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BioPython meme.read MEME output

I am having trouble reading/parsing a meme output file with Biopython. Here is the code I am using:

>>> from Bio import motifs
>>> with open('meme.txt') as f:
    record = motifs.parse(f, 'MEME')

I receive this ValueError:

Traceback (most recent call last):
  File "<pyshell#55>", line 2, in <module>
    record = motifs.parse(f, 'MEME')
  File "C:\Python34\Scripts\Bio\motifs\__init__.py", line 77, in parse
    record = meme.read(handle)
  File "C:\Python34\Scripts\Bio\motifs\meme.py", line 41, in read
    length, num_occurrences, evalue = __read_motif_statistics(line)
  File "C:\Python34\Scripts\Bio\motifs\meme.py", line 219, in __read_motif_statistics
    length = int(ls[3])
ValueError: invalid literal for int() with base 10: '='

How can I fix this so the ValueError does not occur?

biopython
• 5,743 views • link
updated by Ram Ram • written by gable91794 • gable91794

which version of biopython are you using ?

• 1 views • link
written by GouthamAtla GouthamAtla

can you post first few lines of the "meme.txt" file ?

• 1 views • link
written by GouthamAtla GouthamAtla

I believe the output format is the same as all other meme runs I have used.

********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 4.10.1 (Release date: Wed Mar 25 11:40:43 2015 +1000)

For further information on how to interpret these results or to get
a copy of the MEME software please access http://meme-suite.org .

This file may be used as input to the MAST algorithm for searching
sequence databases for matches to groups of motifs.  MAST is available
for interactive use and downloading at http://meme-suite.org .
********************************************************************************

The run was of 4000 peptide sequences.

• 0 views • link
updated by Ram Ram • written by gable91794 • gable91794

See discussions here: https://github.com/biopython/biopython/issues/461

This may be due to format of meme.txt. Whether your file has "MEME" in it like:

MOTIF  1 MEME    width =  19  sites =   3  llr = 43  E-value = 6.9e-002

or just

MOTIF  1        width =  19  sites =   3  llr = 43  E-value = 6.9e-002

?

• 0 views • link
updated by Ram Ram • written by GouthamAtla GouthamAtla

1 answer

I think the length in the file is float,which is supposed to be integer.

int('55063.000000')
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ValueError: invalid literal for int() with base 10: '55063.000000'
• 1 views • link
updated by Ram Ram • written by nvijay.1991 • nvijay.1991

Do you know of a solution for this?

• 0 views • link
written by gable91794 • gable91794

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