Code tide up!
Remove from a title each word of WORDS_TO_REMOVE
---------------------------------
The string with words to removed is set at the top
of the code.
Code tide-up PEP8
---------------------
The pep8 was run and (almost) all error where fixed.
WORDS_TO_REMOVE: remove also upper case of words, e.g. 'A' etc.
----------------------------------------
WORDS_TO_REMOVE: Increased the list of words
-------------------------
DEBUG = False
---------------------
Switch to the non-debug mode.
Tide-up of dichotomic modes of the tool.
-----------------------------------------
There are two modes of running the tool:
1. non-automatic: based on user's pmid/doi
2. automatic: based on DOI from a pdf

It should be now cleaner and easier to work with.
Change the display of a Journal name('Source')
-------------------------------------
Before 'Source' was HUM.MUTAT, now it is HumMutat
(no upper, ' ' replace by '').
Clearer message
----------------------------
Indeed, when one gets this error, it means that
DOI has been found in the pdf
however the PMID was not found in PubMed for that DOI.
Minor changes (PEP8)
-------------------------
Change VERSION --> __version__
-----------------------------------
It will be used in building the package.
Minor edit: do not display hr()
----------------------------------
Main functionality move into main()
--------------------------
The step to build the package.
Package! works :-))
-----------------------
1. pubmex
2. README

magnus@netbook:/usr/local/lib/python2.6/dist-packages/pubmex-0.3a-py2.6.egg$ ls -l
total 40
drwxr-sr-x 2 root staff  4096 Jun  5 21:55 demo
drwxr-sr-x 2 root staff  4096 Jun  5 21:55 EGG-INFO
-rwxr-xr-x 1 root staff 13235 Jun  5 21:55 pubmex.py
-rw-r--r-- 1 root staff 12085 Jun  5 21:55 pubmex.pyc
-rw-r--r-- 1 root staff  1293 Jun  5 21:55 README
Quick-and-dirty test if pdftotext is installed.
----------------------------------
In [44]: subprocess.call(["pdftotext"], stderr=subprocess.PIPE)
---------------------------------------------------------------------------
OSError                                   Traceback (most recent call last)
ble ble ble

install poppler-utils

In [45]: subprocess.call(["pdftotext"])
pdftotext version 0.12.4
Copyright 2005-2009 The Poppler Developers - http://poppler.freedesktop.org
Copyright 1996-2004 Glyph & Cog, LLC
Usage: pdftotext [options] <PDF-file> [<text-file>]
  -f <int>          : first page to convert
  -l <int>          : last page to convert
  -r <fp>           : resolution, in DPI (default is 72)
  -x <int>          : x-coordinate of the crop area top left corner
  -y <int>          : y-coordinate of the crop area top left corner
  -W <int>          : width of crop area in pixels (default is 0)
  -H <int>          : height of crop area in pixels (default is 0)
  -layout           : maintain original physical layout
  -raw              : keep strings in content stream order
  -htmlmeta         : generate a simple HTML file, including the meta information
  -enc <string>     : output text encoding name
  -listenc          : list available encodings
  -eol <string>     : output end-of-line convention (unix, dos, or mac)
  -nopgbrk          : don't insert page breaks between pages
  -opw <string>     : owner password (for encrypted files)
  -upw <string>     : user password (for encrypted files)
  -q                : don't print any messages or errors
  -v                : print copyright and version info
  -h                : print usage information
  -help             : print usage information
  --help            : print usage information
  -?                : print usage information
Out[45]: 99