I forgot to respond to this part of the OP:
If the header element of fasta (eg: FZGA34177.b1) matches <info_name> (eg: <info_name>FZGA34177.b1</info_name>), it will check the hash value (eg: <it_size>35000</it_size>) and write the fasta sequence (header and sequence both), to a new file (eg: 35000.fasta.output). Similarly, there will be various other files corresponding to "it_size". The issue is these XML files and fasta files are multiple files, and I thus need to read all of them all together in order to find the sequence corresponding to <it_size>.

I'm not sure I follow all that, but it sounds like you want to build an index of your fasta files (think of it as a hash, keyed by the "info_name" strings in the fasta files, and having the sequence strings as values), so that as you get the pairs of "info_name" and "it_size" fields from the XML data, you just look up the info_name in the hash index, and do whatever you need to do with the corresponding fasta sequence strings.

In reply to Re: Parse XML and compare with Fasta in Perl by graff
in thread Parse XML and compare with Fasta in Perl by ad23

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