1#!/usr/local/bin/python3.8 2 3import sys 4import collections 5import utils 6try: 7 import argparse as ap 8 import bz2 9 import random 10except ImportError: 11 sys.stderr.write( "argparse not found" ) 12 sys.exit(-1) 13 14def read_params( args ): 15 p = ap.ArgumentParser(description='Convert Usearch ".uc" files in tab-delimited' 16 ' files with the seed as first field followed by the other IDs\n') 17 18 p.add_argument( 'ctxt', nargs='?', default=None, type=str, 19 help= "the input uc file [stdin if not present]") 20 p.add_argument('txt', nargs='?', default=None, type=str, 21 help= "the output txt file compresse if fiven with bz2 extension\n" 22 "[stdout if not present]") 23 p.add_argument('--subsample', metavar="Subsampling rate", 24 default=1.0, type=float ) 25 p.add_argument('-n', action='store_true' ) 26 p.add_argument('-p', metavar="Prefix for taxon names", 27 default="", type=str ) 28 p.add_argument('--sk', action='store_true' ) 29 30 return vars( p.parse_args() ) 31 32if __name__ == "__main__": 33 args = read_params( sys.argv ) 34 uc2cl = collections.defaultdict( set ) 35 36 gint = str if args['sk'] else int 37 38 valin = [] 39 with utils.openr( args['ctxt'] ) as inp: 40 for l in inp: 41 tset = set([gint(a) for a in l.strip().split('\t')][1:]) 42 valin.append(tset) 43 all_t = set() 44 for v in valin: 45 all_t |= v 46 47 res = {} 48 for t in all_t: 49 #if len(t) < args['n']: 50 # continue 51 res[t] = [int(t in v) for v in valin] 52 53 with utils.openw(args['txt']) as out: 54 mat_res = {} 55 for k1 in res: 56 mat_res[k1] = {} 57 for k2 in res: 58 mat_res[k1][k2] = float(len([1 for x,y in zip(res[k1],res[k2]) if x == 1 and y == 1]))/max(sum(res[k1]),sum(res[k2])) 59 60 keys = sorted(res) 61 out.write( "\t".join( ["x"]+keys ) +"\n" ) 62 for k in keys: 63 out.write( "\t".join( [k] + [str(mat_res[k][k2]) for k2 in keys] ) +"\n" ) 64 65 66 """ 67 n = len(res.values()[0]) 68 n_s = int(float(n)*args['subsample']) 69 indok = set(random.sample( list(range(n)), n_s)) 70 out.write( "\t".join(['genes']+["g"+str(v) for v in range(n)]) + "\n" ) 71 72 for k,v in res.items(): 73 out.write( args['p'] + str(k)+"\t"+"\t".join([str(s) for i,s in enumerate(v) if i in indok]) +"\n" ) 74 """ 75