pysam.AlignmentFile not working...

[Matthew Cserhati]

Hello all,

I keep getting this error:

    samfile = pysam.AlignmentFile(infile,"rb")

AttributeError: 'module' object has no attribute 'AlignmentFile'

I've tried conda, pip, manual github install but no luck. My pip version is 0.16.

Thanks, Matthew

[Marcel Martin]

One reason for this could be that you have a leftover or broken pysam
installation in the user site-packages directory
(~/.local/lib/pythonX.Y/site-packages/), which can happen if you have
previously used 'pip install --user' to install pysam.

To debug this, try to find out from where the module is actually imported:

python3 -c 'import pysam; print(pysam.__file__)'

You may want to delete or rename the ~/.local/lib/python* directories.
Alternatively, you can do "export PYTHONNOUSERSITE=1" to temporarily
prevent Python from using the user site directory.

Regards,
Marcel

[Matthew Cserhati]

Hello Marcel,

I erased all site-package directories, and tried reinstalling pysam, but no luck.

I do not have any ~/.local/lib/python* directories.

I also set "export PYTHONNOUSERSITE=1", and tried running my python script but the error persist.

What else can I try?

Thanks,

Matt

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[Marcel Martin]

On 14/06/2021 20.25, Matthew Cserhati wrote:
> I erased all site-package directories, and tried reinstalling pysam, but
> no luck.
> I do not have any ~/.local/lib/python* directories.
> I also set "export PYTHONNOUSERSITE=1", and tried running my python
> script but the error persist.

Are you on Linux or macOS? What does the command that I gave in my
previous mail output? Did you write the script yourself? (Do you know
how to program in Python?) Which exact command did you use for installation?

Posting more extensive log messages might also be helpful.

Marcel

[Matthew Cserhati]

Hi Marcel,

Thanks again for your help.

1. I am on Linux

2. I wrote the python script myself and it has run successfully previously, but now it doesn't.

3. I suspect it is as you say a broken installation

4. I installed pysam-0.16.01 this way:    pip install pysam          at the command prompt

5. error message:

Traceback (most recent call last):
  File "pysam.py", line 40, in <module>
    main(sys.argv[1:])
  File "pysam.py", line 33, in main

    samfile = pysam.AlignmentFile(infile,"rb")
AttributeError: 'module' object has no attribute 'AlignmentFile'

================

the script:

#!/usr/bin/python

import re, os, sys, getopt;
import pysam;

def main(argv):
    infile = ''
    outfile = ''
    chrom, start, end = 0, 0, 0

    try:
        opts, args = getopt.getopt(argv,"hi:o:c:s:e:",["ifile=","ofile=","chrom=","start=","end="])
    except getopt.GetoptError:
        print ('pysam.py -i <inputfile> -o <outputfile> -c <chrom> -s <start> -e <end>')
        sys.exit(2)
    for opt, arg in opts:
        if opt == '-h':
            print ('pysam.py -i <inputfile> -o <outputfile> -c <chrom> -s <start> -e <end>')
            sys.exit()
        elif opt in ("-i", "--ifile"):
            infile = arg
        elif opt in ("-o", "--ofile"):
            outfile = arg
        elif opt in ("-c", "--chrom"):
            chrom = int(arg)
        elif opt in ("-s", "--start"):
            start = (arg)
        elif opt in ("-e", "--end"):
            end = arg

    c = 0

    samfile = pysam.AlignmentFile(infile,"rb")

    for read in samfile.fetch(chrom, start, end):
        c += 1

    print(c)

if __name__ == "__main__":
    main(sys.argv[1:])

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[Marcel Martin]

On 14/06/2021 21.02, Matthew Cserhati wrote:
> Traceback (most recent call last):
>   File "pysam.py", line 40, in <module>
>     main(sys.argv[1:])
>   File "pysam.py", line 33, in main
>     samfile = pysam.AlignmentFile(infile,"rb")
> AttributeError: 'module' object has no attribute 'AlignmentFile'

[...]

>         print ('pysam.py -i <inputfile> -o <outputfile> -c <chrom> -s

Is your script actually called 'pysam.py'? Then it will import itself
when you run "import pysam". Try to rename the file.

Marcel

[Matthew Cserhati]

renamed script but still gives error

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[Matthew Cserhati]

now I get this:

(env) [mcserhati@ftlxsvr08 umi]$ python psam.py -h

Traceback (most recent call last):

  File "psam.py", line 4, in <module>
    import pysam;
ImportError: bad magic number in 'pysam': b'\x03\xf3\r\n'

[Marcel Martin]

On 14/06/2021 21.12, Matthew Cserhati wrote:
> now I get this:
>
> (env) [mcserhati@ftlxsvr08 umi]$ python psam.py -h
> Traceback (most recent call last):
>   File "psam.py", line 4, in <module>
>     import pysam;
> ImportError: bad magic number in 'pysam': b'\x03\xf3\r\n'

We took this off list, and Matthew now got it working by deleting the
.pyc files.

Marcel