Kelly Vincent wrote, On 04/07/2011 11:35 AM:
> That opening-the-entire-file inefficiency in our sam_to_bam.py was 
> fixed quite some time ago (4/30/2010, in 3724:007f175c8b88). It has 
> used getsize since then.

Fixed is one thing, pushed to "dist" is another :)
====
$ hg clone https://bitbucket.org/galaxy/galaxy-dist galaxy_test2
requesting all changes
adding changesets
adding manifests
adding file changes
added 5071 changesets with 21893 changes to 4940 files
updating to branch default
3256 files updated, 0 files merged, 0 files removed, 0 files unresolved
$ cd galaxy_test2/
$ hg tip
changeset:   5070:ca0c4ad2bb39
tag:         tip
user:        Greg Von Kuster <g...@bx.psu.edu>
date:        Wed Feb 16 10:14:24 2011 -0500
summary:     When rendering the contents of a data library, make sure a 
LibraryDataset has an associated LibraryDatasetDatasetAssociation.  There 
should always be an ldda, but some users running their own instances have 
reported that some of their LibraryDatasets are missing these associations.
$ sed -n '148,152p' tools/samtools/sam_to_bam.py 
        if returncode != 0:
            raise Exception, stderr
        if len( open( tmp_aligns_file_name ).read() ) == 0:
            raise Exception, 'Initial BAM file empty'
    except Exception, e:
====
It only exists in "galaxy-central", not in "galaxy-dist" which is what you 
recommend people to use.

Both me and Ryan have this line of code, and I'm sure we've both pulled since 
April 2010.

> It's really just intended to catch weird errors that don't throw an
> actual error (also, I think that if the sam file has no header, no
> info would be output into the bam file).

Nope - look at my example below - an invalid sam file still generates a 
non-empty BAM file.
This happens because of the "-t" parameter: samtools takes the header 
information from another file and generates the BAM file before even reading 
the SAM file.

> It seems somewhat more
> informative to tell the user the file is empty rather than just
> "successfully" output an empty file.
> 

Depends on your definition of "informative" - in this case the error message 
was not so informative at all, to a point a traceback was needed...


-gordon

> 
> 
> On Apr 7, 2011, at 1:05 AM, Assaf Gordon wrote:
> 
>> Just another example why python's misleadingly simple idioms are 
>> quite dangerous in production code (couldn't help myself from 
>> teasing about python... sorry about that).
>> 
>> Seems like line 150 in "sam_to_bam.py" tries to read the entire
>> BAM file into memory just to find out if it's empty or not...
>> 
>> As a stop gap solution with minimal changes, change line 150 from:
>>  if len( open( tmp_aligns_file_name ).read() ) == 0: to if len( 
>> open( tmp_aligns_file_name ).read(10) ) == 0:
>> 
>> Which will read up to the first 10 bytes (instead of the entire 
>> file).
>> 
>> A slightly better (but still wrong) solution is to simply check
>> the file size, with: if os.path.getsize(tmp_aligns_file_name) ==
>> 0:
>> 
>> But it's still wrong because even an invalid sam file will create
>> a non-empty BAM file (when using "samtools view -bt") - the BAM
>> file will still contain the chromosome names and sizes.
>> 
>> Example: ======== $ cat mm9.fa.fai chr1    197195432       6 50
>> 51 chr10   129993255       201139354       50      51 chr11 
>> 121843856       333732482       50      51 chr12   121257530 
>> 458013223       50      51 chr13   120284312       581695911 50
>> 51 chr13_random    400311  704385924       50      51 chr14 
>> 125194864       704794249       50      51 chr15   103494974 
>> 832493018       50      51 ... ...
>> 
>> $ cat 1.sam Hello World This is not a SAM file
>> 
>> $ samtools view -bt mm9.fa.fai -o 1.bam 1.sam [sam_header_read2]
>> 35 sequences loaded. [sam_read1] reference 'This is not a SAM file'
>> is recognized as '*'. [main_samview] truncated file.
>> 
>> $ ls -l 1.* -rw-r--r-- 1 gordon hannon 348 Apr  7 00:57 1.bam 
>> -rw-r--r-- 1 gordon hannon  35 Apr  7 00:57 1.sam ========
>> 
>> 
>> So in short, this whole sam-to-bam wrapper tool is not suitable
>> for large SAM files (if they don't fit entirely in memory), and not
>> for error checking of invalid SAM files.
>> 
>> 
>> -gordon
>> 
>> 
>> On 04/07/2011 12:30 AM, Ryan Golhar wrote:
>>> Here's what I get:
>>> 
>>> (galaxy_env)[galaxy@vail pbs]$ sh ./big.sh Samtools Version: 
>>> 0.1.14 (r933:170) Traceback (most recent call last): File 
>>> "/home/galaxy/galaxy-dist/tools/samtools/sam_to_bam.py", line 
>>> 150, in __main__ if len( open( tmp_aligns_file_name ).read() )
>>> == 0: MemoryError Error extracting alignments from 
>>> (/home/galaxy/galaxy-dist/database/files/000/dataset_785.dat), 
>>> (galaxy_env)[galaxy@vail pbs]$
>>> 
>>> 
>>> 
>>> On 4/6/11 7:29 PM, Assaf Gordon wrote:
>>>> Ryan,
>>>> 
>>>> Since we're shooting in the dark here, best to try and 
>>>> understand what's the exception.
>>>> 
>>>> Add the following line to the beginning of "sam_to_bam.py": 
>>>> import traceback
>>>> 
>>>> and add the following line to "sam_to_bam.py" line 156 (before 
>>>> the call to "stop_err"): traceback.print_exc()
>>>> 
>>>> Hopefully this will print out which exception you're getting, 
>>>> and where is it thrown from.
>>>> 
>>>> -gordon
>>>> 
>> ___________________________________________________________ Please 
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> 

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