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Old 12-18-2009, 01:58 PM   #1
Cresten
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Location: Ithaca, NY

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Default sff_extract Syntax Error

Hello all-

Relatively new to the world of biopython, so I am getting snagged on transferring over to the language. My most recent hangup is in the process of attempting to convert a Roche 454 Titanium .sff file to a fasta file. I am attempting to implement the freely available sff_extract and believe I have been successful of at least getting biopython to read the script (hopefully, I can get the help functionality to spit out the information about the module). However, I get an error when trying to implement it on our .sff file. Here is the error:

>>>sff_extract Test.sff
File "<stdin>", line 1
sff_extract Test.sff
^
SyntaxError: invalid syntax

The pointer is under the little t. Any insight or advice would be most useful!

Thanks in advance.
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Old 12-18-2009, 02:07 PM   #2
maubp
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Hi,

sff_extract is written in Python, but is not part of Biopython. We do however have some SFF support "in the pipeline" based on some code contributed by the ssf_extract author Jose Blanca.

As to your problem, sff_extract is a script designed to be run at the operating system command line, not at the python prompt.

Peter
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Old 12-20-2009, 06:19 PM   #3
Cresten
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Default Thanks!

Hi Peter-

Thanks! Got it working! Now I just have to figure out what the results mean... haha.

-Cresten
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Old 12-21-2009, 12:16 AM   #4
linikujp
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Quote:
Originally Posted by maubp View Post
Hi,

As to your problem, sff_extract is a script designed to be run at the operating system command line, not at the python prompt.

Peter
I got the same problem.
Thank you very much!
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