows:

File3:

>CAGL0D00154g
ATGGAAACAGAACATCAGGCAGACAAAAATGCGGAATTGGGTTATGACAGTGGATCAACCGTTGCTCCCC
CCAATAAATATAGTACATTACGCTCTAGGTTCAATTTAGGACCTGACACTATGAGAAATCATGTTATTGC
CTTTTTTGGGGAGTTGGTTGGCACATTCATGTTTTTATGGTGTGCCTATGTTATTGCAAATATTGCAAAT

>CAGL0D00176g
ATGTCTTCTCAAGTTAACGAACCAGAATTTCAACAAGCTTACCACGAAGTTGTTTCCTCTTTGAAGGACT
CTTCTTTGTTCGAAAAGCACCCAAAATATGCTAAGGTTCTTCCAGTTGTCTCTGTCCCAGAGAGAATCAT
`

Here is what I have done

foreach $line(@File1){
    chomp($line);

($f1,$f2,$f3,$f4,$f5,$f6)=split (/\t+/,$line);
    push(@F1,$f1);
    push(@F2,$f2);

so on... }

@F1 contains Locations colunm(17042..17914,,) @F6 contains Synonym column (CAGL0D00176g)

same way I collected the all the upper limit of location of File 2 i.e(17914,25075,,) @B using

foreach $line(@File2){
    chomp $line;
    if ($line=~/\-(\d*)/){
}

So could anybody help/write code to get output as I specified above

Looking forward for your code

Thank you