[mdb@wistar]

Surprisingly to find that this problem is still not well resolved.

I write a python program "bam2wig.py" that is specially designed for RNA-seq, so it works fine for spliced read, for both single-end and pair-end, for both strand-specific and non-strand specific RNA-seq data.

The input BAM file should be sorted and indexed using SamTools before hand.

http://code.google.com/p/rseqc/downloads/list

Best,

Unfortunately, the bam2wig.py always gives error and quits:
DeprecationWarning: the sets module is deprecated
import sets

and it is not possble to modify the bam2wig.py downloaded from RseqC since it is read only.

[liguow]

Unfortunately, the bam2wig.py always gives error and quits:
DeprecationWarning: the sets module is deprecated
import sets

and it is not possble to modify the bam2wig.py downloaded from RseqC since it is read only.

Interesting. I used it without any problem (I am using python2.7). And, if you can download it, you can do whatever you want.

[mdb@wistar]

Interesting. I used it without any problem (I am using python2.7). And, if you can download it, you can do whatever you want.

funny, I too have python 2.7. I read somewhere that the 'sets' problem began with python 2.4 and using python2.3 or earlier versions may solve the problem. but sam2wig is not supported by older python versions, so I am stuck now
all other packages from RSeQC have worked except bam2wig.

[ESiPS]

funny, I too have python 2.7. I read somewhere that the 'sets' problem began with python 2.4 and using python2.3 or earlier versions may solve the problem. but sam2wig is not supported by older python versions, so I am stuck now
all other packages from RSeQC have worked except bam2wig.

Me too.

$ bam2wig.py -i 3Aligned.out.sorted.bam -s Drosophila_melanogaster.BDGP6.dna.toplevel.fa.fai.chrom.sizes -o 3Aligned.out.sorted.bam --skip-multi-hits -d --strand='1+-,1-+,2++,2--'
Skip multi-hits:True
Processing 211000022279100 ...
Processing 211000022279101 ...
Processing 211000022279102 ...
Processing 211000022279103 ...
Processing 211000022279104 ...
Traceback (most recent call last):
  File "/usr/local/bin/bam2wig.py", line 5, in <module>
    pkg_resources.run_script('RSeQC==2.6.1', 'bam2wig.py')
  File "build/bdist.macosx-10.10-x86_64/egg/pkg_resources/__init__.py", line 696, in run_script
  File "build/bdist.macosx-10.10-x86_64/egg/pkg_resources/__init__.py", line 1614, in run_script
  File "/usr/local/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-macosx-10.10-x86_64.egg/EGG-INFO/scripts/bam2wig.py", line 103, in <module>
    main()
  File "/usr/local/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-macosx-10.10-x86_64.egg/EGG-INFO/scripts/bam2wig.py", line 100, in main
    obj.bamTowig(outfile = options.output_prefix, chrom_sizes = chromSizes, chrom_file = options.chromSize, q_cut = options.map_qual, skip_multi=options.skip_multi,strand_rule = options.strand_rule, WigSumFactor=norm_factor)
  File "/usr/local/lib/python2.7/site-packages/RSeQC-2.6.1-py2.7-macosx-10.10-x86_64.egg/qcmodule/SAM.py", line 2597, in bamTowig
    if strandRule[key] == '+':Fwig[pos] +=1.0
KeyError: '1+'

[ESiPS]

The bam2wig.py worked well after I change the genome version into a new one. Still do not know the reason.