#!/usr/bin/python
# sort_agp.py
import sys
import agp
build_dir = sys.argv[2]
scaffold_file = sys.argv[1]
scaffolds = agp.load(open(scaffold_file))
offset = 0
chrom = 'chrI'
gap_count = 0
cf = open(build_dir + "/contigs.bed", 'w')
sf = open(build_dir + "/scaffolds.bed", 'w')
gf = open(build_dir + "/gaps.bed", 'w')
sc = 0
for length, object_id in sorted([(value,key) for (key,value) in scaffolds.lengths.items()], reverse=True):
for x in scaffolds.objects[object_id]:
name = None
# CONTIG
if x.component_type != 'N':
name = x.component_id
s = "\t".join([str(y) for y in [chrom,
(x.object_beg + offset - 1),
(x.object_end + offset),
name,
1000,
import agp
import status
import Image
def convert_contig_name(cn):
if cn == 'Repeat':
return '|||'
if cn == 'Unmapped':
return '???'
else:
return str(int(cn[6:]))
if __name__ == '__main__':
pairs = status.load_pair_status(open(sys.argv[1]))
scaffolds = agp.load(open('scaffold00023.txt'))
iw = int(scaffolds.length('scaffold00023') / glyphs.SCALE_FACTOR)+1
ih = 300
print scaffolds.length('scaffold00023'), iw, int(iw)+1, ih
contig_offsets = {}
for s in scaffolds.objects['scaffold00023']:
if s.component_type != 'N':
contig_offsets[s.component_id] = s.object_beg
print contig_offsets
scaffold_pairs = []
for t in pairs:
p = pairs[t]
if contig_offsets.get(p.left_contig) or contig_offsets.get(p.right_contig):
scaffold_pairs.append(p)
img = Image.new("RGB", (iw, 16*len(scaffold_pairs)), (200,200,200))
y = 0
#!/usr/bin/python
# sort_agp.py
import sys
import agp
assembly_dir = sys.argv[1]
scaffolds = agp.load(open(assembly_dir + '/454Scaffolds.txt'))
for length, object_id in sorted(
[(value, key) for (key, value) in scaffolds.lengths.items()],
reverse=True):
for x in scaffolds.objects[object_id]:
print x
#!/usr/bin/python
# sort_agp.py
import sys
import agp
assembly_dir = sys.argv[1]
scaffolds = agp.load(open(assembly_dir + '/454Scaffolds.txt'))
for length, object_id in sorted([(value,key) for (key,value) in scaffolds.lengths.items()], reverse=True):
for x in scaffolds.objects[object_id]:
print x
