sff_extract Syntax Error

[Cresten]

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.

[maubp]

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

[Cresten]

Thanks!

Hi Peter-

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

-Cresten

[linikujp]

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!