Mercurial > repos > iuc > ngsutils_bam_filter
annotate ngsutils/support/dbsnp.py @ 0:4e4e4093d65d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
author | iuc |
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date | Wed, 11 Nov 2015 13:04:07 -0500 |
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children | 7a68005de299 |
rev | line source |
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0
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
|
1 ''' |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
|
2 Support package for processing a dbSNP tabix dump from UCSC. |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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3 ''' |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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4 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
|
5 import pysam |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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6 import collections |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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7 import sys |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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8 from ngsutils.support import revcomp |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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9 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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10 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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11 class SNPRecord(collections.namedtuple('SNPRecord', '''bin |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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12 chrom |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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13 chromStart |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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14 chromEnd |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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15 name |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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16 score |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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17 strand |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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18 refNCBI |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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19 refUCSC |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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20 observed |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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21 molType |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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22 clazz |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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23 valid |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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24 avHet |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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25 avHetSE |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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26 func |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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27 locType |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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28 weight |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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29 exceptions |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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30 submitterCount |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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31 submitters |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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32 alleleFreqCount |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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33 alleles |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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34 alleleNs |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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35 alleleFreqs |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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36 bitfields |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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37 ''')): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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38 __slots__ = () |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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39 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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40 @property |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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41 def alleles(self): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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42 alts = [] |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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changeset
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43 for alt in self.observed.split('/'): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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44 if alt != '-' and self.strand == '-': |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
changeset
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45 alt = revcomp(alt) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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46 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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47 alts.append(alt) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
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48 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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49 return alts |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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50 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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51 @property |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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52 def snp_length(self): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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53 return self.chromEnd - self.chromStart |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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54 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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55 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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56 def autotype(ar, length=26): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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57 out = [] |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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58 for el in ar: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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59 val = None |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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60 try: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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61 val = int(el) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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62 except: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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63 try: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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64 val = float(el) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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65 except: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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66 val = el |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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67 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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68 out.append(val) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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69 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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70 if len(out) < 12: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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71 raise TypeError("Invalid dbSNP file! We need at least 12 columns to work with.") |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
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72 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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73 while len(out) < length: |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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74 out.append(None) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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75 return out |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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76 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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77 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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78 class DBSNP(object): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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79 def __init__(self, fname): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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80 self.dbsnp = pysam.Tabixfile(fname) |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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81 self.asTup = pysam.asTuple() |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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82 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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83 def fetch(self, chrom, pos): |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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84 'Note: pos is 0-based' |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff
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85 |
4e4e4093d65d
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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86 # Note: tabix the command uses 1-based positions, but |
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87 # pysam.Tabixfile uses 0-based positions |
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88 |
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89 for tup in self.dbsnp.fetch(chrom, pos, pos + 1, parser=self.asTup): |
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90 snp = SNPRecord._make(autotype(tup)) |
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91 if snp.chromStart == pos: |
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92 yield snp |
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93 |
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94 def close(self): |
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95 self.dbsnp.close() |
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96 |
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97 def dump(self, chrom, op, pos, base, snp, exit=True): |
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98 print |
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99 print ' ->', op, chrom, pos, base |
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100 print snp |
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101 print snp.alleles |
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102 if exit: |
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103 sys.exit(1) |
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104 |
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105 def is_valid_variation(self, chrom, op, pos, seq, verbose=False): |
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106 for snp in self.fetch(chrom, pos): |
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107 if not '/' in snp.observed or snp.clazz not in ['single', 'mixed', 'in-del', 'insertion', 'deletion']: |
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108 # these are odd variations that we can't deal with... (microsatellites, tooLongToDisplay members, etc) |
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109 continue |
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110 |
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111 if op == 0: |
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112 if snp.clazz in ['single', 'mixed'] and seq in snp.alleles: |
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113 return True |
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114 # elif verbose: |
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115 # for alt in snp.alleles: |
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116 # if len(alt) > 1: |
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117 # self.dump(chrom, op, pos, seq, snp, False) |
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118 |
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119 elif op == 1: |
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120 if snp.clazz in ['insertion', 'mixed', 'in-del']: |
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121 if seq in snp.alleles: |
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122 if len(seq) > 1 and verbose: |
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123 self.dump(chrom, op, pos, seq, snp, False) |
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124 return True |
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125 |
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126 if verbose: |
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127 if len(seq) > 1: |
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128 self.dump(chrom, op, pos, seq, snp, False) |
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129 else: |
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130 for alt in snp.alleles: |
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131 if len(alt) > 1: |
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132 self.dump(chrom, op, pos, seq, snp, False) |
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133 |
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134 elif op == 2: |
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135 if snp.clazz in ['deletion', 'mixed', 'in-del']: |
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136 if '-' in snp.alleles and seq in snp.alleles: |
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137 if len(seq) > 1 and verbose: |
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138 self.dump(chrom, op, pos, seq, snp, False) |
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139 return True |
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140 |
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141 return False |