Re: Variables not entering sub routine

A few comments on style and readability

Pick an indentation style and use it. perlstyle gives good advice on one popular choice.
I don't know if your regexen are really complicated or just long. The /x modifier will permit whitespace, including newlines, and comments in the regex. You code could use that.
You haven't shown what the data really looks like. There may be a better way of parsing it. Show some data and we may be able to point you to a better way.
I don't see what benefit you're getting from prototypes.
Uncomment use strict; and pitch in a use warnings;. They are a help in untangling errors.
Your subroutines &check_gene and &check_gene_seq have prototypes, but never look at the argument, only at whatever $_ is at the point of call.
The &extract_seq sub is called with one more argument than the prototype calls for, and the extra is never used.

Update: Just noticed - my 1000th node.

After Compline,
Zaxo

Comment on Re: Variables not entering sub routine

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Re: Re: Variables not entering sub routine by matth (Monk) on Dec 16, 2002 at 13:51 UTC
An example of the two lines of interest in the intput text is shown below: `<gene id = "251" label = "gene_of_interest"> <gene_seq id = "321" status = "Sanger source DNA code" CDS_number += "1" number_of_CDSs = "" sequence_source "/data/databases/flatfiles/ +sequences/species/genome/embl/ch1.embl" startpos = "2435591" endpos = + "2436562" startopen = "1" endopen = "1" complement = "F"/>` [download] If I could ask an XML question in relation to this. Does any XML convention suggest that the two ids here should have the same value?	[reply] [d/l]
Re: Re: Re: Variables not entering sub routine by Zaxo (Archbishop) on Dec 16, 2002 at 13:59 UTC
If your data is valid XML, run, don't walk, to the XML namespace. Something there will save you a bazillion headaches and make this job easy. Yes, you haven't yet reached a closing </gene> tag so the gene_seq data is part of gene's data. If there is no closing tag, you don't have valid XML. After Compline, Zaxo	[reply]