Merge branch 'hotfix/fix_output' into develop

genmod/commands/annotate.py

@@ -204,10 +204,12 @@ def check_tabix_index(compressed_file, file_type='cadd', verbose=False):
 def annotate(family_file, variant_file, family_type, vep, silent, phased, strict, cadd_raw, whole_gene, 
                 annotation_dir, cadd_file, cadd_1000g, cadd_esp, cadd_indels, thousand_g, exac, outfile,
                 chr_prefix, processes, verbose):
-    """Annotate variants in a VCF file.
-        It is possible to annotate from sources shown as options only
-        If a ped file is provided then the genetic inheritance patterns for all individuals are followed.
-        Individuals that are not present in ped file will not be considered in the analysis.
+    """Annotate variants in a VCF file.\n
+        The main function with genmod is to annotate genetic inheritance patterns for variants in families. 
+        Use flag --family together with a .ped file to describe which individuals in the vcf you wish to check inheritance for in the analysis.
+        Individuals that are not present in the ped file will not be considered in the analysis.\n
+        It is also possible to use genmod without a family file. In this case the variants will be annotated with a variety of options seen below.
+        Please see docuentation on github.com/moonso/genmod or genmod/examples/readme.md for more information.
     """    
     verbosity = verbose
 
@@ -248,20 +250,23 @@ def annotate(family_file, variant_file, family_type, vep, silent, phased, strict
             if individual not in individuals:
                 warning.warning('All individuals in ped file must be in vcf file! Aborting...')
                 warning.warning('Individuals in PED file: %s' % ' '.join(list(family_parser.individuals.keys())))
-                warning.warning('Individuals in VCF file: %s' % ' '.join(list(variant_parser.individuals)))
+                warning.warning('Individuals in VCF file: %s' % ' '.join(individuals))
                 sys.exit()
 
     if verbosity:
         if family_file:
             print('Starting analysis of families: %s' % ','.join(list(families.keys())))
-            print('Individuals included in analysis: %s\n' % ','.join(list(individuals.keys())))
+            print('Individuals included in analysis: %s\n' % ','.join(list(family_parser.individuals.keys())))
     ######### Connect to the annotations #########
 
     gene_trees = {}
     exon_trees = {}
 
     if not vep:
 
+        if verbosity:
+            print('Reading annotations...\n')
+
         gene_db = pkg_resources.resource_filename('genmod', 'annotations/genes.db')
         exon_db = pkg_resources.resource_filename('genmod', 'annotations/exons.db')
 

scripts/genmod

@@ -56,7 +56,10 @@ def print_version(ctx, param, value):
                 is_eager=True
 )
 def run_genmod():
-    """Annotate genetic models in variant files."""
+    """Tool for annotating and analyzing genetic variants in the vcf format.\n
+        For more information, please run:
+        genmod COMMAND --help \n
+        """
     pass
 
 run_genmod.add_command(build_annotation.build_annotation)

setup.py

@@ -16,7 +16,7 @@
 #     long_description = file.read()
 
 setup(name='genmod',
-    version='1.8.2',
+    version='1.8.3',
     description='Annotate genetic inheritance models in variant files',
     author = 'Mans Magnusson',
     author_email = '[email protected]',