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  • HTSeq errors

    Hi, dear patrons

    i had an error when running HT-seq in python.

    ******$ python
    Python 2.6.1 (r261:67515, Aug 2 2010, 20:10:18)
    [GCC 4.2.1 (Apple Inc. build 5646)] on darwin
    Type "help", "copyright", "credits" or "license" for more information.
    >>> import HTSeq
    >>> import numpy
    >>> htseq-count --mode=intersection-nonempty CAR01_tophatHits_sorted.bam merged.gtf >> CAR01_gene_counts.txt
    File "<stdin>", line 1
    htseq-count --mode=intersection-nonempty CAR01_tophatHits_sorted.bam merged.gtf >> CAR01_gene_counts.txt
    ^
    SyntaxError: invalid syntax

    i cannot figure out the problem. Can anyone give me some suggestions and hints?

    I will appreciated it a lot.

    Best wishes
    Li

  • #2
    Try executing the htseq-count command from the command line rather than within python.

    Comment


    • #3
      Thanks, dpryan!

      I made a file named as htseq_count.py and then execute it in the terminal.

      The content of the file is as follows:
      #!/usr/bin/python2.6 -tt

      import numpy
      import HTSeq

      htseq-count --mode=intersection-nonempty /users/shared/HTSeq/CAR01_tophatHits_sorted.bam /users/shared/HTSeq/merged.gtf >> CAR01_gene_count.txt

      But I still got errors shown here:
      File "./htseq_count.py", line 6
      htseq-count --mode=intersection-nonempty /users/shared/HTSeq/CAR01_tophatHits_sorted.bam /users/shared/HTSeq/merged.gtf >> CAR01_gene_count.txt
      SyntaxError: can't assign to operator

      It seems that python cannot find htseq-count. In python shell, i typed dir(HTSeq) and didnot find "htseq-count".

      It is my first experience with python. Sorry for my naive questions. Can someone point out my error? Thanks!

      Comment


      • #4
        Don't bother with python, execute the command directly in the shell. No shell scripting, nothing like that. Just open a terminal and type:
        Code:
        htseq-count --mode=intersection-nonempty /users/shared/HTSeq/CAR01_tophatHits_sorted.bam /users/shared/HTSeq/merged.gtf > CAR01_gene_count.txt
        from an appropriate location.

        Comment


        • #5
          Thanks a lot, dpryan! It works!

          Comment

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