8.4. Handling Input and Output

8.4.1. Handling Sequences

Under the wEMBOSS interface the pages for programs that operate on sequences provide a radio button Sequence(s) with 3 options :

from the EMBOSS databases or a current project file

Here you get a box where you can type in an USA as you would while working at the command line. You can operate on a "public" sequence using the dbname:seqname syntax or on a "private" sequence by typing just the name of the data file that contains the sequence. You can also use List Files and the asis syntax. A minor restriction is that under the current version of wEMBOSS a complete databank must always be specified as dbname:*, not as dbname, and that the first item in a List File should not contain a wild card * or ?. The [begin:end:reverse] range specifications however do not work, but you can use the begin/end/rev boxes. To get your personal sequences into a data file you can, of course, use the New file or the Upload functions in the Project Management page (see above).

from the local computer/PC

You can input sequences from files (naturally, in any format) stored on your own local computer. You can type the name of the file directly into the box (e.g. C:\Tmp\my.seq) or use the Browse button. The sequence file will be copied to the server and stored in the project.

from the sequence selector (nucList or protList)

This is the default option and was designed by M. Colet to save excessive typing when you want to run many jobs using the same sequence. When you create a new project, files named nucList and protList are automatically created. You can edit them and type in the USAs of the sequences you most often use. The content of these files will appear in a selector, from which you can choose them. Note that you cannot select more than one sequence. If you want to operate on several sequences at the same time, you must create separate List Files (with any name you find appropriate); you can type the USA pointing to such a List File in nucList or protList as list::xxx. Note that, to make your work easier still, the New file function in the Program Management page offers an add filename to nucList/protList option. Note also that if a program has written its output as a List File and you want to work with sequences from this list, you can always rename nucList to something else and then rename your result file to become the new nucList.

For programs that write sequences you can choose the format you want with the Output file format selector, which can be found in the OUTPUT section near the bottom of the page for that program.

8.4.2. Handling Graphical Output

wEMBOSS by default saves graphical output in PNG format but allows PostScript as alternative. PNG is displayed inside the program output page. You can save it if you wish. PostScript is not displayed, but you can save it.

8.4.3. Handling Various Kinds of Input/Output Data

For programs that take as their input a data file and use, by default, a file from the EMBOSS distribution wEMBOSS offers you 3 different ways to select alternatives:

from EMBOSS data

You can choose, from a selector, a file from the EMBOSS distribution. For nucleotide symbol comparison tables, amino acid symbol comparison tables and codon usage tables wEMBOSS gives you a list with the relevant choices. For other data you get a list with all the available *.dat files (although this will of course rarely be useful).

from project(s) data

You can choose from a selector that contains the names of the data files in the current project and also the names of the files in the projects higher up in the hierarchy. Note that you can use this feature by installing into a "project" a file with data needed by different "subprojects". You can run the program embossdata with the Fetch a data file? switch set to y to put a copy of an EMBOSS distribution file into your project and then Edit it.

from local data

You can import a file stored on your PC.

wEMBOSS has selectors for Report formats, Alignment formats and Codon Usage Table formats, which allow to choose which format you want for your output. You can find them in the OUTPUT section near the bottom of the page for the program.