This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Please Suggest Some Command-Line Tools For Displaying Abi Trace File On Windows Os, Just Like Abiview.

Hi,

I need to display ABI trace file in PNG format in command-line way. I try abiview but failed on my computer. So, do any other command-line tools available for this task?

software command-line
• 6,857 views • link
updated by Biostar Biostar • written by Wubin Qu Wubin Qu

In what way did it fail? Do you mean it failed because it is not a Win32 application?

• 0 views • link
written by Sabrewolfy • Sabrewolfy

you will only waste time with Windows, as its support for command line tools and terminals is very poor. Moreover, it will be complicated to install mostly any command line tool. Ubuntu is free and you can install it in 20 minutes.

• 125 views • link
written by Giovanni M Dall'Olio Giovanni M Dall'Olio

What do you mean by "command-line"?

• 0 views • link
written by Sabrewolfy • Sabrewolfy

3 answers

Try trev from Staden although I suspect this means you will have to compile it from source, I don't think Staden release Windows binaries. Mind you neither will abiview work on Windows - as EMBOSS is a Unix set of packages..

• 0 views • link
written by User 59 User 59

Thanks! I will have a try.

• 0 views • link
written by Wubin Qu Wubin Qu

FinchTV has worked for me in the past and supports OSX, Windows, Linux, and Solaris. Plus your traces look nice and pretty.

• 1 views • link
written by Aaronquinlan Aaronquinlan

The poster is looking for a command-line tool.

• 0 views • link
written by Sabrewolfy • Sabrewolfy

@aaron: The link you posted above shows command-line usage in non-Win32 cases, non of which show how to automatically export a PNG image (see OP question) of the trace data. The OP wants a command-line program for Windows to create an image file of the trace, presumably to use as part of a pipeline.

• 0 views • link
written by Sabrewolfy • Sabrewolfy

You're quite right. Poor answer on my part. Apologies.

• 0 views • link
written by Aaronquinlan Aaronquinlan
  • There is an official Windows port of the EMBOSS suite. I've not managed to get abiview to produce good-quality output. It exports the trace as separate image files of 40 bases (default) each. This can be changed with the -window parameter. However, abiview then exported the entire trace into one image file which was the same size as each of the separate files, so that the entire trace was squashed into 800 pixels. abiview may not be the best solution, unless someone else can post further assistance.
  • BioEdit/BioLign (click the image for download or go here) have an option "Edit -> Copy trace window as a bitmap" which works well. It's not a "command-line" program though.
• 0 views • link
updated by Ram Ram • written by Sabrewolfy • Sabrewolfy

Thanks. abiview is OK and I solved the problem when I using the abiview first time. Now it's pretty good.

• 0 views • link
written by Wubin Qu Wubin Qu

Log in to answer this question.

More posts like this