updating readme.

README.md

@@ -2,54 +2,57 @@
 A tool for generating an EMBL-formatted submission of a standard novel HLA allele. 
 
 ##Run using Python
-Run this program using standard python call:
-$python AlleleSubmissionEMBL.py
+Run this program using standard python call:  
+```
+python AlleleSubmissionEMBL.py
+```
 
 ##To configure Anaconda:
-Anaconda uses separate environments to run your programs in.
-Install Anaconda for python 2.7.
-https://www.continuum.io/downloads
-To set up the environment in anaconda, run this in console:
-$conda create --name AlleleSubEnvironment biopython
+Anaconda uses separate environments to run your programs in.  
+Install Anaconda for python 2.7.  
+https://www.continuum.io/downloads  
+To set up the environment in anaconda, run this in console:  
+```
+conda create --name AlleleSubEnvironment biopython
+```
 
 ##Run using a bash or .bat script using anaconda
-You can execute the following scripts to run the tool inside of Anaconda:
-Linux/Mac:
-bash Run_allele_submission.sh
-Windows:
+You can execute the following scripts to run the tool inside of Anaconda:  
+Linux/Mac:  
+```
+bash Run_allele_submission.sh  
+```
+Windows:  
+```
 Run_allele_submission.bat
+```
 
-Input data sequence consists of 
-1) 5' UTR 
+##Input Data
+Input data sequence consists of  
+1) 5' UTR  
 2) An odd number of Exons, with an Even number of introns between them.  
 3) 3' UTR
 
 Introns, Exons, and UTRs are to be specified using capital or lowercase letters.  
 Exons are capital, while introns and UTRs are lowercase.
 
-Like this:
-
-fiveprimeutrEXONONEintrononeEXONTWOintrontwoEXONTHREEthreeprimeutr
-
+Like this:  
+fiveprimeutrEXONONEintrononeEXONTWOintrontwoEXONTHREEthreeprimeutr  
 agctagctagctAGCTAGCtagctagctAGCTAGCtagctagctAGCTAGCTAgctagctagctag
 
 All spaces, tabs, and newlines are not interpreted by this program,  They are removed.
 If you wish, you may use those characters for more convenient visualization of splice sites:
-agctagctagct
-AGCTAGC
-tagctagct
-AGCTAGC
-tagctagct
-AGCTAGCTA
-gctagctagctag
-
-For more information on EMBL's ENA format:
-
-http://www.ebi.ac.uk/ena/submit/sequence-submission
-
-http://www.ebi.ac.uk/ena/submit/entry-upload-templates\n
-ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt
-
-ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html
-
-http://www.ebi.ac.uk/ena/software/flat-file-validator
+agctagctagct  
+AGCTAGC  
+tagctagct  
+AGCTAGC  
+tagctagct  
+AGCTAGCTA  
+gctagctagctag  
+
+##For more information on EMBL's ENA format:  
+http://www.ebi.ac.uk/ena/submit/sequence-submission  
+http://www.ebi.ac.uk/ena/submit/entry-upload-templates  
+ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/usrman.txt  
+ftp://ftp.ebi.ac.uk/pub/databases/embl/doc/FT_current.html  
+http://www.ebi.ac.uk/ena/software/flat-file-validator