Question

Please Suggest Some Command-Line Tools For Displaying Abi Trace File On Windows Os, Just Like Abiview.

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14.2 years ago

Wubin Qu ▴ 170

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 • 5.5k views

ADD COMMENT • link updated 11.1 years ago by Biostar 20 • written 14.2 years ago by Wubin Qu ▴ 170

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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.

ADD REPLY • link 13.7 years ago by Giovanni M Dall'Olio 28k

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

ADD REPLY • link 13.7 years ago by Sabrewolfy ▴ 80

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What do you mean by "command-line"?

ADD REPLY • link 13.7 years ago by Sabrewolfy ▴ 80

score 2 · Answer 1 · 2010-09-24

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14.2 years ago

User 59 13k

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..

ADD COMMENT • link 14.2 years ago by User 59 13k

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Thanks! I will have a try.

ADD REPLY • link 14.2 years ago by Wubin Qu ▴ 170

Ram · Answer 2 · 2011-03-11

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13.7 years ago

Aaronquinlan 12k

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

ADD COMMENT • link 13.7 years ago by Aaronquinlan 12k

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

ADD REPLY • link 13.7 years ago by Aaronquinlan 12k

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The poster is looking for a command-line tool.

ADD REPLY • link 13.7 years ago by Sabrewolfy ▴ 80

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Sorry, I neglected that. It works from the command line too. http://www.geospiza.com/finchtv/help/pages/C-WorkingWithYourData/01-OpenFiles.html

ADD REPLY • link updated 5.2 years ago by Ram 44k • written 13.7 years ago by Aaronquinlan 12k

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@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.

ADD REPLY • link 13.7 years ago by Sabrewolfy ▴ 80

Ram · Answer 3 · 2011-03-11

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13.7 years ago

Sabrewolfy ▴ 80

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.

ADD COMMENT • link updated 5.2 years ago by Ram 44k • written 13.7 years ago by Sabrewolfy ▴ 80

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

ADD REPLY • link 13.7 years ago by Wubin Qu ▴ 170