#!/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