On 4/7/11 12:13 PM, Assaf Gordon wrote:
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... -gordonOn 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 keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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