Minor (And Not So Minor) Annoyances in Bioinformatics. An Ongoing Saga

So today started out as a pretty frustrating morning due to random (not really random) failure in some analysis pipelines on some data I am trying to work on for a collaborator. The analysis has already taken far longer than expected for various reasons, some of which are my fault, and some of which aren’t. But given some of the issues that crop up I was inspired to post a little bit of a vent concerning things that end up just annoying me as a researcher in bioinformatics. Some of these are specific to today, some arent but I am putting them all here today anyway. In some cases I may call out specific software. In all cases I appreciate the work put into the tool by its developers. Often it is a tool I use a lot. Sometimes it is a specific case where it is symptomatic of larger issues in Bioinformatics software design. After all, if I thought the tool was complete garbage I wouldn’t care enough to vent about it (unless it was really widely used and terrible, but thats something for other posts). Ok, so in no particular order:

Inflexible and overly restrictive parsers

This particular complaint is something I just ran into when running the whole tuxedo suite on some data where I am doing something non-standard with non-standard references. Working on some viral transcriptomics where I have created synthetic genome and transcriptome references for the virus + human data, as both will be present in the RNA-Seq data and we want to capture the whole system. And this particular complaint is most frustrating when it happens while using a tool that is in the middle of a longer tool chain. Often it necessitates changing something about the reference data, which may necessitate going back and re-doing previous steps. In this case it doesn’t, it has just put the brakes on the analysis until I fix the reference and re-run this particular step.

In this case it is cuffmerge and the FASTA reference. Why, in 2016, does the parser for a widely used tool, require that all sequence containing lines in a FASTA record have the same length? That is ridiculous. We have had pretty flexible FASTA parsers for longer than cuffmerge was even a tool. Parsing FASTA isn’t THAT hard, even if the records end up being a bit non-standard.

This is an ongoing Saga of Rants… Stay Tuned

Written on June 10, 2016