REST works for EMBL now

HEADER

@@ -1,16 +1,15 @@
-# This file is part of EMBL-HLA-Submission.
+# This file is part of saddle-bags.
 #
-# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# saddle-bags is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# EMBL-HLA-Submission is distributed in the hope that it will be useful,
+# saddle-bags is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 # GNU Lesser General Public License for more details.
 #
 # You should have received a copy of the GNU Lesser General Public License
-# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+# along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
-# Version 1.0

MakeExecutables.bat

@@ -1,17 +1,17 @@
-:: This file is part of EMBL-HLA-Submission.
+:: This file is part of saddle-bags.
 ::
-:: EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+:: saddle-bags is free software: you can redistribute it and/or modify
 :: it under the terms of the GNU Lesser General Public License as published by
 :: the Free Software Foundation, either version 3 of the License, or
 :: (at your option) any later version.
 ::
-:: EMBL-HLA-Submission is distributed in the hope that it will be useful,
+:: saddle-bags is distributed in the hope that it will be useful,
 :: but WITHOUT ANY WARRANTY; without even the implied warranty of
 :: MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 :: GNU Lesser General Public License for more details.
 ::
 :: You should have received a copy of the GNU Lesser General Public License
-:: along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+:: along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
 :: Version 1.0
 

MakeExecutables.sh

@@ -1,19 +1,18 @@
-# This file is part of EMBL-HLA-Submission.
+# This file is part of saddle-bags.
 #
-# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# saddle-bags is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# EMBL-HLA-Submission is distributed in the hope that it will be useful,
+# saddle-bags is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 # GNU Lesser General Public License for more details.
 #
 # You should have received a copy of the GNU Lesser General Public License
-# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+# along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
-# Version 1.0
 
 # This isn't working in it's current state.  The spec file is apparently just for windows, 
 # it's still pulling in windows DLLs.  

README.md

@@ -1,16 +1,15 @@
-# Bhast
-Ben's HLA Allele Submission Tool
-
-A tool for generating an EMBL-formatted submission of a standard novel HLA allele. 
+# Saddlebags
+A tool for generating allele submissions for the EMBL and IMGT nucleotide databases. 
 
 ## Download the executable
 Download an executable for Windows from the Release page.
-[Download Bhast for Windows Here](https://github.com/transplantation-immunology/EMBL-HLA-Submission/releases)
+[Download Saddlebags for Windows Here](https://github.com/transplantation-immunology/saddle-bags/releases)
 
 ## Run using Python
-Alternatively, you can run this program using Python 2.7. This works for Mac and Linux users (or Windows). There are prerequesites, you can install them inside an Anaconda environment.
+Alternatively, you can run this program using Python 2.7. This works for Mac and Linux users (or Windows). There are prerequesites, I recommend you install them inside an Anaconda environment. See Run_allele_submission.sh and Run_allele_submission.bat for an example of this in Linux and Windows environments, respectively.
+
 ```
-python AlleleSubmissionEMBL.py
+python AlleleSubmissionMain.py
 ```
 
 ## To configure Anaconda
@@ -21,7 +20,7 @@ To set up the environment in anaconda:
 
 Linux/Mac:  
 ```
-conda create --name AlleleSubEnvironment biopython six  
+conda create --name AlleleSubEnvironment biopython six pycurl 
 source activate AlleleSubEnvironment  
 pip install pyinstaller packaging  
 source deactivate  
@@ -68,11 +67,17 @@ AGCTAGCTA
 gctagctagctag  
 
 ## Annotating your exons
-Identifying the exons in your HLA sequence is a nontrivial challenge. We have provided a list of common sequences surrounding exon boundaries. See the [Release Page](https://github.com/transplantation-immunology/EMBL-HLA-Submission/releases) for a .pdf reference.  These sequences can probably be found within your HLA consensus sequence at exon boundary sites. It may also help to use the [IMGT/HLA sequence alignment tool](http://www.ebi.ac.uk/ipd/imgt/hla/align.html) for more information on common exon patterns.
+Identifying the exons in your HLA sequence is a nontrivial challenge. We have provided a list of common sequences surrounding exon boundaries. See the [Release Page](https://github.com/transplantation-immunology/saddle-bags/releases) for a .pdf reference.  These sequences can probably be found within your HLA consensus sequence at exon boundary sites. It may also help to use the [IMGT/HLA sequence alignment tool](http://www.ebi.ac.uk/ipd/imgt/hla/align.html) for more information on common exon patterns.
+
+## EMBL Metadata Input format
+Sample ID: Specified by the submitting laboratory, you may use a value that is informative to you.
+Gene:
+Class I or II:
+Allele Local Name:
 
-## 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
+Saddlebags will submit to EMBL Test environment by default, you must specify that the software target the Live / Production environment.
 
+EMBL sequence submissions must be associated with a Study/Project. You may specify the accession number of an existing EMBL study (Get this accession number from [EMBL Webin](https://www.ebi.ac.uk/ena/submit/sra/#home) ), or Saddlebags can create a new project to your specifications.
 
 
 ## For more information on EMBL's ENA format:  
@@ -81,3 +86,7 @@ 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  
+
+## For more information on IMGT metadata:
+
+TODO: Put a description of the IMGT metadata form. There is lots of information that goes in here, and much of it is confusing.  How should Primers and Sequencing methodology be provided? What are the options for Ethnic Origin or Sex or Cosanguineous?

Run_allele_submission.bat

@@ -1,21 +1,21 @@
-:: This file is part of EMBL-HLA-Submission.
+:: This file is part of saddle-bags.
 ::
-:: EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+:: saddle-bags is free software: you can redistribute it and/or modify
 :: it under the terms of the GNU Lesser General Public License as published by
 :: the Free Software Foundation, either version 3 of the License, or
 :: (at your option) any later version.
 ::
-:: EMBL-HLA-Submission is distributed in the hope that it will be useful,
+:: saddle-bags is distributed in the hope that it will be useful,
 :: but WITHOUT ANY WARRANTY; without even the implied warranty of
 :: MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 :: GNU Lesser General Public License for more details.
 ::
 :: You should have received a copy of the GNU Lesser General Public License
-:: along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
+:: along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
 :: Version 1.0
 
 :: See the file README.MD for how to set up your anaconda environment.
 
-activate AlleleSubEnvironment && cd src && python AlleleSubmissionEMBL.py && deactivate
+activate AlleleSubEnvironment && cd src && python AlleleSubmissionMain.py && deactivate
 

Run_allele_submission.sh

@@ -1,19 +1,17 @@
-# This file is part of EMBL-HLA-Submission.
+# This file is part of saddle-bags.
 #
-# EMBL-HLA-Submission is free software: you can redistribute it and/or modify
+# saddle-bags is free software: you can redistribute it and/or modify
 # it under the terms of the GNU Lesser General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# EMBL-HLA-Submission is distributed in the hope that it will be useful,
+# saddle-bags is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 # GNU Lesser General Public License for more details.
 #
 # You should have received a copy of the GNU Lesser General Public License
-# along with EMBL-HLA-Submission. If not, see <http://www.gnu.org/licenses/>.
-
-# Version 1.0
+# along with saddle-bags. If not, see <http://www.gnu.org/licenses/>.
 
 # See the file README.MD for how to set up your anaconda environment.