start = f.location.nofuzzy_start stop = f.location.nofuzzy_end geneList.append([record.name, start, stop, 0, 0]) sysid = record.name+";"+str(start+1)+'-'+str(stop+1) f.qualifiers['sysid'] = [sysid] if 'locus_tag' in f.qualifiers: locus_tag = f.qualifiers['locus_tag'][0] else: #if the locus_tag is missing from the genbank record make up a tag locus_tag = "tag_" + str(start+1)+'-'+str(stop+1) geneCoverList.append([record.name+'__'+locus_tag]) repliconList.append([record.name,len(record),feature_count]) largest_key = 0 for replicon in repliconList: key = get_key(replicon[0]) if key > largest_key: largest_key = key replicon_index = [] for i in range((largest_key)): replicon_index.append([]) count = 0 for replicon in repliconList: key = get_key(replicon[0]) replicon_index[(key-1)].append([replicon[0],count]) count += 1 geneSlice = [] sliceSize = [] #slice the geneList by coordinates and replicon count = 0
from Bio.Seq import Seq from Bio.SeqRecord import SeqRecord from pipe_utils import get_key reference = sys.argv[1] coverFile = open(sys.argv[2]) chromosomes = [] output = "" for record in SeqIO.parse(reference, "fasta"): chromosomes.append([record.id, len(record), 0, 0]) largest_key = 0 for chromosome in chromosomes: key = get_key(chromosome[0]) if key > largest_key: largest_key = key chromosome_index = [] for i in range((largest_key)): chromosome_index.append([]) count = 0 for chromosome in chromosomes: key = get_key(chromosome[0]) chromosome_index[(key-1)].append([chromosome[0],count]) count += 1 previous_replicon = ""