compare two Fasta files

[acyrocks]

Hi,
I am new in NGS and have very little knowledge in tools used for analyzing sequences generated by NGS. Here, I have a problem and think somebody with good perl script skill may be able to help me out:
I have two Fasta files like below:

File1:
>a
GVKKDVKCTTTGGG
.
.
>f
AAATTTGGGCCCEEE
>g
SSSGGGYYYTTTGTFR
.
.
>x
DDDGGGYYYTTTGTFR
.
.
.

File2:
1>
GVKKDVKCTTTGGG
.
.
>41
FFFGGGYYYTTTGTFR
.
.
>200
AAATTTGGGCCCEEE
.
.
>1000
SSSGGGYYYTTTGTFR
.
.
.

Many but not all sequences are identical in these two files. I would like to compare each sequence of the first file with the second file and make a following table:

a GVKKDVKCTTTGGG 1
f AAATTTGGGCCCEEE 200
g SSSGGGYYYTTTGTFR 1000
x DDDGGGYYYTTTGTFR 0
.
.
.

In the table, the first column is the header of each sequence of the first file. The second column is each sequence of the first file and the third column is the header of the second file with the identical sequence with the first file. If there is no sequence identical in the second file, then use number zero instead.
Appreciate if someone can help me out.
Thanks a lot.
Acyrocks

[Torst]

Is this a homework question?

[krobison]

It sounds like one, but in any case it is pretty simple to hash this out in not much code :-)

[Torst]

Agreed, I think you've given him the key idea.

[acyrocks]

Thanks for replying. No, it's not a home work. I don't have much Perl knowledge, except have read couple of chapters and know how to run a script. I may spend more time in future to learn it if I found some time. If you guys can help me out, I appreciate it.

[Torst]

Do you know how to program in any particular language? Perhaps we could assist you to implement it in a language you have experience in. If not, someone will probably give you a solution to try.

[rahularjun86]

Dear acyrocks,
Please run the attached code using following command(unix):
perl for_seqanswer_fasta_formatter.pl file1.fasta file2.fasta out.fasta
It is working fine here
Best wishes,
Rahul

[acyrocks]

Thanks so much, Rahul.
I tried your code and it works for most parts. However, it skip the sequences in file1 which are not identical to any sequences in the file2. I hope these sequences are still include in out file and with zero printed on the third column. I think this could be easy fix for you. Thanks again.