コード例 #1
0
ファイル: deriveAllRepGeneCover.py プロジェクト: d-j-e/euRD
            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
コード例 #2
0
ファイル: getCoverByRep.py プロジェクト: d-j-e/euRD
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 = ""