#!user/bin/env python

import pygr.Data

from pygr.seqdb import BlastDB, AnnotationDB

seqdb = BlastDB('/somepath/hg18.fa')

exon_slices = pygr.Data.Collection(path='exon_slices.db',mode='c',writeback=False) # Store on disk

exon_db = AnnotationDB(exon_slices, seqdb,sliceAttrDict=dict(id=0, exon_id=1, orientation=2, gene_id=3, start=4, stop=5))

from pygr.cnestedlist import NLMSA

nlmsa = NLMSA('exonAnnot','w',use_virtual_lpo=True,bidirectional=False)

ifile = file('exonslice.txt')

for line in ifile:

row = [x for x in line.split()] # CONVERT TO LIST SO MUTABLE

row[1] = int(row[1]) # CONVERT FROM STRING TO INTEGER

exon_slices[row[1]] = row

exon = exon_db[row[1]] # GET THE ANNOTATION OBJECT FOR THIS EXON

nlmsa.addAnnotation(exon) # SAVE IT TO GENOME MAPPING

exon_db.clear()

nlmsa.build() # FINALIZE GENOME ALIGNMENT INDEXES

ifile.close()

pygr.Data.Bio.Seq.Genome.hg18 = seqdb # SAVE TO pygr.Data

pygr.Data.Bio.Annotation.hg18.exons = exon_db

pygr.Data.Bio.Annotation.hg18.exonmap = nlmsa

pygr.Data.schema.Bio.Annotation.hg18.exonmap = \

pygr.Data.ManyToManyRelation(seqdb,bindAttrs=('exons',))

pygr.Data.save()

# [Note that to work with these results using the pygr.Data schema (i.e. to search a piece of genomic sequence using its "exons" attribute), you should make sure to load the data from pygr.Data. To do this, start a new Python session and run a test like the following:]

import pygr.Data

hg18 = pygr.Data.Bio.Seq.Genome.hg18()

chr16 = seqdb['chr1']

qint = chr16[10000:20000] # an arbitrary genomic interval containing genes...

for exon in qint.exons:

print(exon)