Hi,
Infernal is a very helpful suite of tools.
Unfortunately, the cmscan tabular output have issues related to fields delimiter (although we all know that Infernal’s guide says “tab-delimited files are a minor evil in the world”).
Using the galaxy.eu version of cmscan, we always have to manually correct the tabular outputs in order to plot/interpret results;
Bad times whenever the term “Betaproteobacteria_toxic_sRNA RF02278” appears;
This record has
[target name] [space] [target accession] format:
| target name | target accession |
|---|---|
| Betaproteobacteria_toxic_sRNA RF02278 | |
| Betaproteobacteria_toxic_sRNA RF02278 | |
| . |
The correct would be
[target name] [tab] [target accession]:
| target name | target accession |
|---|---|
| mir-515 | RF00639 |
| sn2417 | RF01222 |
| bxd_4 | RF01932 |
| . |
Also, headers and values of some columns are pretty messed up:
| strand | trunc | pass | gc | bias | score | E-value | inc | description of target |
|---|---|---|---|---|---|---|---|---|
| no | 1 0.40 | 1.1 | 14.9 | 0.5 ? | microRNA mir-515 | |||
| no | 1 0.45 | 0.2 | 12.2 | 1.2 ? | Small nucleolar RNA sn2417 | |||
| no | 1 0.42 | 2.5 | 11.7 | 1.5 ? | Bithoraxoid conserved region 4 | |||
| no | 3 0.30 | 0.4 | 12.7 | 2 ? | Renin stability regulatory element (REN-SRE) | |||
| no | 1 0.46 | 0.3 | 14.6 | 2.2 ? | Small nucleolar RNA R72 | |||
| . | ||||||||
| I think it would be good for the galaxy.eu users if this was corrected, as it could prevent misinterpretations of hits counts and it would save a good time of manual correction. |
Is it feasible? Or ‘it is what it is’ because it’s from Infernal itself?
Thanks.