def main():
'It reads the map data and writes it'
base_path = '/home/peio/melonomics/datos_originales/mapa_genetico'
markers_path = 'mapa_icugi/melon_markers.csv'
merged_map_path = 'mapa_icugi/framework_merged_map.csv'
irta_maps_path = 'mapa_genetico_irta.csv'
icugi_qtls = 'mapa_icugi/all_qtls.csv'
bin_map_path = 'mapa_icugi/bin_mapping.csv'
out_path = 'out.gff3'
mcf_path = 'out.mcf'
correl_fpath = os.path.join(base_path, 'mapa_icugi/markers.dat')
markers_path = os.path.join(base_path, markers_path)
merged_map_path = os.path.join(base_path, merged_map_path)
irta_maps_path = os.path.join(base_path, irta_maps_path)
out_path = os.path.join(base_path, out_path)
mcf_path = os.path.join(base_path, mcf_path)
bin_map_path = os.path.join(base_path, bin_map_path)
qtls_path = os.path.join(base_path, icugi_qtls)
#qtls_fix_path = os.path.join(base_path, icugi_fix_qtls)
cmap = create_empty_cmap()
#Correlations file
marker_corr = parse_markersfile(open(correl_fpath))
#get Monforte marker data
read_markers(open(markers_path), cmap, marker_corr)
#get irta maps
cmap_fhand = open(irta_maps_path)
read_maps(cmap_fhand, cmap, marker_corr)
#get data from icugi map
read_icugi_map(open(merged_map_path), cmap, marker_corr)
#fix the marker types
fix_marker_types(cmap)
#get icugi qtls
read_qtls(open(qtls_path), cmap, marker_corr)
#read bin map
read_bin_map(open(bin_map_path), cmap, marker_corr)
# import pprint
# pprint.pprint(cmap)
# return
#write gff3 file
gff_fhand = open(out_path, 'w')
cmap_to_gff(cmap, gff_fhand)
#write mcf file
mcf_fhand = open(mcf_path, 'w')
cmap_to_mcf(cmap, mcf_fhand)
def main():
'The main part'
# set parameters
infhands, markersfname, name_cor, type_cor, sequence_cor = set_parameters()
#read markes file if exists
if os.path.exists(markersfname):
markersfhand = open(markersfname)
markers = parse_markersfile(markersfhand)
markersfhand.close()
else:
markers = {}
# add files to marker structure
for infhand in infhands:
add_markers(infhand, markers, name_cor, type_cor, sequence_cor)
# write markers to file:
markersfhand = open(markersfname, 'w')
write_markers(markersfhand, markers)
markersfhand.close()
