Biopython Indentation Error

Question

[priyasshah]

Hi,

I've been dabbling in biopython for about a year and I recently upgraded to Biopython release 1.59. I've been refreshing my skills with some tutorials (taken verbatim from the Biopython Cookbook) but I always get the error below when I run a for loop and any module from the biopython library:

IndentationError: expected an indented block

I only get this error when I call the .py file that I wrote in Komodo Edit version 7.0.2 from the command line terminal:

Priyas-iMac:~ Priya$ python /Users/priya/Documents/Python/Tutorials/BioParse.py
Traceback (most recent call last):
  File "/Users/priya/Documents/Python/Tutorials/BioParse.py", line 4, in <module>
    SeqIO.write(rc, "/Users/priya/Documents/Python/Tutorials/ls_orchid_rc.fasta", "fasta")
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/SeqIO/__init__.py", line 400, in write
    from Bio import AlignIO
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/AlignIO/__init__.py", line 147, in <module>
    import NexusIO
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/AlignIO/NexusIO.py", line 19, in <module>
    from Bio.Nexus import Nexus
  File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/Nexus/Nexus.py", line 15, in <module>
    import os,sys, math, random, copy
  File "/Users/Priya/Documents/Python/Tutorials/random.py", line 27
    randLowHigh(5,10)
    ^
IndentationError: expected an indented block

But when I start up python directly and type in the tutorial example line by line it works fine:

Priyas-iMac:~ Priya$ python 
Python 2.7.3 (default, Apr 19 2012, 00:55:09) 
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio import SeqIO
>>> for seq_record in SeqIO.parse("/Users/priya/Documents/Python/Tutorials/ls_orchid.txt","fasta"):
...      print seq_record.id
... 
gi|2765658|emb|Z78533.1|CIZ78533
gi|2765657|emb|Z78532.1|CCZ78532

I can also still run old code that I wrote a year ago that has for loops and calls biopython modules, just not anything new that I write.

Any insight into this problem would be greatly appreciated!

Priya

[Niek De Klein]

Make sure that your indentation is consistent. In most editors there is an option to change space-tabs into tabs or tabs into space tabs. Try doing that for random.py. If that doesn't work, post the code as bow suggested.

[st.ph.n]

What version of Python are you using with your BioPython upgrade? Make sure they're compatible. I had some issues with indentation errors with the new Biopython 1.64 and Python 2.6.6, where the new biopython would work perfectly with 2.7.

Answer 1

[bow]

Hi priyasshah,

It looks like there's an error in this file: "/Users/Priya/Documents/Python/Tutorials/random.py". Could you paste the contents here: http://pastebin.com/?