Same error as before: 'Not a HASH reference at line 12' (which is: push @{$ret},join '|',).

The statement isn't over, keep following the comma 

  push @{$ret},join '|', 
      $_->{Hit_def}, ## HASH ACCESS
      $_->{Hit_num}, ## HASH ACCESS
      $_->{Hit_hsps}->{Hsp}->{Hsp_identity};  ## HASH OF HASH OF HASH 
+ACCESS

[download]

So is it related to the input file?

Absolutely, sometimes a Hit_hsps doesn't have a Hsp_identity or an Hsp ... if the data isn't there its not there

You can cure death with judicious use of block eval and subroutines and Data::Diver :) See Re: Parsing SOAP::Lite results (with Data::Diver), Re: $var{el} += 1 vs $var{el} = $var{el} + 1, Re: Problem with counting the nodes in a hash created by XML::Simple (use XML::Rules, Data::Diver )

So is it related to the input file? Maybe my XML file is somehow messed up.

Yes, its because you're using XML::Simple when you want to use XML::Rules

XML::Rules does by default what folks expect from XML::Simple

See examples Re: XML::Simple Not getting the proper output. ( xml2XMLRules, Re^3: Parsing XML (XML::Rules xml2XMLRules )

The more files you give xml2XMLRules the better the rules it spits out for you to plug into XML::Rules, the more stable the resulting data structure

... ? ... ! ...

You can always use rehohy to visualize your data like Re^3: Parsing a JSON response, Re: A "simple" question regarding accessing a value in a complex data structure., Re^2: Array of structures within an array of structures.

See also references quick reference, hashes are curly
Re: How to traverse a two dimentional array in a constructor?, Re: Parsing SOAP::Lite results,, Re: Trouble accessing Hash of Arrays (troubleshooting basics),
Re^5: Combining 3 files,

In reply to Re^7: multiple XML fields in one line by Anonymous Monk
in thread multiple XML fields in one line by smice

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