diff --git a/README.md b/README.md index 780d178..53ee46c 100644 --- a/README.md +++ b/README.md @@ -1,17 +1,17 @@ -#Bhast +# Bhast Ben's HLA Allele Submission Tool A tool for generating an EMBL-formatted submission of a standard novel HLA allele. -##Download the executable +## Download the executable When the compiled executable is available, i'll put a link for the file download here. -##Run using Python +## Run using Python Run this program using standard python call: ``` python AlleleSubmissionEMBL.py ``` -##To configure Anaconda +## To configure Anaconda Anaconda uses separate environments to run your programs in. Install Anaconda for python 2.7. https://www.continuum.io/downloads @@ -30,7 +30,7 @@ conda create --name AlleleSubEnvironment biopython six pywin32 call activate AlleleSubEnvironment && pip install pyinstaller packaging && call deactivate ``` -##Run using a bash or .bat script using anaconda +## Run using a bash or .bat script using anaconda You can execute the following scripts to run the tool inside of Anaconda: Linux/Mac: ``` @@ -41,7 +41,7 @@ Windows: Run_allele_submission.bat ``` -##Input Data +## Input Data Input data sequence must consist of 1) 5' UTR 2) Any number of Exons, with an introns distributed between them. @@ -65,10 +65,10 @@ tagctagct AGCTAGCTA gctagctagctag -##Output Data +## Output Data The resulting report is in the form of an EMBL HLA Novel Allele submission flatfile. You can submit this to EMBL as a new HLA allele. -##For more information on EMBL's ENA format: +## 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