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writing_appliance script example: smiting perl from yet one more place #705

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writing_appliance script example: smiting perl from yet one more place #705

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6 changes: 3 additions & 3 deletions docs/_writing_scripts.rst
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Expand Up @@ -5,10 +5,10 @@ Many common bioinformatics applications are available on the `Tool Shed`_
already and so a common development task is to integrate scripts of
various complexity into Galaxy.

Consider the following small Perl script.
Consider the following small Python script.

.. literalinclude:: writing/gc_content.pl
:language: perl
.. literalinclude:: writing/gc_content.py
:language: python

One can build a tool for this script as follows and place the script in
the same directory as the tool XML file itself. The special value
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23 changes: 0 additions & 23 deletions docs/writing/gc_content.pl
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20 changes: 20 additions & 0 deletions docs/writing/gc_content.py
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@@ -0,0 +1,20 @@
#!/usr/bin/env python2
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python2? why not python3? ;)

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Haha, I'd love to, but I figured let's not go crazy here.

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Actually, this made me do some research.. can OS X people confirm whether python2 is on your PATH?

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By default, no. At least only python is on the $PATH on macOS Sierra 10.12.5, not python2.

$ uname
Darwin
$ which python2
$ python2
-bash: python2: command not found
$ which python
/usr/bin/python
$ python --version
Python 2.7.10

import sys

# usage : python gc_content.py <FASTA file> <output file>

name = None
with open(sys.argv[1]) as infile:
with open(sys.argv[2], 'w') as outfile:
for line_raw in infile:
line = line_raw.rstrip('\r\n')
if line.startswith('>'):
if name is not None:
outfile.write(name+': '+str(gc/float(total))+'\n')
name = line[1:]
gc = 0
total = 0
else:
gc += line.count('G') + line.count('C')
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not case insensitive, unlike the perl version.

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True, true. Didn't know if it was more important to be complete or keep it simple. I can make the edit if you guys want.

total += len(line)
outfile.write(name+': '+str(gc/float(total))+'\n')
2 changes: 1 addition & 1 deletion docs/writing/gc_content.xml
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@@ -1,6 +1,6 @@
<tool id="gc_content" name="Compute GC content">
<description>for each sequence in a file</description>
<command>perl $__tool_directory__/gc_content.pl $input output.tsv</command>
<command>python $__tool_directory__/gc_content.py $input output.tsv</command>
<inputs>
<param format="fasta" name="input" type="data" label="Source file"/>
</inputs>
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