Re: [Samtools-help] SAM to BAM

[Mic]

Hello,

is it a way to do it with pysam?

Thank you in advance.

On Mon, Oct 17, 2011 at 11:15 PM, Tim Fennell <tfen...@broadinstitute.org> wrote:

And if you're not tied to pysam you can use Picard's sort sam to do it all in one pass:
       java -Xmx2g -jar SortSam.jar I=your.sam O=your.bam CREATE_INDEX=true

-t

On Oct 17, 2011, at 9:06 AM, Peter Cock wrote:

> On Mon, Oct 17, 2011 at 1:11 PM, Mic <mict...@gmail.com> wrote:
>> Hello,
>> Is there a way to convert SAM file to sorted BAM file and generate also BAI
>> file with pysam?
>> Thank you in advance.
>
> With samtools at the command line,
>
> samtools view -b -S example.sam | samtools sort - example
> samtools index example.bam
>
> I know you can easy call samtools from pysam, not sure if you
> can do the pipe trick to avoid extra steps:
>
> samtools view -b -S example.sam > example_unsorted
> samtools sort example_unsorted.bam example
> rm example_unsorted.bam
> samtools index example.bam
>
> Peter
>

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[Brett Bowman]

I am also curious about this.

I'm using PySam to QC some very large BAM files, but I'm starting to get some SAMs as well.  The problem is the unsorted SAMs take a lot longer to access, so I'd like to convert them to BAM and sort them as a pre-processing step.

I've tried pysam.view(), but it says the -o option is disabled.  In addition, since its within Python I can't use a command-line redirect '>' to do it either.

Is this currently possible?  If so how.

-Brett

Thank you in advance.

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[Ben Schiller]

As a workaround, I do -ofoo to save to foo, but it can fail on some systems, so use carefully

Ben

[Brett Bowman]

Sweet, that works.  Thanks Ben.

Are there any plans for when/if a non-workaround option will be made available?

/b/

[Ben Schiller]

Andreas would know. I forget why it was disabled in the first place -- I think it may have been an issue with Windows or Mac? You can remove the check and recompile your own copy if you want. It's in pysam/csamtools.pyx line 2867 (in the current hg source):

if "-o" in args: raise ValueError("option -o is forbidden in samtools view")

So if you need, just add a comment (#) and delete the csamtools.c file (don't commit that to the upstream code, obviously)

I went a different route and wrapped the command line samtools because I wanted to pipe things more easily. You can look at my align.py script if you want https://github.com/benjschiller/seriesoftubes . Note: the PolledPipe class I wrote does not support Windows.

Ben

[Mic]

http://code.google.com/p/pysam/issues/detail?id=48