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POBiopython Indentation Error
 

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  1. POBiopython Indentation Error
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    <p>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 but I always get the error below when I run a for loop and any module from the biopython library:</p> <pre><code> IndentationError: expected an indented block </code></pre> <p>I only get this error when I call the .py file written in Komodo Edit version 7.0.2 from the command line terminal:</p> <pre><code> 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 &lt;module&gt; 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 &lt;module&gt; import NexusIO File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/Bio/AlignIO/NexusIO.py", line 19, in &lt;module&gt; 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 &lt;module&gt; import os,sys, math, random, copy File "/Users/Priya/Documents/Python/Tutorials/random.py", line 27 randLowHigh(5,10) ^ IndentationError: expected an indented block </code></pre> <p>When I use the command line to call old .py files that I wrote a year ago as above they run fine. And when I start up python directly and type in the tutorial example line by line it works fine:</p> <pre><code> 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. &gt;&gt;&gt; from Bio import SeqIO &gt;&gt;&gt; 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 </code></pre> <p>How can I fix my .py file so I can just run it from the terminal?</p> <p>Any insight into this problem would be greatly appreciated!</p> <p>Priya</p>
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    1. COCould you post the .py file? Probably, you forgot to indent line 27.
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      1. USRafał Rawicki
    2. COI'm not sure how to post a file directly, could you tell me how?
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