Is there a utility to detect how sff files are compressed?

[LizBent]

Hi all. My lab partner has given me some sff files to work with, file name format NAME.sff.

They seem to be compressed- the biopieces command read_sff does not work with them, and when I try to look at the files I get a warning that they may be in binary format, then when the file is open I see only gibberish.

How can I tell how they were compressed? there is nothing in the file name to indicate that the files are compressed, or how. My lab partner is off on vacation and I can't reach him, so I have no way to know if he took off a file extension or used some kind of compression software before he gave me these files. Is there a utility that can help with this? I also have fasta and qual files I can work with that seem uncompressed, but I would prefer to use the sff files since the read_sff command in biopieces allows for automatic trimming of adapter keys using the -c option, and that would be pretty nice.

[maasha]

sff files are binary encoded but not compressed.

Read about sff files here.

If Biopieces read_sff fail it may very well indicate a corrupt file. You can test if the file is compressed with the UNIX command "file". On my system this shows:

maasha@mel:~$ file test.sff.gz 
test.sff.gz: gzip compressed data, was "test.sff", from Unix, last modified: Tue Feb  8 20:46:46 2011
maasha@mel:~$ gunzip test.sff.gz 
maasha@mel:~$ file test.sff 
test.sff: data

[LizBent]

Thanks a lot- the file does seem to be corrupt (I tried a different sff file and it was read OK by read_sff, so it may just be the one file) and not compressed. This makes sense now.

[maubp]

I'd look at the first few bytes with hexdump - that is enough to spot commonly used compression formats, or if it is an SFF file.