def buildJunctionExonAnnotations(species,array_type,specific_array_type,force,genomic_build):
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'; run_from_scratch = 'yes'; force='no'
export_all_associations = 'no' ### YES only for protein prediction analysis
#buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force)
### Get genomic locations and initial annotations for exon sequences (exon pobesets and junctions)
import JunctionArray
import JunctionArrayEnsemblRules
""" The following functions:
1) Extract transcript cluster-to-gene annotations
2) Extract exon sequences for junctions and exon probesets from the Affymetrix annotation file (version 2.0),
3) Map these sequences to Ensembl gene sequences (build specific) plus and minus 2KB, upstream and downstream
4) Obtain AltAnalyze exon region annotations and obtain full-length exon sequences for each exon probeset
5) Consoladate these into an Ensembl_probeset.txt file (rather than Ensembl_junction_probeset.txt) with junctions
having a single probeset identifier.
6) Determine which junctions and junction-exons represent recipricol junctions using:
a) AltAnalyze identified recipricol junctions from Ensembl and UCSC and
b) Affymetrix suggested recipricol junctions based on common exon cluster annotations, creating
Mm_junction_comps_updated.txt.
c) De novo comparison of all exon-junction region IDs for all junctions using the EnsemblImport method compareJunctions().
"""
### Steps 1-3
JunctionArray.getJunctionExonLocations(species,array_type,specific_array_type)
### Step 4
JunctionArrayEnsemblRules.getAnnotations(species,array_type,'yes',force)
### Step 5-6
JunctionArray.identifyJunctionComps(species,array_type,specific_array_type)
def buildJunctionExonAnnotations(species, array_type, specific_array_type,
force, genomic_build):
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'
run_from_scratch = 'yes'
force = 'no'
export_all_associations = 'no' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species, mRNA_Type, export_all_associations,
run_from_scratch, force)
### Get genomic locations and initial annotations for exon sequences (exon pobesets and junctions)
import JunctionArray
import JunctionArrayEnsemblRules
""" The following functions:
1) Extract transcript cluster-to-gene annotations
2) Extract exon sequences for junctions and exon probesets from the Affymetrix annotation file (version 2.0),
3) Map these sequences to Ensembl gene sequences (build specific) plus and minus 2KB, upstream and downstream
4) Obtain AltAnalyze exon region annotations and obtain full-length exon sequences for each exon probeset
5) Consoladate these into an Ensembl_probeset.txt file (rather than Ensembl_junction_probeset.txt) with junctions
having a single probeset identifier.
6) Determine which junctions and junction-exons represent recipricol junctions using:
a) AltAnalyze identified recipricol junctions from Ensembl and UCSC and
b) Affymetrix suggested recipricol junctions based on common exon cluster annotations, creating
Mm_junction_comps_updated.txt.
c) De novo comparison of all exon-junction region IDs for all junctions using the EnsemblImport method compareJunctions().
"""
### Steps 1-3
JunctionArray.getJunctionExonLocations(species, array_type,
specific_array_type)
### Step 4
JunctionArrayEnsemblRules.getAnnotations(species, array_type, 'yes', force)
### Step 5-6
JunctionArray.identifyJunctionComps(species, array_type,
specific_array_type)
def buildAltMouseExonAnnotations(species,array_type,force,genomic_build):
"""Code required to:
1) Extract out Affymetrix provided exon sequence (probeset sequence extracted from "probeset_sequence_reversed.txt", derived
directly from the Affymetrix AltMouse probe annotation file), from the "SEQUENCE-transcript-dbase.txt" (built using
dump-chip1 .gff sequence and AltMerge-Peptide Informatics script "sequence_analysis_AltMouse_refseq.py").
2) Once exported, grab full length exon sequences using exon/intron coordinates matches to full-length gene sequences with 2kb
flanking sequence to efficiently predict microRNA binding site exclusion (reAnnotateCriticalExonSequences) and later for
coordinate mapping to get exons aligning with UCSC annotated splicing annotations and exons. This sequence data replaced
the previous file (don't need to re-run this - see rederive_exonseq == 'yes' below for reference).
3) Match the updated exon sequences to the most recent genomic coordinates and build the exact equivalent of the exon array
Mm_Ensembl_probeset.txt database (same structure and ExonArrayEnsemblRules.py code). This involves running EnsemblImport.
This code should be run before the exon array location build code since the "Mm_Ensembl_probeset.txt" is created and then re-
written as "Mm_AltMouse_Ensembl_probeset.txt".
"""
import JunctionArray
import JunctionArrayEnsemblRules
rederive_exonseq = 'no'
### Only needs to be run once, to export exon sequence for AltMouse array the original (1 and 2 above)
if rederive_exonseq == 'yes':
import AltAnalyze
import ExonAnnotate_module
import ExonAnalyze_module
agglomerate_inclusion_probesets = 'no'; onlyAnalyzeJunctions='no'
probeset_annotations_file = "AltDatabase/"+species+"/"+array_type+"/"+"MASTER-probeset-transcript.txt"
verifyFile(probeset_annotations_file,array_type) ### Will force download if missing
exon_db={}; filtered_arrayids={};filter_status='no'
constituitive_probeset_db,exon_db,genes_being_analyzed = AltAnalyze.importSplicingAnnotationDatabase(probeset_annotations_file,array_type,filtered_arrayids,filter_status)
alt_junction_db,critical_exon_db,exon_dbase,exon_inclusion_db,exon_db = ExonAnnotate_module.identifyPutativeSpliceEvents(exon_db,constituitive_probeset_db,{},agglomerate_inclusion_probesets,onlyAnalyzeJunctions)
ExonAnnotate_module.exportJunctionComparisons(alt_junction_db,critical_exon_db,exon_dbase)
print "Finished exporting junctions used in AltMouse array comparisons."
ExonAnalyze_module.exportAltMouseExonSequence()
JunctionArray.reAnnotateCriticalExonSequences(species,array_type)
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'; run_from_scratch = 'yes'
export_all_associations = 'no' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species,mRNA_Type,export_all_associations,run_from_scratch,force)
reannotate_exon_seq = 'yes'
print 'genomic_build', genomic_build
if genomic_build == 'new':
### Need to run with every new genomic build (match up new coordinates
print "Begining to derive exon sequence from new genomic build"
JunctionArray.identifyCriticalExonLocations(species,array_type)
reannotate_exon_seq = 'yes'
JunctionArrayEnsemblRules.getAnnotations(species,array_type,reannotate_exon_seq,force)
### Download files required during AltAnalyze analysis but not during the database build process
filename = "AltDatabase/"+species+"/"+array_type+"/"+"MASTER-probeset-transcript.txt"
verifyFile(filename,array_type) ### Will force download if missing
filename = "AltDatabase/"+species+'/'+ array_type+'/'+array_type+"_annotations.txt"
verifyFile(filename,array_type) ### Will force download if missing
def buildAltMouseExonAnnotations(species, array_type, force, genomic_build):
"""Code required to:
1) Extract out Affymetrix provided exon sequence (probeset sequence extracted from "probeset_sequence_reversed.txt", derived
directly from the Affymetrix AltMouse probe annotation file), from the "SEQUENCE-transcript-dbase.txt" (built using
dump-chip1 .gff sequence and AltMerge-Peptide Informatics script "sequence_analysis_AltMouse_refseq.py").
2) Once exported, grab full length exon sequences using exon/intron coordinates matches to full-length gene sequences with 2kb
flanking sequence to efficiently predict microRNA binding site exclusion (reAnnotateCriticalExonSequences) and later for
coordinate mapping to get exons aligning with UCSC annotated splicing annotations and exons. This sequence data replaced
the previous file (don't need to re-run this - see rederive_exonseq == 'yes' below for reference).
3) Match the updated exon sequences to the most recent genomic coordinates and build the exact equivalent of the exon array
Mm_Ensembl_probeset.txt database (same structure and ExonArrayEnsemblRules.py code). This involves running EnsemblImport.
This code should be run before the exon array location build code since the "Mm_Ensembl_probeset.txt" is created and then re-
written as "Mm_AltMouse_Ensembl_probeset.txt".
"""
import JunctionArray
import JunctionArrayEnsemblRules
rederive_exonseq = 'no'
### Only needs to be run once, to export exon sequence for AltMouse array the original (1 and 2 above)
if rederive_exonseq == 'yes':
import AltAnalyze
import ExonAnnotate_module
import ExonAnalyze_module
agglomerate_inclusion_probesets = 'no'
onlyAnalyzeJunctions = 'no'
probeset_annotations_file = "AltDatabase/" + species + "/" + array_type + "/" + "MASTER-probeset-transcript.txt"
verifyFile(probeset_annotations_file,
array_type) ### Will force download if missing
exon_db = {}
filtered_arrayids = {}
filter_status = 'no'
constituitive_probeset_db, exon_db, genes_being_analyzed = AltAnalyze.importSplicingAnnotationDatabase(
probeset_annotations_file, array_type, filtered_arrayids,
filter_status)
alt_junction_db, critical_exon_db, exon_dbase, exon_inclusion_db, exon_db = ExonAnnotate_module.identifyPutativeSpliceEvents(
exon_db, constituitive_probeset_db, {},
agglomerate_inclusion_probesets, onlyAnalyzeJunctions)
ExonAnnotate_module.exportJunctionComparisons(alt_junction_db,
critical_exon_db,
exon_dbase)
print "Finished exporting junctions used in AltMouse array comparisons."
ExonAnalyze_module.exportAltMouseExonSequence()
JunctionArray.reAnnotateCriticalExonSequences(species, array_type)
### Get UCSC associations (download databases if necessary)
mRNA_Type = 'mrna'
run_from_scratch = 'yes'
export_all_associations = 'no' ### YES only for protein prediction analysis
buildUCSCAnnoationFiles(species, mRNA_Type, export_all_associations,
run_from_scratch, force)
reannotate_exon_seq = 'yes'
print 'genomic_build', genomic_build
if genomic_build == 'new':
### Need to run with every new genomic build (match up new coordinates
print "Begining to derive exon sequence from new genomic build"
JunctionArray.identifyCriticalExonLocations(species, array_type)
reannotate_exon_seq = 'yes'
JunctionArrayEnsemblRules.getAnnotations(species, array_type,
reannotate_exon_seq, force)
### Download files required during AltAnalyze analysis but not during the database build process
filename = "AltDatabase/" + species + "/" + array_type + "/" + "MASTER-probeset-transcript.txt"
verifyFile(filename, array_type) ### Will force download if missing
filename = "AltDatabase/" + species + '/' + array_type + '/' + array_type + "_annotations.txt"
verifyFile(filename, array_type) ### Will force download if missing