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()