def make_cns_to_at_map(blast_file, tair_desc, gff, query, subject, outdir):
"""
take the cns vs at blast file, find the best at hit for the cns,
and find teh tair desc for that hit, create a datastructure like:
{'cns_id' : ('at_name', 'at_desc') ... }
e.g.
{'q1|5766644|5766724|3|2158237|2158317' : ('AT2G38030', 'pre-tRNA')}
this can then be used in make_better_datasheet.
"""
shelve = get_shelve(outdir, query, subject)
from blast_misc import blast_array
b = blast_array(blast_file, best_hit=True)
seen = {}
updated = 0
for row in b:
if str(row['query']) in seen: continue
seen[str(row['query'])] = True
besthit = sorted(b[b['query'] == row['query']],
key=operator.itemgetter('eval'),
reverse=True)[0]
# 1: get rid of starting SB or OS
key = str(row['query'])[3:]
current = shelve[key]
current["at_rna"] = str(row['subject']) + ';;eval(' + str(
row['eval']) + ')' + tair_desc[str(row['subject'])]
updated += 1
shelve[key] = current
print >> sys.stderr, "%i cns's tagged as hitting at_rna" % updated
shelve.close()
def make_cns_to_at_map(blast_file, tair_desc, gff, query, subject, outdir):
"""
take the cns vs at blast file, find the best at hit for the cns,
and find teh tair desc for that hit, create a datastructure like:
{'cns_id' : ('at_name', 'at_desc') ... }
e.g.
{'q1|5766644|5766724|3|2158237|2158317' : ('AT2G38030', 'pre-tRNA')}
this can then be used in make_better_datasheet.
"""
shelve = get_shelve(outdir, query, subject)
from blast_misc import blast_array
b = blast_array(blast_file, best_hit=True)
seen = {}
updated = 0
for row in b:
if str(row["query"]) in seen:
continue
seen[str(row["query"])] = True
besthit = sorted(b[b["query"] == row["query"]], key=operator.itemgetter("eval"), reverse=True)[0]
# 1: get rid of starting SB or OS
key = str(row["query"])[3:]
current = shelve[key]
current["at_rna"] = str(row["subject"]) + ";;eval(" + str(row["eval"]) + ")" + tair_desc[str(row["subject"])]
updated += 1
shelve[key] = current
print >> sys.stderr, "%i cns's tagged as hitting at_rna" % updated
shelve.close()
def find_colinear_hits(blastfile, qeval, seval, mask='query', as_str=False):
sqlite_file = blastfile[:blastfile.rfind(".")] + ".sqlite"
db = sqlite3.connect(sqlite_file)
cur = db.cursor()
# need these to convert the absolute coords in sqlite to match
# the local positions in the fresh blast
qmin, smin = [x[0] for x in cur.execute('SELECT bpmin FROM image_info ORDER BY id')]
# so we mask the new blast with anything that's NOT an HSP
sql = "SELECT image_id, bpmin, bpmax FROM image_data WHERE type != 'HSP'"
if mask == 'query': sql += ' AND image_id = 1'
b = blast_array(blastfile, dopickle=False, best_hit=0, maxkeep=99999)
if plot:
pylab.plot(b['qstart'], b['sstart'], "kx")
b = b[(b['eval'] < qeval) & (b['eval'] < seval)]
if plot:
pylab.plot(b['qstart'], b['sstart'], "ro")
# TODO: remove stuff that's way off the diagonal?
for row in cur.execute(sql).fetchall():
(start, stop, lmin) = row[0] == 1 and ('qstart', 'qstop', qmin) or ('sstart', 'sstop', smin)
assert (start, stop) == ('qstart', 'qstop') # for now, always only using query
cds_start, cds_stop = row[1] - lmin + 1, row[2] - lmin + 1
bstart, bstop = b[start], b[stop]
b = b[numexpr.evaluate("(((bstart < cds_start) & (bstop < cds_start)) | ((bstop > cds_stop ) & (bstart > cds_stop)))")]
r = 0
if not b.shape[0]: return None
delta = 0.2 * b['sstart'].max()
# here, try to find a sort of line, and keep removing outliers to only get linear cnss
for i in range(4):
slope, intercept, r, zy, zz = linregress(b['qstart'], b['sstart'])
#print >>sys.stderr, slope, intercept, r, zy, zz
if r > 0.8: break
bqstart = b['qstart']
expected = numexpr.evaluate('intercept + slope * bqstart')
bsstart = b['sstart']
s = b.shape[0]
b = b[numexpr.evaluate('bsstart - expected < delta')]
if s == b.shape[0]: break # not removing anything.
if plot:
pylab.plot(b['qstart'], b['sstart'], "bo")
pylab.savefig('/var/www/ms_tmp/d.png')
cnss = []
start_stops = [map(lambda p: int(p) + qmin - 1, pair) for pair in zip(b['qstart'], b['qstop'])]
for qstart, qstop in start_stops:
qres = cur.execute('SELECT xmin, ymin, xmax, ymax, id, pair_id FROM image_data WHERE image_id = 1 AND bpmin = ? AND bpmax = ?', (qstart, qstop)).fetchone()
this_cns = [qres[:-1]]
if not qres: continue
sres = cur.execute('SELECT xmin, ymin, xmax, ymax, id FROM image_data WHERE id = ?', (qres[-1],)).fetchone()
this_cns.append(sres)
cnss.append(this_cns)
return cnss
def find_colinear_hits(blastfile, qeval, seval, mask='query', as_str=False):
sqlite_file = blastfile[:blastfile.rfind(".")] + ".sqlite"
db = sqlite3.connect(sqlite_file)
cur = db.cursor()
# need these to convert the absolute coords in sqlite to match
# the local positions in the fresh blast
qmin, smin = [
x[0] for x in cur.execute('SELECT bpmin FROM image_info ORDER BY id')
]
# so we mask the new blast with anything that's NOT an HSP
sql = "SELECT image_id, bpmin, bpmax FROM image_data WHERE type != 'HSP'"
if mask == 'query': sql += ' AND image_id = 1'
b = blast_array(blastfile, dopickle=False, best_hit=0, maxkeep=99999)
if plot:
pylab.plot(b['qstart'], b['sstart'], "kx")
b = b[(b['eval'] < qeval) & (b['eval'] < seval)]
if plot:
pylab.plot(b['qstart'], b['sstart'], "ro")
# TODO: remove stuff that's way off the diagonal?
for row in cur.execute(sql).fetchall():
(start, stop,
lmin) = row[0] == 1 and ('qstart', 'qstop', qmin) or ('sstart',
'sstop', smin)
assert (start, stop) == ('qstart', 'qstop'
) # for now, always only using query
cds_start, cds_stop = row[1] - lmin + 1, row[2] - lmin + 1
bstart, bstop = b[start], b[stop]
b = b[numexpr.evaluate(
"(((bstart < cds_start) & (bstop < cds_start)) | ((bstop > cds_stop ) & (bstart > cds_stop)))"
)]
r = 0
if not b.shape[0]: return None
delta = 0.2 * b['sstart'].max()
# here, try to find a sort of line, and keep removing outliers to only get linear cnss
for i in range(4):
slope, intercept, r, zy, zz = linregress(b['qstart'], b['sstart'])
#print >>sys.stderr, slope, intercept, r, zy, zz
if r > 0.8: break
bqstart = b['qstart']
expected = numexpr.evaluate('intercept + slope * bqstart')
bsstart = b['sstart']
s = b.shape[0]
b = b[numexpr.evaluate('bsstart - expected < delta')]
if s == b.shape[0]: break # not removing anything.
if plot:
pylab.plot(b['qstart'], b['sstart'], "bo")
pylab.savefig('/var/www/ms_tmp/d.png')
cnss = []
start_stops = [
map(lambda p: int(p) + qmin - 1, pair)
for pair in zip(b['qstart'], b['qstop'])
]
for qstart, qstop in start_stops:
qres = cur.execute(
'SELECT xmin, ymin, xmax, ymax, id, pair_id FROM image_data WHERE image_id = 1 AND bpmin = ? AND bpmax = ?',
(qstart, qstop)).fetchone()
this_cns = [qres[:-1]]
if not qres: continue
sres = cur.execute(
'SELECT xmin, ymin, xmax, ymax, id FROM image_data WHERE id = ?',
(qres[-1], )).fetchone()
this_cns.append(sres)
cnss.append(this_cns)
return cnss
import sys sys.path.insert(0,".") import blast_misc import time import operator blast_file = 'data/t.blast' b = blast_misc.blast_array(blast_file, best_hit=0, maxkeep=999999, dopickle=0) print b print b.shape
