Mercurial > repos > jjohnson > mzsqlite_psm_align

annotate profmt.py @ 0:492f98d89e26 draft

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planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
author jjohnson
date Tue, 10 Apr 2018 09:57:49 -0400
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492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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1 #!/usr/bin/env python
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2016, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13 """
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14
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15 import sys,re
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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16 from operator import itemgetter, attrgetter
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17 from twobitreader import TwoBitFile
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18
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19 """
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20 1 QNAME string spectrum name *
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21 2 FLAG int bitwise FLAG (see further) *
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22 3 RNAME string reference sequence name *
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23 4 POS int 1-based lefmost mapping position 0
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24 5 MAPQ int unused in proBAM 255
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25 6 CIGAR string extended cigar string (see further) *
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26 7 RNEXT string unused in proBAM *
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27 8 PNEXT int unused in proBAM 0
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28 9 TLEN int unused in proBAM 0
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29 10 SEQ string coding sequence *
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30 11 QUAL string unused in proBAM *
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31 """
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32 """
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33 bit description FLAG
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34 0x00 peptide maps to the forward strand 0
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35 0x10 peptide maps to the reverse strand 16
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36 0x100 peptide is not the rank=1 peptide for the spectrum 256
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37 0x400 decoy peptide 1024
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38 0x4 unmapped peptide 4
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39 """
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40
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41 """
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42 tag type description
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43 --- ---- -----------
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44 NH int number of genomic locations to which the peptide sequence maps
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45 XL int number of peptides to which the spectrum maps
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46 XP string peptide sequence
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47 XR string reference peptide sequence
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48 XS float PSM score
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49 XQ float PSM q-value PSM FDR (i.e. q-value or 1-PEP).
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50 XC int peptide charge
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51 XA int Whether the peptide is annotated 0:yes; 1:parially unknown; 2:totally unknown;
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52 XM string Modification(s): semicolon seperated list of position,modName
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53 XN int number of missed cleavages
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54 XT int tryptic state: 0:non-tryptic 1:semi-tryptic 2:tryptic
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55 XG string peptide type: N:normal peptide V:variant peptide J:novel junction peptide D:decoy peptide U:unmappped
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56 XB string Semicolon-separated list of mass in the following format: massdiff; experimental mass; calculated mass massdiff can be calculated by experimental mass - calculated mass. If any number is unavailable, the value should be left blank (such as 0.01;;).
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57 XE int
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58 XF string Reading frame of the peptide (0, 1, 2) (See section 4.4.6).
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59 XG char Peptide type (see Table 6 and Figure 1)
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60 XI float Peptide intensity
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61 XO string This field indicates the uniqueness of the peptide mapping
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62 XU string
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63
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64
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65 NH i NH:i:1
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66 XO Z XO:Z:unique
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67 XL i XL:i:1
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68 XP Z XP:Z:ATLELTHNWGTEDDATQSYHNGNSDPR
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69 YP Z YP:Z:ENSP00000362463_rs4746:E111A
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70 XF Z XF:Z:1,1
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71 XI f XI:f:*
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72 XB f XB:f:0.70082940064
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73 XR Z XR:Z:ATLELTHNWGTEDDETQSYHNGNSDPR
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74 YB Z YB:Z:RK
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75 YA Z YA:Z:GF
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76 XS f XS:f:73.1426
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77 XQ f XQ:f:0
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78 XC i XC:i:3
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79 XA i XA:i:0
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80 XM Z XM:Z:*
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81 XN i XN:i:0
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82 XT i XT:i:2
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83 XE i XE:i:1
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84 XG Z XG:Z:V
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85 XU Z klc_070108x_PH_P7_COLO_205_D13.pepXML
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diff changeset
86
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
87 NH:i:1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
88 XO:Z:unique
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
89 XL:i:1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
90 XP:Z:ATLELTHNWGTEDDATQSYHNGNSDPR
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
91 YP:Z:ENSP00000362463_rs4746:E111A
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
92 XF:Z:1,1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
93 XI:f:*
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
94 XB:f:0.70082940064
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
95 XR:Z:ATLELTHNWGTEDDETQSYHNGNSDPR
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
96 YB:Z:RK
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
97 YA:Z:GF
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
98 XS:f:73.1426
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
99 XQ:f:0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
100 XC:i:3
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
101 XA:i:0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
102 XM:Z:*
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
103 XN:i:0
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
104 XT:i:2
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
105 XE:i:1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
106 XG:Z:V
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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diff changeset
107 XU:Z:klc_070108x_PH_P7_COLO_205_D13.pepXML
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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108
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109
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jjohnson
parents:
diff changeset
110 NH:i:*
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
111 XO:Z:unique
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
112 XL:i:1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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diff changeset
113 XP:Z:ATLELTHNWGTEDDATQSYHNGNSDPR
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
114 YP:Z:ENSP00000362463_rs4746:E111A
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
115 XF:Z:1,1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
116 XI:f:*
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
117 XB:f:0.70082940064
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
118 XR:Z:ATLELTHNWGTEDDETQSYHNGNSDPR
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jjohnson
parents:
diff changeset
119 YB:Z:RK
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
120 YA:Z:GF
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
121 XS:f:73.1426
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
diff changeset
122 XQ:f:0
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jjohnson
parents:
diff changeset
123 XC:i:3
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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parents:
diff changeset
124 XA:i:0
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jjohnson
parents:
diff changeset
125 XM:Z:*
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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diff changeset
126 XN:i:0
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jjohnson
parents:
diff changeset
127 XT:i:2
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jjohnson
parents:
diff changeset
128 XE:i:1
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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diff changeset
129 XG:Z:V
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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130 XU:Z:klc_070108x_PH_P7_COLO_205_D13.pepXML
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131 """
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132
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133
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134 PROBAM_TAGS = ['NH', 'XO', 'XL', 'XP', 'YP', 'XF', 'XI', 'XB', 'XR', 'YB', 'YA', 'XS', 'XQ', 'XC', 'XA', 'XM', 'XN', 'XT', 'XE', 'XG', 'XU']
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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135
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136
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137 PROBAM_TYTPES = {
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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138 'NH' : 'i', #number of genomic locations to which the peptide sequence maps
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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139 'XO' : 'Z', #uniqueness of the peptide mapping
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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140 'XL' : 'i', #number of peptides to which the spectrum maps
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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141 'XP' : 'Z', #peptide sequence
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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142 'YP' : 'Z', #Protein accession ID from the original search result
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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143 'XF' : 'Z', #Reading frame of the peptide (0, 1, 2)
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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144 'XI' : 'f', #Peptide intensity
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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145 'XB' : 'Z', #massdiff; experimental mass; calculated mass massdiff can be calculated by experimental mass - calculated mass. If any number is unavailable, the value should be left blank (such as 0.01;;).
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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146 'XR' : 'Z', #reference peptide sequence
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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147 'YB' : 'Z', #Preceding amino acids (2 AA, B stands for before).
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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148 'YA' : 'Z', #Following amino acids (2 AA, A stands for after).
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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149 'XS' : 'f', #PSM score
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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150 'XQ' : 'f', #PSM FDR (i.e. q-value or 1-PEP).
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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151 'XC' : 'i', #peptide charge
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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152 'XA' : 'i', #Whether the peptide is annotated 0:yes; 1:parially unknown; 2:totally unknown;
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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153 'XM' : 'Z', #Modifications
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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154 'XN' : 'i', #Number of missed cleavages in the peptide (XP)
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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155 'XT' : 'i', #Enzyme specificity
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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156 'XE' : 'i', #Enzyme used in the experiment
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157 'XG' : 'A', #Peptide type
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158 'XU' : 'Z', #URI
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159 }
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160
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161
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162 PROBAM_DEFAULTS = {
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163 'NH' : -1, #number of genomic locations to which the peptide sequence maps
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164 'XO' : '*', #uniqueness of the peptide mapping
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165 'XL' : -1, #number of peptides to which the spectrum maps
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166 'XP' : '*', #peptide sequence
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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167 'YP' : '*', #Protein accession ID from the original search result
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168 'XF' : '*', #Reading frame of the peptide (0, 1, 2)
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169 'XI' : -1, #Peptide intensity
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170 'XB' : '*', #massdiff; experimental mass; calculated mass massdiff can be calculated by experimental mass - calculated mass. If any number is unavailable, the value should be left blank (such as 0.01;;).
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diff changeset
171 'XR' : '*', #reference peptide sequence
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172 'YB' : '*', #Preceding amino acids (2 AA, B stands for before).
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173 'YA' : '*', #Following amino acids (2 AA, A stands for after).
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diff changeset
174 'XS' : -1, #PSM score
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diff changeset
175 'XQ' : -1, #PSM FDR (i.e. q-value or 1-PEP).
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176 'XC' : -1, #peptide charge
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177 'XA' : -1, #Whether the peptide is annotated 0:yes; 1:parially unknown; 2:totally unknown;
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178 'XM' : '*', #Modifications
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179 'XN' : -1, #Number of missed cleavages in the peptide (XP)
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180 'XT' : -1, #Enzyme specificity
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181 'XE' : -1, #Enzyme used in the experiment
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182 'XG' : '*', #Peptide type
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183 'XU' : '*', #URI
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184 }
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185
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186 def cmp_alphanumeric(s1,s2):
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187 if s1 == s2:
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188 return 0
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189 a1 = re.findall("\d+|[a-zA-Z]+",s1)
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190 a2 = re.findall("\d+|[a-zA-Z]+",s2)
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191 for i in range(min(len(a1),len(a2))):
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192 if a1[i] == a2[i]:
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193 continue
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diff changeset
194 if a1[i].isdigit() and a2[i].isdigit():
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195 return int(a1[i]) - int(a2[i])
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196 return 1 if a1[i] > a2[i] else -1
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197 return len(a1) - len(a2)
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198
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199
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200 def sort_chrom_names(names):
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201 rnames = sorted(names,cmp=cmp_alphanumeric)
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202 if 'chrM' in rnames:
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203 rnames.remove('chrM')
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204 rnames.insert(0,'chrM')
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205 if 'MT' in rnames:
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206 rnames.remove('MT')
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207 rnames.append('MT')
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208 return rnames
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209
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210 def as_int_list(obj):
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211 if obj is None:
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212 return None
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213 if isinstance(obj, list):
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diff changeset
214 return [int(x) for x in obj]
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215 elif isinstance(obj, str):
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216 return [int(x) for x in obj.split(',')]
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217 else: # python2 unicode?
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218 return [int(x) for x in str(obj).split(',')]
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diff changeset
219
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diff changeset
220
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diff changeset
221 class ProBEDEntry (object):
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diff changeset
222 def __init__(self, chrom, chromStart, chromEnd, name, score, strand,
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223 blockCount, blockSizes, blockStarts,
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224 protacc, peptide, uniqueness, genomeReference,
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225 psmScore='.', fdr='.', mods='.', charge='.',
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diff changeset
226 expMassToCharge='.', calcMassToCharge='.',
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227 psmRank='.', datasetID='.', uri='.'):
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228 self.chrom = chrom
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229 self.chromStart = int(chromStart)
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230 self.chromEnd = int(chromEnd)
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diff changeset
231 self.name = name
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232 self.score = int(score) if score is not None else 0
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diff changeset
233 self.strand = '-' if str(strand).startswith('-') else '+'
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diff changeset
234 self.thickStart = self.chromStart
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diff changeset
235 self.thickEnd = self.chromEnd
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diff changeset
236 self.itemRgb = '0'
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237 self.blockCount = int(blockCount)
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238 self.blockSizes = as_int_list(blockSizes)
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diff changeset
239 self.blockStarts = as_int_list(blockStarts)
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diff changeset
240 self.protacc = protacc
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diff changeset
241 self.peptide = peptide
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diff changeset
242 self.uniqueness = uniqueness
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diff changeset
243 self.genomeReference = genomeReference
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diff changeset
244 self.psmScore = psmScore
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diff changeset
245 self.fdr = fdr
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diff changeset
246 self.mods = mods
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247 self.charge = charge
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diff changeset
248 self.expMassToCharge = expMassToCharge
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diff changeset
249 self.calcMassToCharge = calcMassToCharge
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diff changeset
250 self.psmRank = psmRank
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diff changeset
251 self.datasetID = datasetID
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252 self.uri = uri
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253
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254 def __str__(self):
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255 return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \
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256 (self.chrom, self.chromStart, self.chromEnd,
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257 self.name, self.score, self.strand,
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258 self.thickStart, self.thickEnd, self.itemRgb,
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259 self.blockCount, self.blockSizes, self.blockStarts,
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260 self.protacc, self.peptide, self.uniqueness,
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261 self.genomeReference,
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262 self.psmScore, self.fdr, self.mods,
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263 self.charge, self.expMassToCharge, self.calcMassToCharge,
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264 self.psmRank, self.datasetID, self.uri)
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265
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266
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267 class ProBED ( object ):
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268 def __init__(self,species=None,assembly=None,comments=[]):
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269 self.species = species
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270 self.assembly = assembly
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271 self.comments = comments
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272 self.entries = dict()
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273
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274 def add_entry(self,entry):
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275 if not entry.chrom in self.entries:
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276 self.entries[entry.chrom] = []
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277 self.entries[entry.chrom].append(entry)
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278
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279 def write(self,fh):
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280 rnames = sort_chrom_names(self.entries.keys())
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281 for sn in rnames:
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282 if sn not in self.entries:
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283 continue
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284 ##for pbe in sorted(self.entries[sn], key=lambda probam_entry: probam_entry.pos):
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285 for pbe in sorted(self.entries[sn], key=attrgetter('chromStart','chromEnd')):
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286 fh.write('%s\n' % str(pbe))
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287
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288
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289 class ProBAMEntry (object):
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290 def __init__(self, qname='', flag=0, rname='', pos=0, mapq=255, cigar='', rnext='*', pnext='0', tlen='0', seq='*', qual='*', optional=PROBAM_DEFAULTS):
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291 self.qname = qname
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292 self.flag = flag
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293 self.rname = rname
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294 self.pos = pos
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295 self.mapq = mapq
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296 self.cigar = cigar
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297 self.rnext = rnext
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298 self.pnext = pnext
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299 self.tlen = tlen
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300 self.seq = seq
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301 self.qual = qual
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302 self.optional = optional
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303 def __str__(self):
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304 opt_cols = '\t%s' % '\t'.join(['%s:%s:%s' % (t,PROBAM_TYTPES[t],self.optional[t]) for t in PROBAM_TAGS]) if self.optional else ''
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305 return '%s\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s%s' % (
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306 self.qname,self.flag,self.rname,self.pos,self.mapq,self.cigar,
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307 str(self.rnext) if self.rnext else '',
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308 str(self.pnext) if self.pnext else '',
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309 str(self.tlen) if self.tlen else '',
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310 self.seq,
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311 self.qual, opt_cols)
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312 def add_optional(self,tag,value):
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313 self.optional[tag] = value
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314
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315
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316 class ProBAM ( object ):
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317 def __init__(self,species=None,assembly=None,seqlens={},comments=[]):
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318 self.species = species
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319 self.assembly = assembly
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320 self.seqlens = seqlens
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321 self.comments = comments
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322 self.entries = dict()
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323 self.opt_columns = set()
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324 self.rg = []
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325
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326 def add_entry(self,pb_entry):
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327 if not pb_entry.rname in self.entries:
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328 self.entries[pb_entry.rname] = []
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329 self.entries[pb_entry.rname].append(pb_entry)
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330 if pb_entry.optional:
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331 self.opt_columns | set(pb_entry.optional.keys())
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332
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333 def add_entry_from_bed(self,bed_entry,optional=dict()):
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334 if bed_entry.pep:
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335 optional['XP:Z'] = bed_entry.pep
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336 qname=bed_entry.name
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337 flag = 0 if bed_entry.strand == '+' else 16
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338 rname = bed_entry.chrom
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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339 pos = bed_entry.chromStart + 1
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340 cigar = bed_entry.get_cigar()
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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341 seq = bed_entry.get_spliced_seq(strand='+') if bed_entry.seq else '*'
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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342 pb_entry = ProBAMEntry(qname=qname, flag=flag, rname=rname, pos=pos,cigar=cigar,seq=seq,optional=optional)
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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343 self.add_entry(pb_entry)
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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344 ## print >> sys.stderr,('add_entry_from_bed:%s\n %s\n %s' % (self.entries.keys(),bed_entry,pb_entry))
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
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345
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jjohnson
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346 def write(self,fh):
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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347 fh.write('@HD VN:1.0 SO:coordinate\n')
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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348 rnames = sort_chrom_names(self.seqlens.keys())
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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349 for sn in rnames:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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350 fh.write('@SQ\tSN:%s\tLN:%d\n' % (sn,self.seqlens[sn]))
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
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351 for rg in self.rg:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
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352 fh.write('@RG\tID:%s\n' % (rg))
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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353 fh.write('@PG\tID:SampleSpecificGenerator\n')
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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354 for comment in self.comments:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
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355 fh.write('@CO\t%s\n' % comment)
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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356 for sn in rnames:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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357 if sn not in self.entries:
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
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358 continue
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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359 ##for pbe in sorted(self.entries[sn], key=lambda probam_entry: probam_entry.pos):
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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360 for pbe in sorted(self.entries[sn], key=attrgetter('pos')):
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
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361 fh.write('%s\n' % str(pbe))
492f98d89e26 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/mzsqlite_psm_align commit 88e2fb9c31fbd687a0956924a870137d1fb9bee3-dirty
jjohnson
parents:
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362