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:
        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, 
        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.

$ 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.


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:
Error extracting alignments from
(galaxy_env)[galaxy@vail pbs]$

On 4/6/11 7:29 PM, Assaf Gordon wrote:

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"):

Hopefully this will print out which exception you're getting, and
where is it thrown from.


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