Mercurial > repos > iuc > ngsutils_bam_filter

annotate ngsutils/support/__init__.py @ 2:7a68005de299 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
author iuc
date Sun, 27 Nov 2016 15:01:21 -0500
parents 4e4e4093d65d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
1 import collections
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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2 import gzip
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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3 import os
2
7a68005de299 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
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4 import re
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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5 import sys
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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6 try:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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7 from eta import ETA
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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8 except:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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9 pass
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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10
2
7a68005de299 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
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11
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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12 class FASTARead(collections.namedtuple('FASTARecord', 'name comment seq')):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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13 def __repr__(self):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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14 if self.comment:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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15 return '>%s %s\n%s\n' % (self.name, self.comment, self.seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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16 return '>%s\n%s\n' % (self.name, self.seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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17
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18 def subseq(self, start, end, comment=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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19 if self.comment:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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20 comment = '%s %s' % (self.comment, comment)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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21
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22 return FASTARead(self.name, comment, self.seq[start:end])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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24 def clone(self, name=None, comment=None, seq=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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25 n = name if name else self.name
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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26 c = comment if comment else self.comment
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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27 s = seq if seq else self.seq
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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29 return FASTARead(n, c, s)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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31 def write(self, out):
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32 out.write(repr(self))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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34
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35 class FASTA(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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36 def __init__(self, fname=None, fileobj=None, qual=False):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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37 self.fname = fname
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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38 self.qual = qual
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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39 if fileobj:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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40 self.fileobj = fileobj
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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41 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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42 if self.fname == '-':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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43 self.fileobj = sys.stdin
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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44 elif self.fname[-3:] == '.gz' or self.fname[-4:] == '.bgz':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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45 self.fileobj = gzip.open(os.path.expanduser(self.fname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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46 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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47 self.fileobj = open(os.path.expanduser(self.fname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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48
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49 if not self.fileobj:
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50 raise ValueError("Missing valid filename or fileobj")
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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51
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52 def close(self):
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53 if self.fileobj != sys.stdout:
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54 self.fileobj.close()
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55
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56 def tell(self):
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57 # always relative to uncompressed...
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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58 return self.fileobj.tell()
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59
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60 def seek(self, pos, whence=0):
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61 self.fileobj.seek(pos, whence)
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62
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63 def fetch(self, quiet=False):
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64 name = ''
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65 comment = ''
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66 seq = ''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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67
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68 if not quiet and self.fname and self.fname != '-':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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69 eta = ETA(os.stat(self.fname).st_size, fileobj=self.fileobj)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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70 else:
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71 eta = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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72
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73 for line in self.fileobj:
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74 line = line.strip()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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75 if not line:
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76 continue
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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77 if line[0] == '#':
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78 continue
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79
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80 if line[0] == '>':
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81 if name and seq:
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82 if eta:
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83 eta.print_status(extra=name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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84 yield FASTARead(name, comment, seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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85
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86 spl = re.split(r'[ \t]', line[1:], maxsplit=1)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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87 name = spl[0]
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88 if len(spl) > 1:
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89 comment = spl[1]
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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90 else:
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iuc
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diff changeset
91 comment = ''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
92 seq = ''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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93
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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94 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
95 if self.qual:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
96 seq = seq + ' ' + line
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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97 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
98 seq += line
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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99
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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100 if name and seq:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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101 if eta:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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102 eta.print_status(extra=name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
103 yield FASTARead(name, comment, seq)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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104
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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105 if eta:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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106 eta.done()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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107
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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108
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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109 def gzip_reader(fname, quiet=False, callback=None, done_callback=None, fileobj=None):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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110 if fileobj:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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111 f = fileobj
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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112 elif fname == '-':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
113 f = sys.stdin
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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114 elif fname[-3:] == '.gz' or fname[-4:] == '.bgz':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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115 f = gzip.open(os.path.expanduser(fname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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116 else:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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117 f = open(os.path.expanduser(fname))
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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118
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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119 if quiet or fname == '-':
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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120 eta = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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121 else:
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iuc
parents:
diff changeset
122 eta = ETA(os.stat(fname).st_size, fileobj=f)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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123
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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124 for line in f:
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iuc
parents:
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125 if eta:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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126 if callback:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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127 extra = callback()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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128 else:
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iuc
parents:
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129 extra = ''
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130
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iuc
parents:
diff changeset
131 eta.print_status(extra=extra)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
132 yield line
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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133
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iuc
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134 if done_callback and done_callback():
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
135 break
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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136
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iuc
parents:
diff changeset
137 if f != sys.stdin:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
138 f.close()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
139
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
140 if eta:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
141 eta.done()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
142
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
143
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
144 class Symbolize(object):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
145 'Converts strings to symbols - basically a cache of strings'
2
7a68005de299 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 9a243c616a4a3156347e38fdb5f35863ae5133f9
iuc
parents: 0
diff changeset
146
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
147 def __init__(self):
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iuc
parents:
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148 self.__cache = {}
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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149
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iuc
parents:
diff changeset
150 def __getitem__(self, k):
2
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iuc
parents: 0
diff changeset
151 if k not in self.__cache:
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
152 self.__cache[k] = k
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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153
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
154 return self.__cache[k]
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diff changeset
155
2
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iuc
parents: 0
diff changeset
156
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
157 symbols = Symbolize()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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diff changeset
158
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iuc
parents:
diff changeset
159 _compliments = {
2
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iuc
parents: 0
diff changeset
160 'a': 't',
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iuc
parents: 0
diff changeset
161 'A': 'T',
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iuc
parents: 0
diff changeset
162 'c': 'g',
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iuc
parents: 0
diff changeset
163 'C': 'G',
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iuc
parents: 0
diff changeset
164 'g': 'c',
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iuc
parents: 0
diff changeset
165 'G': 'C',
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iuc
parents: 0
diff changeset
166 't': 'a',
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iuc
parents: 0
diff changeset
167 'T': 'A',
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iuc
parents: 0
diff changeset
168 'n': 'n',
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iuc
parents: 0
diff changeset
169 'N': 'N'
0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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diff changeset
170 }
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171
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172
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iuc
parents:
diff changeset
173 def revcomp(seq):
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iuc
parents:
diff changeset
174 '''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
175 >>> revcomp('ATCGatcg')
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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parents:
diff changeset
176 'cgatCGAT'
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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parents:
diff changeset
177 '''
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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diff changeset
178 ret = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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179
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180 for s in seq:
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iuc
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diff changeset
181 ret.append(_compliments[s])
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182
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iuc
parents:
diff changeset
183 ret.reverse()
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
184 return ''.join(ret)
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185
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186
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187 class Counts(object):
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188 '''
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189 Setup simple binning. Bins are continuous 0->max. Values are added to
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190 bins and then means / distributions can be calculated.
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191 '''
2
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192
0
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193 def __init__(self):
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194 self.bins = []
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195
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196 def add(self, val):
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197 while len(self.bins) <= val:
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198 self.bins.append(0)
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199 self.bins[val] += 1
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200
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201 def mean(self):
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202 acc = 0
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203 count = 0
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204
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205 for i, val in enumerate(self.bins):
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206 acc += (i * val)
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207 count += val
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208
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209 if count > 0:
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210 return float(acc) / count
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211
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212 def max(self):
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213 return len(self.bins) - 1
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214
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215
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216 def memoize(func):
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217 if 'TESTING' in os.environ or 'DEBUG' in os.environ:
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218 return func
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219
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220 __cache = {}
2
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221
0
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222 def inner(*args, **kwargs):
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223 k = (args, tuple(kwargs.iteritems()))
2
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224 if k not in __cache:
0
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225 __cache[k] = func(*args, **kwargs)
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226 return __cache[k]
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227
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228 inner.__doc__ = '(@memoized %s)\n%s' % (func.__name__, func.__doc__)
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229 return inner
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230
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231
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232 def quoted_split(s, delim, quote_char='"'):
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233 tokens = []
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234
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235 buf = ""
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236 inquote = False
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237
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238 for c in s:
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239 if inquote:
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240 buf += c
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241 if c == quote_char:
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242 inquote = False
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243 elif c == delim:
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244 tokens.append(buf)
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245 buf = ""
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246 else:
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247 buf += c
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248 if c == quote_char:
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249 inquote = True
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250
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251 if buf:
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252 tokens.append(buf)
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253
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254 return tokens