As a rule, don't trust data. Or rather, trust but verify.

I recommend that you put in sanity checks to confirm that the first line, the last line, and everything in between, is what you expect. For example, what happens if you get a first column that does not match the pattern /Chr\d+/ (aka chromosome21), but instead get ChrX, or Chr?, or ? instead? What happens if instead of getting a reference sequence id (e.g. NT_113958) that you can pass on to the genome browser, you get something unique to the research organization providing the data (e.g. adhoc_1234)? Those are just two examples of gotchas that bit me when processing supposedly well formed genetics data.

I raise specific issues around bioinformations, but the mindset applies to all processing. If you have source data assumptions, have your program verify them.

Scott\b

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.