comparison libs/special_gene_test_assemblies.py @ 7:3d6680af0bec draft

planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty

6:b6281a377a18

    hspbit=[]
    alignmentlist=[]
    for record in records:
      for alignment in record.alignments:
        if x in alignment.hit_def: #multi gene database, so...
          print x,"got a hit, evaluating the hit quality..."
          score=0
          for hsp in alignment.hsps:
            if hsp.expect<E_thresh:
              score+=hsp.bits
          alignment=alignment.hit_def+':'+str(score)

    for Htype in scorelist:
      if scorelist[Htype]>score:
        First_Choice=Htype
        score=scorelist[Htype]
    if float(score)>=0.1*aver_len:
      print "$$$",First_Choice,"got a hit, score:",score
    else:
      print "$$$No ",x,"exists"
  os.system("rm "+database+"_db.*")##########1/28/2015
  os.system("rm "+xml_file)##########1/28/2015

database=sys.argv[1]
target_file=sys.argv[2]

7:3d6680af0bec

    hspbit=[]
    alignmentlist=[]
    for record in records:
      for alignment in record.alignments:
        if x in alignment.hit_def: #multi gene database, so...
          print(x,"got a hit, evaluating the hit quality...")
          score=0
          for hsp in alignment.hsps:
            if hsp.expect<E_thresh:
              score+=hsp.bits
          alignment=alignment.hit_def+':'+str(score)

    for Htype in scorelist:
      if scorelist[Htype]>score:
        First_Choice=Htype
        score=scorelist[Htype]
    if float(score)>=0.1*aver_len:
      print("$$$",First_Choice,"got a hit, score:",score)
    else:
      print("$$$No ",x,"exists")
  os.system("rm "+database+"_db.*")##########1/28/2015
  os.system("rm "+xml_file)##########1/28/2015

database=sys.argv[1]
target_file=sys.argv[2]