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Re^5: (OT) help reading a bgzip file

by pmqs (Pilgrim)
on May 04, 2011 at 10:49 UTC ( #902846=note: print w/replies, xml ) Need Help??


in reply to Re^4: (OT) help reading a bgzip file
in thread (OT) help reading a bgzip file

If file is really just a gzip file then try checking that it isn't corrupt
gunzip -tv file.bgzip
Looking at http://samtools.sourceforge.net/SAM1.pdf (which I think is the reference for the file format used by bgzip) it looks like the payload data (BAM) in the bgzip file is not ascii text - that would explain why you are seeing non-ascii text when you run it through zless.

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[tobyink]: *in your grep block
[tobyink]: You can use grep { $_ =~ /.*$in.*/; } @my_modules but why not stick to grep(/.*$in.*/, @my_modules)? (The latter is faster.)
[shmem]: Lady_Aleena, in the first example grep evaluates the result from grep and if true, returns $_. In the second, it always returns $_
[shmem]: ..the result from the pattern match
[Lady_Aleena]: tobyink, I did after I failed to get the BLOCK to work. I can't seem to get my brain around grep BLOCK, though I'm okay with grep EXPR.
[shmem]: so in the second example grep returns all true elements of the list passed
[Lady_Aleena]: Okay, so grep BLOCK is not like map BLOCK where something might need to be returned at the end.
[tobyink]: grep { $_ =~ /.*$in.*/; } @my_modules should work just fine. The problem is that you were adding on ;$_ at the end of the block. Why were you doing that?
[Lady_Aleena]: tobyink, I was thinking map.
[tobyink]: Something does need to be returned at the end not $_ though. You need to return (something that will be evaluated as) a boolean.

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