def get_scaff_from_minimus(contig):
'''takes <contig> filename, returns GFF.File of scaffolding, e.g.
LS146000 . . 1 946 . - . contig_end=1904;contig=8;contig_start=1004
'''
contigs = GFF.File()
for l in open(contig):
match = re.search(
'#(?P<seqid>.+?)\(\d+\)\s(?P<strand>.+?)\s.+?\{(?P<sstart>\d+)\s(?P<send>\d+)\}\s\<(?P<cstart>\d+)\s(?P<cend>\d+)\>',
l)
if l.startswith('##'):
num = l.split()[0][2:]
elif match:
m = match.groupdict()
r = GFF.Region()
r['seqid'] = m['seqid']
r['start'], r['end'] = [
str(s) for s in sorted((int(m['sstart']), int(m['send'])))
]
r['attribute_contig'] = num
r['attribute_cstart'], r['attribute_cend'] = [
str(s) for s in sorted((int(m['cstart']), int(m['cend'])))
]
if m['strand'] == '[RC]':
r['strand'] = '-'
else:
r['strand'] = '+'
contigs.append(r)
return contigs
def draw_bs_plot(sites,sp_order,site_styles,seq_lens,offsets=None,maxheight=0.8,minheight=0.4,
fig=1,subpl=111,clear_plot=True,filename=None,**figargs):
by_factor = dict(zip(set([r['source'] for r in sites]),[GFF.File() for i in set([r['source'] for r in sites])]))
for r in sites:
cut = site_styles[r['source']]['cut']
if r['score'] < cut and r['seqid'] in sp_order:
by_factor[r['source']].append(r)
print by_factor
for k,v in by_factor.items():
normscores = Util.normalize([r['score'] for r in v],minheight,maxheight,to_abs=1)
for i,vn in enumerate(normscores):
by_factor[k][i]['score'] = vn
sites_to_plot = []
for f in by_factor.values():
sites_to_plot.extend(f)
figo = pylab.figure(fig,**figargs)
if clear_plot:
figo.clf()
figo = pylab.figure(fig,**figargs)
ax = figo.add_subplot(subpl)
ax.set_yticks([])
#calc offsets, draw lines
if offsets is None:
offsets = [None]*(len(sp_order)+1)
midpt = max([v for k,v in seq_lens.items() if k in sp_order])/2
for i,sp in enumerate(sp_order):
rank = len(sp_order) - i
if offsets[rank] is None:
off = midpt - seq_lens[sp]/2
offsets[rank] = off
print off,rank,seq_lens[sp]+off,rank
ax.text(5,rank,sp)
ax.add_line(matplotlib.lines.Line2D((offsets[rank],seq_lens[sp]+offsets[rank]),(rank,rank),color='k',alpha=0.25,lw=5))
for site in sites_to_plot:
fc = site_styles[site['source']]['color']
ec = fc
rank = len(sp_order) - sp_order.index(site['seqid'])
ax.add_patch(matplotlib.patches.Ellipse( (site['start']+offsets[rank],rank),
len(site),
site['score'],
fc=fc,ec=ec,alpha=site['score'] )
)
if filename:
ax.autoscale_view()
figo.savefig(filename)
else:
pylab.plot()
#test Fasta class (loading, editing, writing)
test_fasta = Fasta("/home/brant/py_util/unit_test_data/seq.fasta")
print "%s\n%s" % (test_fasta.filename, test_fasta.seq_len())
for k in test_fasta.iterkeys():
test_fasta[k] += "TGGCG"
test_fasta.write_to_file("/home/brant/temp/temp.fa", 1)
print "%s\n%s" % (test_fasta.filename, test_fasta.seq_len())
other_test_fasta = Fasta("/home/brant/temp/temp.fa")
print other_test_fasta.seq_len()
#end Fasta test
print other_test_fasta.order
print "test substr_from_gff\n"
import GFF
seqfile = os.path.join(paths['py_testdata'], "eve.ceratitis_capitata.fa")
gfffile = os.path.join(paths['py_testdata'],
"eve.ceratitis_capitata.fa.gff3")
seq = Fasta(seqfile)
gff = GFF.File(gfffile)
evegene = seq.substr_from_gff([
region for region in gff if 'gene_name' in region['attributes'].keys()
and region['attributes']['gene_name'] == 'eve'
],
name_key='gene_name',
plus_strand=1)
print evegene
#gff sqlite action
import GFF, os, sqlite3
def InsertGFFRegion(curobj, vals):
curobj.execute('INSERT INTO gff VALUES (null,?,?,?,?,?,?,?,?,?,?)', vals)
gff_filename = r"G:\AllBrantsStuff\python\ephinaroun\sqlite\dmel-all-r4.3.filtered.gff"
DB_filename = os.path.join(os.path.dirname(gff_filename),
'.' + os.path.basename(gff_filename) + '.DB')
gff = GFF.File(gff_filename)
connection = sqlite3.connect(DB_filename)
cursor = connection.cursor()
try:
cursor.execute('drop table gff')
connection.commit()
except:
pass
cursor.execute('''CREATE TABLE gff (
id INTEGER PRIMARY KEY AUTOINCREMENT,
sequence_name TEXT NOT NULL,
source TEXT NOT NULL,
type TEXT NOT NULL,
start INTEGER NOT NULL,
end INTEGER NOT NULL,
score REAL NOT NULL,
strand TEXT NOT NULL,
