Mercurial > repos > galaxyp > mzsqlite_psm_align

annotate mzsqlite_psm_align.py @ 1:4f8cf8fbef57 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit b0c57cac4e558d974a16b14d4498cf8d4ba9e0c7
author galaxyp
date Thu, 19 Apr 2018 14:30:28 -0400
parents f2dc9805107a
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f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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1 #!/usr/bin/env python
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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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 2017, 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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f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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15 from __future__ import print_function
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17 import argparse
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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18 import re
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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19 import sys
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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20 import sqlite3 as sqlite
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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21 from time import time
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24 from Bio.Seq import reverse_complement, translate
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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27 import pysam
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28 from twobitreader import TwoBitFile
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30 from profmt import PROBAM_DEFAULTS,ProBAM,ProBAMEntry,ProBED,ProBEDEntry
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33 def regex_match(expr, item):
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34 return re.match(expr, item) is not None
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37 def regex_search(expr, item):
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38 return re.search(expr, item) is not None
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41 def regex_sub(expr, replace, item):
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42 return re.sub(expr, replace, item)
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45 def get_connection(sqlitedb_path, addfunctions=True):
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46 conn = sqlite.connect(sqlitedb_path)
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47 if addfunctions:
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48 conn.create_function("re_match", 2, regex_match)
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49 conn.create_function("re_search", 2, regex_search)
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50 conn.create_function("re_sub", 3, regex_sub)
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51 return conn
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52
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53
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54 ## Peptide Spectral Match (PSM)s
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55 PSM_QUERY = """\
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56 SELECT
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57 pe.dBSequence_ref,
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58 pe.start,
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59 pe.end,
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60 pe.pre,
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61 pe.post,
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62 pep.sequence,
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63 sr.id,
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64 sr.spectrumTitle,
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65 si.rank,
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66 si.chargeState,
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67 si.calculatedMassToCharge,
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68 si.experimentalMassToCharge,
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69 si.peptide_ref
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70 FROM spectrum_identification_results sr
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71 JOIN spectrum_identification_result_items si ON si.spectrum_identification_result_ref = sr.id
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72 JOIN peptide_evidence pe ON si.peptide_ref = pe.peptide_ref
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73 JOIN peptides pep ON pe.peptide_ref = pep.id
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74 WHERE pe.isDecoy = 'false'
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75 ORDER BY sr.spectrumTitle,si.rank
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76 """
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77
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78
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79 ## Peptide Post Translational Modifications
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80 PEP_MODS_QUERY = """\
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81 SELECT location, residue, name, modType, '' as "unimod"
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82 FROM peptide_modifications
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83 WHERE peptide_ref = :peptide_ref
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84 ORDER BY location, modType, name
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85 """
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86
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87
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88 ## number of peptides to which the spectrum maps
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
89 ## spectrum_identification_results => spectrum_identification_result_items -> peptide_evidence
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
90 SPECTRUM_PEPTIDES_QUERY = """\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
91 SELECT count(distinct pep.sequence)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
92 FROM spectrum_identification_results sr
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
93 JOIN spectrum_identification_result_items si ON si.spectrum_identification_result_ref = sr.id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
94 JOIN peptide_evidence pe ON si.peptide_ref = pe.peptide_ref
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
95 JOIN peptides pep ON pe.peptide_ref = pep.id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
96 WHERE pe.isDecoy = 'false'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
97 AND sr.id = :sr_id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
98 GROUP BY sr.id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
99 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
100
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
101
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
102 ## number of genomic locations to which the peptide sequence maps
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
103 ## uniqueness of the peptide mapping
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
104 ## peptides => peptide_evidence -> db_sequence -> location
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
105 ## proteins_by_peptide
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
106 PEPTIDE_ACC_QUERY = """\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
107 SELECT
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
108 pe.dBSequence_ref,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
109 pe.start,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
110 pe.end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
111 FROM peptide_evidence pe
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
112 JOIN peptides pep ON pe.peptide_ref = pep.id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
113 WHERE pe.isDecoy = 'false'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
114 AND pep.sequence = :sequence
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
115 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
116
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
117
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
118 MAP_QUERY = """\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
119 SELECT distinct *
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
120 FROM feature_cds_map
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
121 WHERE name = :acc
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
122 AND :p_start < cds_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
123 AND :p_end >= cds_start
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
124 ORDER BY name,cds_start,cds_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
125 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
126
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
127
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
128 GENOMIC_POS_QUERY = """\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
129 SELECT distinct chrom, CASE WHEN strand = '+' THEN start + :cds_offset - cds_start ELSE end - :cds_offset - cds_start END as "pos"
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
130 FROM feature_cds_map
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
131 WHERE name = :acc
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
132 AND :cds_offset >= cds_start
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
133 AND :cds_offset < cds_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
134 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
135
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
136
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
137 FEATURE_QUERY = """\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
138 SELECT distinct seqid,start,end,featuretype,strand,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
139 CAST(frame AS INTEGER) as "frame", CAST(frame AS INTEGER)==:frame as "in_frame",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
140 CASE WHEN :strand = '+' THEN start - :start ELSE end - :end END as "start_pos",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
141 CASE WHEN :strand = '+' THEN end - :end ELSE start - :start END as "end_pos",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
142 parent as "name"
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
143 FROM features JOIN relations ON features.id = relations.child
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
144 WHERE seqid = :seqid
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
145 AND parent in (
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
146 SELECT id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
147 FROM features
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
148 WHERE seqid = :seqid
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
149 AND featuretype = 'transcript'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
150 AND start <= :tstart AND :tend <= end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
151 )
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
152 AND :end >= start AND :start <= end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
153 AND featuretype in ('CDS','five_prime_utr','three_prime_utr','transcript')
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
154 ORDER BY strand = :strand DESC, featuretype
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
155 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
156
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
157 ## Use order by to get best matches
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
158 ## one_exon strand, featuretype, contained, inframe,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
159 ## first_exon strand, featuretype, contained, end_pos,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
160 ## middle_exon strand, featuretype, contained, start_pos, end_pos,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
161 ## last_exon strand, featuretype, contained, start_pos,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
162
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
163 ONLY_EXON_QUERY = FEATURE_QUERY + """,\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
164 start <= :start AND end >= :end DESC,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
165 in_frame DESC, end - start DESC, start DESC, end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
166 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
167
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
168 FIRST_EXON_QUERY = FEATURE_QUERY + """,\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
169 start <= :start AND end >= :end DESC,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
170 in_frame DESC, abs(end_pos), start DESC, end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
171 """
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
172
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
173 MIDDLE_EXON_QUERY = FEATURE_QUERY + """,\
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
174 start <= :start AND end >= :end DESC,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
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175 in_frame DESC, abs(start_pos), abs(end_pos), start DESC, end
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176 """
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177
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178 LAST_EXON_QUERY = FEATURE_QUERY + """,\
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179 start <= :start AND end >= :end DESC,
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180 in_frame DESC, abs(start_pos), start DESC, end
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181 """
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182
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183
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184 def __main__():
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185 parser = argparse.ArgumentParser(
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186 description='Generate proBED and proBAM from mz.sqlite')
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187 parser.add_argument('mzsqlite', help="mz.sqlite converted from mzIdentML")
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188 parser.add_argument('genomic_mapping_sqlite', help="genomic_mapping.sqlite with feature_cds_map table")
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189 parser.add_argument(
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190 '-R', '--genomeReference', default='Unknown',
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191 help='Genome reference sequence in 2bit format')
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192 parser.add_argument(
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193 '-t', '--twobit', default=None,
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194 help='Genome reference sequence in 2bit format')
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195 parser.add_argument(
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196 '-r', '--reads_bam', default=None,
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197 help='reads alignment bam path')
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198 parser.add_argument(
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199 '-g', '--gffutils_sqlite', default=None,
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200 help='gffutils GTF sqlite DB')
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201 parser.add_argument(
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202 '-B', '--probed', default=None,
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203 help='proBed path')
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204 parser.add_argument(
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205 '-s', '--prosam', default=None,
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206 help='proSAM path')
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207 parser.add_argument(
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208 '-b', '--probam', default=None,
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209 help='proBAM path')
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210 parser.add_argument(
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211 '-l', '--limit', type=int, default=None,
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212 help='limit numbers of PSMs for testing')
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213 parser.add_argument('-v', '--verbose', action='store_true', help='Verbose')
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214 parser.add_argument('-d', '--debug', action='store_true', help='Debug')
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215 args = parser.parse_args()
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216
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217 def get_sequence(chrom, start, end):
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218 if twobit:
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219 if chrom in twobit and 0 <= start < end < len(twobit[chrom]):
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220 return twobit[chrom][start:end]
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221 contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
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222 if contig in twobit and 0 <= start < end < len(twobit[contig]):
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223 return twobit[contig][start:end]
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224 return ''
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225 return None
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226
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227 twobit = TwoBitFile(args.twobit) if args.twobit else None
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228 samfile = pysam.AlignmentFile(args.reads_bam, "rb" ) if args.reads_bam else None
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229 seqlens = twobit.sequence_sizes()
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230
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231 probed = open(args.probed,'w') if args.probed else sys.stdout
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232
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233 gff_cursor = get_connection(args.gffutils_sqlite).cursor() if args.gffutils_sqlite else None
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234 map_cursor = get_connection(args.genomic_mapping_sqlite).cursor()
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235 mz_cursor = get_connection(args.mzsqlite).cursor()
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236
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237 unmapped_accs = set()
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238 timings = dict()
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239 def add_time(name,elapsed):
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240 if name in timings:
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241 timings[name] += elapsed
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242 else:
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243 timings[name] = elapsed
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244
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245 XG_TYPES = ['N','V','W','J','A','M','C','E','B','O','T','R','I','G','D','U','X','*']
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246 FT_TYPES = ['CDS','five_prime_utr','three_prime_utr','transcript']
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247 def get_exon_features(exons):
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248 efeatures = None
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249 transcript_features = dict()
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250 t_start = min(exons[0][2],exons[-1][2])
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251 t_end = max(exons[0][3],exons[-1][3])
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252 if gff_cursor:
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253 ts = time()
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254 (acc,gc,gs,ge,st,cs,ce) = exons[0]
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255 ft_params = {"seqid" : str(gc).replace('chr',''), 'strand' : st, 'tstart': t_start, 'tend': t_end}
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256 efeatures = [None] * len(exons)
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257 for i,exon in enumerate(exons):
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258 (acc,gc,gs,ge,st,cs,ce) = exon
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diff changeset
259 fr = cs % 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
260 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
261 print('exon:\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % (acc,gc,gs,ge,st,cs,ce,fr),file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
262 ft_params = {"seqid" : str(gc).replace('chr',''), "start" : gs + 1, "end" : ge, 'strand' : st, 'frame' : fr, 'tstart': t_start, 'tend': t_end}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
263 if len(exons) == 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
264 q = ONLY_EXON_QUERY
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
265 elif i == 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
266 q = FIRST_EXON_QUERY
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
267 elif len(exons) - i == 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
268 q = LAST_EXON_QUERY
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
269 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
270 q = MIDDLE_EXON_QUERY
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
271 features = [f for f in gff_cursor.execute(q,ft_params)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
272 transcripts = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
273 efeatures[i] = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
274 for j,f in enumerate(features):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
275 transcript = f[-1]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
276 ftype = f[3]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
277 if ftype == 'transcript':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
278 if i > 0 or efeatures[i]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
279 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
280 if i == 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
281 if transcript not in transcript_features:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
282 transcript_features[transcript] = [[] for _ in range(len(exons))]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
283 transcript_features[transcript][i].append(f)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
284 efeatures[i].append(f)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
285 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
286 if transcript in transcript_features:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
287 transcript_features[transcript][i].append(f)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
288 efeatures[i].append(f)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
289 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
290 del transcript_features[transcript]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
291 if not efeatures[i]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
292
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
293 efeatures[i] = transcripts
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
294 for f in efeatures[i]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
295 (seqid,start,end,featuretype,strand,frame,in_frame,start_offset,end_offset,parent) = f
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
296 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
297 print('feat%d:\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % \
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
298 (i,seqid,start,end,featuretype,strand,frame,str(in_frame) == '1',start_offset,end_offset,parent),file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
299 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
300 print('fmap:\t%s' % transcript_features,file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
301 return (efeatures,transcript_features)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
302
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
303 def is_structural_variant(exons):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
304 if len(exons) > 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
305 (acc,gc,gs,ge,st,cs,ce) = exons[0]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
306 for i in range(1,len(exons)):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
307 if gc != exons[i][1] or st != exons[i][4]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
308 return True
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
309 return False
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
310
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
311 XG_TYPES = ['N','V','W','J','A','M','C','E','B','O','T','R','I','G','D','U','X','*']
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
312 FT_TYPES = ['CDS','five_prime_utr','three_prime_utr','transcript']
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
313 def classify_transcript(exons,transcript_features,ref_prot,peptide):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
314 etypes = ['*'] * len(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
315 features = transcript_features[0]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
316 (acc,gc,gs,ge,st,cs,ce) = exons[0]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
317 if len(features) == 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
318 (seqid,start,end,featuretype,strand,frame,in_frame,start_offset,end_offset,parent) = features[0]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
319 if strand == st:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
320 if featuretype == 'CDS':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
321 if start <= gs and ge <= end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
322 if in_frame:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
323 if ref_prot == peptide:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
324 if len(exons) > 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
325 pass
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
326 return 'N'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
327 elif len(ref_prot) != len(peptide):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
328 return 'W'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
329 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
330 return 'V'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
331 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
332 return 'O'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
333 elif strand == '+' and start <= gs or ge > end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
334 return 'C'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
335 elif strand == '-' and start <= gs and ge <= end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
336 return 'C'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
337 elif featuretype == 'five_prime_utr':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
338 return 'E'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
339 elif featuretype == 'three_prime_utr':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
340 return 'B'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
341 elif featuretype == 'transcript':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
342 return 'I'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
343 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
344 return 'R'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
345 elif len(features) > 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
346 ftypes = [f[3] for f in features]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
347 if 'five_prime_utr' in ftypes:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
348 return 'E'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
349 elif 'three_prime_utr' in ftypes:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
350 return 'B'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
351 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
352 return 'C'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
353 return '*'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
354
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
355 def classify_peptide(exons,ref_prot,peptide,pep_cds,probam_dict):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
356 if ref_prot != peptide and samfile:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
357 try:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
358 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
359 print('name: %s \nref: %s\npep: %s\n' % (scan_name,ref_prot,peptide), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
360 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
361 for exon in exons:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
362 (acc,chrom,start,end,strand,c_start,c_end) = exon
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
363 a_start = c_start / 3 * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
364 a_end = c_end / 3 * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
365 if ref_prot[a_start:a_end] != peptide[a_start:a_end]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
366 pileup = get_exon_pileup(chrom,start,end)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
367 for i, (bi,ai,ao) in enumerate([(i,i / 3, i % 3) for i in range(c_start, c_end)]):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
368 if ao == 0 or i == 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
369 if ref_prot[ai] != peptide[ai]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
370 codon = get_pep_codon(pileup, bi - c_start, peptide[ai], ao)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
371 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
372 print('%d %d %d %s : %s %s %s' % (bi,ai,ao, peptide[ai], str(pep_cds[:bi]), str(codon), str(pep_cds[bi+3:])), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
373 if codon:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
374 pep_cds = pep_cds[:bi] + codon + pep_cds[bi+3:]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
375 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
376 add_time('var_cds',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
377 except Exception as e:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
378 print('name: %s \nref: %s\npep: %s\n%s\n' % (scan_name,ref_prot,peptide,e), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
379 probam_dict['XG'] = '*'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
380 if is_structural_variant(exons):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
381 probam_dict['XG'] = 'G'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
382 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
383 (efeatures,transcript_features) = get_exon_features(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
384 n = len(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
385 if efeatures and efeatures[0]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
386 for f in efeatures[0]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
387 transcript = f[9]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
388 features = transcript_features[transcript]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
389 xg = classify_transcript(exons,features,ref_prot,peptide)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
390 if xg != '*':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
391 probam_dict['XG'] = xg
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
392 break
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
393 return pep_cds
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
394
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
395 def get_variant_cds(exons,ref_prot,peptide,pep_cds):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
396 if ref_prot != peptide and samfile:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
397 try:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
398 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
399 print('name: %s \nref: %s\npep: %s\n' % (scan_name,ref_prot,peptide), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
400 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
401 for exon in exons:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
402 (acc,chrom,start,end,strand,c_start,c_end) = exon
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
403 a_start = c_start / 3 * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
404 a_end = c_end / 3 * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
405 if ref_prot[a_start:a_end] != peptide[a_start:a_end]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
406 pileup = get_exon_pileup(chrom,start,end)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
407 for i, (bi,ai,ao) in enumerate([(i,i / 3, i % 3) for i in range(c_start, c_end)]):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
408 if ao == 0 or i == 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
409 if ref_prot[ai] != peptide[ai]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
410 codon = get_pep_codon(pileup, bi - c_start, peptide[ai], ao)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
411 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
412 print('%d %d %d %s : %s %s %s' % (bi,ai,ao, peptide[ai], str(pep_cds[:bi]), str(codon), str(pep_cds[bi+3:])), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
413 if codon:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
414 pep_cds = pep_cds[:bi] + codon + pep_cds[bi+3:]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
415 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
416 add_time('var_cds',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
417 except Exception as e:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
418 print('name: %s \nref: %s\npep: %s\n%s\n' % (scan_name,ref_prot,peptide,e), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
419 return pep_cds
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
420
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
421 def get_mapping(acc,pep_start,pep_end):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
422 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
423 p_start = (pep_start - 1) * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
424 p_end = pep_end * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
425 map_params = {"acc" : acc, "p_start" : p_start, "p_end" : p_end}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
426 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
427 print('%s' % map_params, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
428 locs = [l for l in map_cursor.execute(MAP_QUERY,map_params)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
429 exons = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
430 ## ========= pep
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
431 ## --- continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
432 ## --- trim
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
433 ## --- copy
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
434 ## --- trim
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
435 ## --- break
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
436 c_end = 0
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
437 for i, (acc,chrom,start,end,strand,cds_start,cds_end) in enumerate(locs):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
438 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
439 print('Prot: %s\t%s:%d-%d\t%s\t%d\t%d' % (acc,chrom,start,end,strand,cds_start,cds_end),file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
440 c_start = c_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
441 if cds_end < p_start:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
442 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
443 if cds_start >= p_end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
444 break
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
445 if strand == '+':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
446 if cds_start < p_start:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
447 start += p_start - cds_start
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
448 if cds_end > p_end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
449 end -= cds_end - p_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
450 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
451 if cds_start < p_start:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
452 end -= p_start - cds_start
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
453 if cds_end > p_end:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
454 start += cds_end - p_end
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
455 c_end = c_start + abs(end - start)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
456 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
457 print('Pep: %s\t%s:%d-%d\t%s\t%d\t%d' % (acc,chrom,start,end,strand,cds_start,cds_end),file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
458 exons.append([acc,chrom,start,end,strand,c_start,c_end])
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
459 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
460 add_time('get_mapping',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
461 return exons
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
462
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
463 def get_cds(exons):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
464 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
465 seqs = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
466 for i, (acc,chrom,start,end,strand,cds_start,cds_end) in enumerate(exons):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
467 seq = get_sequence(chrom, min(start,end), max(start,end))
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
468 if strand == '-':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
469 seq = reverse_complement(seq)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
470 seqs.append(seq)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
471 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
472 add_time('get_cds',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
473 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
474 print('CDS: %s' % str(seqs),file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
475 return ''.join(seqs) if seqs else ''
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
476
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
477 def genomic_mapping_count(peptide):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
478 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
479 params = {"sequence" : peptide}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
480 acc_locs = [l for l in mz_cursor.execute(PEPTIDE_ACC_QUERY,params)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
481 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
482 add_time('PEPTIDE_ACC_QUERY',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
483 if acc_locs:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
484 if len(acc_locs) == 1:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
485 return 1
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
486 locations = set()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
487 for i,acc_loc in enumerate(acc_locs):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
488 (acc,pep_start,pep_end) = acc_loc
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
489 if acc in unmapped_accs:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
490 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
491 try:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
492 add_time('GENOMIC_POS_QUERY_COUNT',1)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
493 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
494 p_start = pep_start * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
495 p_end = pep_end * 3
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
496 params = {"acc" : acc, "cds_offset" : p_start}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
497 (start_chrom,start_pos) = map_cursor.execute(GENOMIC_POS_QUERY, params).fetchone()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
498 params = {"acc" : acc, "cds_offset" : p_end}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
499 (end_chrom,end_pos) = map_cursor.execute(GENOMIC_POS_QUERY, params).fetchone()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
500 locations.add('%s:%s-%s:%s' % (start_chrom,start_pos,end_chrom,end_pos))
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
501 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
502 add_time('GENOMIC_POS_QUERY',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
503 except:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
504 unmapped_accs.add(acc)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
505 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
506 print('Unmapped: %s' % acc, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
507 return len(locations)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
508 return -1
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
509
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
510 def spectrum_peptide_count(spectrum_id):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
511 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
512 params = {"sr_id" : spectrum_id}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
513 pep_count = mz_cursor.execute(SPECTRUM_PEPTIDES_QUERY, params).fetchone()[0]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
514 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
515 add_time('SPECTRUM_PEPTIDES_QUERY',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
516 return pep_count
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
517
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
518 def get_exon_pileup(chrom,chromStart,chromEnd):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
519 cols = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
520 for pileupcolumn in samfile.pileup(chrom, chromStart, chromEnd):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
521 if chromStart <= pileupcolumn.reference_pos <= chromEnd:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
522 bases = dict()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
523 col = {'depth' : 0, 'cov' : pileupcolumn.nsegments, 'pos': pileupcolumn.reference_pos, 'bases' : bases}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
524 for pileupread in pileupcolumn.pileups:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
525 if not pileupread.is_del and not pileupread.is_refskip:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
526 col['depth'] += 1
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
527 base = pileupread.alignment.query_sequence[pileupread.query_position]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
528 if base not in bases:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
529 bases[base] = 1
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
530 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
531 bases[base] += 1
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
532 cols.append(col)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
533 return cols
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
534
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
535 codon_map = {"TTT":"F", "TTC":"F", "TTA":"L", "TTG":"L",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
536 "TCT":"S", "TCC":"S", "TCA":"S", "TCG":"S",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
537 "TAT":"Y", "TAC":"Y", "TAA":"*", "TAG":"*",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
538 "TGT":"C", "TGC":"C", "TGA":"*", "TGG":"W",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
539 "CTT":"L", "CTC":"L", "CTA":"L", "CTG":"L",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
540 "CCT":"P", "CCC":"P", "CCA":"P", "CCG":"P",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
541 "CAT":"H", "CAC":"H", "CAA":"Q", "CAG":"Q",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
542 "CGT":"R", "CGC":"R", "CGA":"R", "CGG":"R",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
543 "ATT":"I", "ATC":"I", "ATA":"I", "ATG":"M",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
544 "ACT":"T", "ACC":"T", "ACA":"T", "ACG":"T",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
545 "AAT":"N", "AAC":"N", "AAA":"K", "AAG":"K",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
546 "AGT":"S", "AGC":"S", "AGA":"R", "AGG":"R",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
547 "GTT":"V", "GTC":"V", "GTA":"V", "GTG":"V",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
548 "GCT":"A", "GCC":"A", "GCA":"A", "GCG":"A",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
549 "GAT":"D", "GAC":"D", "GAA":"E", "GAG":"E",
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
550 "GGT":"G", "GGC":"G", "GGA":"G", "GGG":"G",}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
551
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
552 aa_codon_map = dict()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
553 for c,a in codon_map.items():
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
554 aa_codon_map[a] = [c] if a not in aa_codon_map else aa_codon_map[a] + [c]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
555
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
556 aa_na_map = dict() # m[aa]{bo : {b1 : [b3]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
557 for c,a in codon_map.items():
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
558 if a not in aa_na_map:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
559 aa_na_map[a] = dict()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
560 d = aa_na_map[a]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
561 for i in range(3):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
562 b = c[i]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
563 if i < 2:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
564 if b not in d:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
565 d[b] = dict() if i < 1 else set()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
566 d = d[b]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
567 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
568 d.add(b)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
569
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
570 def get_pep_codon(pileup, idx, aa, ao):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
571 try:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
572 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
573 bases = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
574 for i in range(3):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
575 if i < ao:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
576 bases.append(list(set([c[i] for c in aa_codon_map[aa]])))
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
577 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
578 bases.append([b for b, cnt in reversed(sorted(pileup[idx + i]['bases'].iteritems(), key=lambda (k,v): (v,k)))])
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
579 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
580 print('%s' % bases,file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
581 for b0 in bases[0]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
582 if b0 not in aa_na_map[aa]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
583 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
584 for b1 in bases[1]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
585 if b1 not in aa_na_map[aa][b0]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
586 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
587 for b2 in bases[2]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
588 if b2 in aa_na_map[aa][b0][b1]:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
589 return '%s%s%s' % (b0,b1,b2)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
590 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
591 add_time('pep_codon',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
592 except Exception as e:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
593 print("get_pep_codon: %s %s %s %s"
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
594 % (aa, ao, idx, pileup), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
595 raise e
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
596 return None
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
597
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
598 def write_probed(chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
599 spectrum,protacc,peptide,uniqueness,genomeReference,score=1000,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
600 psmScore='.', fdr='.', mods='.', charge='.',
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
601 expMassToCharge='.', calcMassToCharge='.',
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
602 psmRank='.', datasetID='.', uri='.'):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
603 probed.write('%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' % \
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
604 (chrom,chromStart,chromEnd,spectrum,score,strand,chromStart,chromEnd,'0',blockCount,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
605 ','.join([str(v) for v in blockSizes]),
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
606 ','.join([str(v) for v in blockStarts]),
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
607 protacc,peptide,uniqueness, genomeReference,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
608 psmScore, fdr, mods, charge, expMassToCharge, calcMassToCharge, psmRank, datasetID, uri))
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
609
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
610 def get_genomic_location(exons):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
611 chrom = exons[0][1]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
612 strand = exons[0][4]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
613 pos = [exon[2] for exon in exons] + [exon[3] for exon in exons]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
614 chromStart = min(pos)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
615 chromEnd = max(pos)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
616 blockCount = len(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
617 blockSizes = [abs(exon[3] - exon[2]) for exon in exons]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
618 blockStarts = [min(exon[2],exon[3]) - chromStart for exon in exons]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
619 return (chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
620
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
621 def get_psm_modifications(peptide_ref):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
622 mods = []
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
623 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
624 params = {"peptide_ref" : peptide_ref}
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
625 pepmods = [m for m in mz_cursor.execute(PEP_MODS_QUERY, params)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
626 if pepmods:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
627 for (location, residue, name, modType, unimod) in pepmods:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
628 mods.append('%s-%s' % (location, unimod if unimod else '%s%s' % (name,residue)))
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
629 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
630 add_time('PEP_MODS_QUERY',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
631 return ';'.join(mods)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
632
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
633 ## iterate through PSMs
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
634 psm_cursor = get_connection(args.mzsqlite).cursor()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
635 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
636 psms = psm_cursor.execute(PSM_QUERY)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
637 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
638 add_time('PSM_QUERY',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
639 proBAM = ProBAM(species=None,assembly=args.genomeReference,seqlens=seqlens,comments=[]) if args.prosam or args.probam else None
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
640 proBED = ProBED(species=None,assembly=args.genomeReference,comments=[]) if args.probed else None
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
641 for i, psm in enumerate(psms):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
642 probam_dict = PROBAM_DEFAULTS.copy()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
643 (acc,pep_start,pep_end,aa_pre,aa_post,peptide,spectrum_id,spectrum_title,rank,charge,calcmass,exprmass,pepref) = psm
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
644 scan_name = spectrum_title if spectrum_title else spectrum_id
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
645 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
646 print('\nPSM: %d\t%s' % (i, '\t'.join([str(v) for v in (acc,pep_start,pep_end,peptide,spectrum_id,scan_name,rank,charge,calcmass,exprmass)])), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
647 exons = get_mapping(acc,pep_start,pep_end)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
648 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
649 print('%s' % exons, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
650 if not exons:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
651 continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
652 mods = get_psm_modifications(pepref)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
653 (chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts) = get_genomic_location(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
654 ref_cds = get_cds(exons)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
655 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
656 print('%s' % ref_cds, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
657 ref_prot = translate(ref_cds)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
658 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
659 print('%s' % ref_prot, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
660 print('%s' % peptide, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
661 spectrum_peptides = spectrum_peptide_count(spectrum_id)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
662 peptide_locations = genomic_mapping_count(peptide)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
663 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
664 print('spectrum_peptide_count: %d\tpeptide_location_count: %d' % (spectrum_peptides,peptide_locations), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
665 uniqueness = 'unique' if peptide_locations == 1 else 'not-unique[unknown]'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
666 if proBED is not None:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
667 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
668 proBEDEntry = ProBEDEntry(chrom,chromStart,chromEnd,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
669 '%s_%s' % (acc,scan_name),
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
670 1000,strand,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
671 blockCount,blockSizes,blockStarts,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
672 acc,peptide,uniqueness,args.genomeReference,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
673 charge=charge,expMassToCharge=exprmass,calcMassToCharge=calcmass,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
674 mods=mods if mods else '.', psmRank=rank)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
675 proBED.add_entry(proBEDEntry)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
676 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
677 add_time('add_probed',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
678 if proBAM is not None:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
679 if len(ref_prot) != len(peptide):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
680 pass
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
681 # continue
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
682 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
683 probam_dict['NH'] = peptide_locations
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
684 probam_dict['XO'] = uniqueness
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
685 probam_dict['XL'] = peptide_locations
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
686 probam_dict['XP'] = peptide
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
687 probam_dict['YP'] = acc
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
688 probam_dict['XC'] = charge
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
689 probam_dict['XB'] = '%f;%f;%f' % (exprmass - calcmass, exprmass, calcmass)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
690 probam_dict['XR'] = ref_prot # ? dbSequence
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
691 probam_dict['YA'] = aa_post
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
692 probam_dict['YB'] = aa_pre
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
693 probam_dict['XM'] = mods if mods else '*'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
694 flag = 16 if strand == '-' else 0
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
695 if str(rank)!=str(1) and rank!='*' and rank!=[] and rank!="":
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
696 flag += 256
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
697 probam_dict['XF'] = ','.join([str(e[2] % 3) for e in exons])
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
698 ## what if structural variant, need to split into multiple entries
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
699 ## probam_dict['XG'] = peptide_type
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
700 pep_cds = classify_peptide(exons,ref_prot,peptide,ref_cds,probam_dict)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
701 ## probam_dict['MD'] = peptide
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
702
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
703 ## FIX SAM sequence is forward strand
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
704 seq = pep_cds if strand == '+' else reverse_complement(pep_cds)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
705 ## cigar based on plus strand
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
706 cigar = ''
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
707 if strand == '+':
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
708 blkStarts = blockStarts
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
709 blkSizes = blockSizes
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
710 else:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
711 blkStarts = [x for x in reversed(blockStarts)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
712 blkSizes = [x for x in reversed(blockSizes)]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
713 for j in range(blockCount):
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
714 if j > 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
715 intron = blkStarts[j] - (blkStarts[j-1] + blkSizes[j-1])
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
716 if intron > 0:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
717 cigar += '%dN' % intron
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
718 cigar += '%dM' % blkSizes[j]
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
719 proBAMEntry = ProBAMEntry(qname=scan_name, flag=flag, rname=chrom, pos=chromStart+1,
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
720 cigar=cigar,seq=seq,optional=probam_dict)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
721 proBAM.add_entry(proBAMEntry)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
722 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
723 add_time('add_probam',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
724 if args.debug:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
725 print('%s' % probam_dict, file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
726 if args.limit and i >= args.limit:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
727 break
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
728 if args.probed:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
729 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
730 with open(args.probed,'w') as fh:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
731 proBED.write(fh)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
732 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
733 add_time('write_probed',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
734 if args.prosam or args.probam:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
735 samfile = args.prosam if args.prosam else 'temp.sam'
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
736 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
737 with open(samfile,'w') as fh:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
738 proBAM.write(fh)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
739 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
740 add_time('write_prosam',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
741 if args.probam:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
742 ts = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
743 bamfile = args.prosam.replace('.sam','.bam')
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
744 pysam.view(samfile, '-b', '-o', args.probam, catch_stdout=False)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
745 te = time()
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
746 add_time('write_probam',te - ts)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
747 pysam.index(args.probam)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
748
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
749 if args.verbose:
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
750 print('\n%s\n' % str(timings), file=sys.stderr)
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
751
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
752 if __name__ == "__main__":
f2dc9805107a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
galaxyp
parents:
diff changeset
753 __main__()