Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #16
    Originally posted by liguow View Post
    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.



    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.

    Comment


    • #17
      Originally posted by mdb@wistar View Post
      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.

      Comment


      • #18
        Originally posted by liguow View Post
        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.

        Comment


        • #19
          Originally posted by mdb@wistar View Post
          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.

          Code:
          $ 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+'

          Comment


          • #20
            The bam2wig.py worked well after I change the genome version into a new one. Still do not know the reason.

            Comment

            Latest Articles

            Collapse

            • seqadmin
              Strategies for Sequencing Challenging Samples
              by seqadmin


              Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
              03-22-2024, 06:39 AM
            • seqadmin
              Techniques and Challenges in Conservation Genomics
              by seqadmin



              The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

              Avian Conservation
              Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
              03-08-2024, 10:41 AM

            ad_right_rmr

            Collapse

            News

            Collapse

            Topics Statistics Last Post
            Started by seqadmin, 03-27-2024, 06:37 PM
            0 responses
            12 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-27-2024, 06:07 PM
            0 responses
            11 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-22-2024, 10:03 AM
            0 responses
            53 views
            0 likes
            Last Post seqadmin  
            Started by seqadmin, 03-21-2024, 07:32 AM
            0 responses
            69 views
            0 likes
            Last Post seqadmin  
            Working...
            X