Merge pull request #62 from apriha/develop

v2.0.0

.travis.yml

@@ -30,6 +30,8 @@ script:
     if [ $TRAVIS_BRANCH == "master" ]; then
       if [ $SELECTED_JOB != $JOB_ID ]; then
         aws s3 cp s3://lineage-resources/resources.tar.gz resources.tar.gz
+      else
+        DOWNLOADS_ENABLED=True
       fi
     else
       aws s3 cp s3://lineage-resources/resources.tar.gz resources.tar.gz
@@ -49,7 +51,7 @@ stages:
   - check formatting
   - test
   - name: deploy
-    if: branch = master
+    if: tag IS present
 
 jobs:
   include:

CONTRIBUTORS.rst

@@ -26,6 +26,8 @@ Listed in alphabetical order.
 Name            GitHub
 =============== =============
 Anatoli Babenia `@abitrolly`_
+Yoan Bouzin     `@Tuisto59`_
 =============== =============
 
 .. _@abitrolly: https://github.com/abitrolly
+.. _@Tuisto59: https://github.com/Tuisto59

README.rst

@@ -5,9 +5,7 @@
 lineage
 =======
 ``lineage`` provides a framework for analyzing genotype (raw data) files from direct-to-consumer
-DNA testing companies (e.g., `23andMe <https://www.23andme.com>`_,
-`Family Tree DNA <https://www.familytreedna.com>`_, and `Ancestry <http://www.ancestry.com>`_),
-primarily for the purposes of genetic genealogy.
+(DTC) DNA testing companies, primarily for the purposes of genetic genealogy.
 
 Capabilities
 ------------
@@ -18,13 +16,23 @@ Capabilities
 - Find discordant SNPs between child and parent(s)
 - Remap SNPs between assemblies / builds (e.g., convert SNPs from Build 36 to Build 37, etc.)
 
+Supported Genotype Files
+------------------------
+``lineage`` supports genotype files from the following DTC DNA testing companies:
+
+- `23andMe <https://www.23andme.com>`_
+- `Ancestry <https://www.ancestry.com>`_
+- `Family Tree DNA <https://www.familytreedna.com>`_
+- `MyHeritage <https://www.myheritage.com>`_
+
 Dependencies
 ------------
 ``lineage`` requires `Python <https://www.python.org>`_ 3.5+ and the following Python packages:
 
 - `numpy <http://www.numpy.org>`_
 - `pandas <http://pandas.pydata.org>`_
 - `matplotlib <http://matplotlib.org>`_
+- `atomicwrites <https://github.com/untitaker/python-atomicwrites>`_
 
 On Linux systems, the following system-level installs may also be required::
 
@@ -210,12 +218,12 @@ Loading resources/4584.ftdna-illumina.3483.csv.gz
 Now let's find the shared genes:
 
 >>> one_chrom_shared_dna, two_chrom_shared_dna, one_chrom_shared_genes, two_chrom_shared_genes = l.find_shared_dna(user4583, user4584, shared_genes=True)
-Saving output/shared_dna_User4583_User4584.png
-Saving output/shared_dna_one_chrom_User4583_User4584_GRCh37.csv
 Downloading resources/knownGene_hg19.txt.gz
 Downloading resources/kgXref_hg19.txt.gz
-Saving output/shared_genes_one_chrom_User4583_User4584_GRCh37.csv
+Saving output/shared_dna_User4583_User4584.png
+Saving output/shared_dna_one_chrom_User4583_User4584_GRCh37.csv
 Saving output/shared_dna_two_chroms_User4583_User4584_GRCh37.csv
+Saving output/shared_genes_one_chrom_User4583_User4584_GRCh37.csv
 Saving output/shared_genes_two_chroms_User4583_User4584_GRCh37.csv
 
 The plot that illustrates the shared DNA is shown below. Note that in addition to outputting the

setup.py

@@ -106,7 +106,7 @@
     },
     keywords="dna genes genetics genealogy snps chromosomes genotype "
     "bioinformatics ancestry",
-    install_requires=["numpy==1.15.1", "pandas==0.23.4", "matplotlib==2.2.3"],
+    install_requires=["numpy", "pandas", "matplotlib", "atomicwrites"],
     python_requires=">=3.5",
     platforms=["any"],
 )