return "\n".join(outstr)
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
# test code
from SAP.Bio import SeqIO
from ._FeatureSet import FeatureSet
from ._GraphSet import GraphSet
from random import normalvariate
genbank_entry = SeqIO.read('/data/genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk', 'gb')
gdfs1 = FeatureSet(0, 'Nanoarchaeum equitans CDS - CDS')
gdfs2 = FeatureSet(1, 'Nanoarchaeum equitans CDS - gene')
for feature in genbank_entry.features:
if feature.type == 'CDS':
gdfs1.add_feature(feature)
if feature.type == 'gene':
gdfs2.add_feature(feature)
gdt = Track()
gdt.add_set(gdfs1)
gdt.add_set(gdfs2)
graphdata = []
for pos in range(1, len(genbank_entry.seq), 1000):
"""
outstr = [
"\n<%s: %s %d features>" %
(self.__class__, self.name, len(self.features))
]
return "\n".join(outstr)
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == '__main__':
from SAP.Bio import SeqIO
genbank_entry = SeqIO.read(
'/data/Genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk', 'gb')
# Test code
gdfs = FeatureSet(0, 'Nanoarchaeum equitans CDS')
for feature in genbank_entry.features:
if feature.type == 'CDS':
gdfs.add_feature(feature)
#print len(gdfs)
#print gdfs.get_ids()
#gdfs.del_feature(560)
#print gdfs.get_ids()
#print gdfs.get_features()
#for feature in gdfs.get_features():
# print feature.id, feature.start, feature.end
#print gdfs[500]
""" __str__(self) -> ""
Returns a formatted string with information about the feature set
"""
outstr = ["\n<%s: %s %d features>" % (self.__class__, self.name, len(self.features))]
return "\n".join(outstr)
################################################################################
# RUN AS SCRIPT
################################################################################
if __name__ == "__main__":
from SAP.Bio import SeqIO
genbank_entry = SeqIO.read("/data/Genomes/Bacteria/Nanoarchaeum_equitans/NC_005213.gbk", "gb")
# Test code
gdfs = FeatureSet(0, "Nanoarchaeum equitans CDS")
for feature in genbank_entry.features:
if feature.type == "CDS":
gdfs.add_feature(feature)
# print len(gdfs)
# print gdfs.get_ids()
# gdfs.del_feature(560)
# print gdfs.get_ids()
# print gdfs.get_features()
# for feature in gdfs.get_features():
# print feature.id, feature.start, feature.end
# print gdfs[500]
