Mercurial > repos > galaxyp > mzsqlite_psm_align
changeset 0:f2dc9805107a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mzsqlite_psm_align commit 464e05be1084ed9a65b542c8eabb18147d425666
| author | galaxyp |
|---|---|
| date | Mon, 16 Apr 2018 18:00:53 -0400 |
| parents | |
| children | 4f8cf8fbef57 |
| files | mzsqlite_psm_align.py mzsqlite_psm_align.xml profmt.py tool-data/twobit.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 5 files changed, 1145 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzsqlite_psm_align.py Mon Apr 16 18:00:53 2018 -0400 @@ -0,0 +1,753 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2017, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +from __future__ import print_function + +import argparse +import re +import sys +import sqlite3 as sqlite +from time import time + + +from Bio.Seq import reverse_complement, translate + + +import pysam +from twobitreader import TwoBitFile + +from profmt import PROBAM_DEFAULTS,ProBAM,ProBAMEntry,ProBED,ProBEDEntry + + +def regex_match(expr, item): + return re.match(expr, item) is not None + + +def regex_search(expr, item): + return re.search(expr, item) is not None + + +def regex_sub(expr, replace, item): + return re.sub(expr, replace, item) + + +def get_connection(sqlitedb_path, addfunctions=True): + conn = sqlite.connect(sqlitedb_path) + if addfunctions: + conn.create_function("re_match", 2, regex_match) + conn.create_function("re_search", 2, regex_search) + conn.create_function("re_sub", 3, regex_sub) + return conn + + +## Peptide Spectral Match (PSM)s +PSM_QUERY = """\ +SELECT + pe.dBSequence_ref, + pe.start, + pe.end, + pe.pre, + pe.post, + pep.sequence, + sr.id, + sr.spectrumTitle, + si.rank, + si.chargeState, + si.calculatedMassToCharge, + si.experimentalMassToCharge, + si.peptide_ref +FROM spectrum_identification_results sr +JOIN spectrum_identification_result_items si ON si.spectrum_identification_result_ref = sr.id +JOIN peptide_evidence pe ON si.peptide_ref = pe.peptide_ref +JOIN peptides pep ON pe.peptide_ref = pep.id +WHERE pe.isDecoy = 'false' +ORDER BY sr.spectrumTitle,si.rank +""" + + +## Peptide Post Translational Modifications +PEP_MODS_QUERY = """\ +SELECT location, residue, name, modType, '' as "unimod" +FROM peptide_modifications +WHERE peptide_ref = :peptide_ref +ORDER BY location, modType, name +""" + + +## number of peptides to which the spectrum maps +## spectrum_identification_results => spectrum_identification_result_items -> peptide_evidence +SPECTRUM_PEPTIDES_QUERY = """\ +SELECT count(distinct pep.sequence) +FROM spectrum_identification_results sr +JOIN spectrum_identification_result_items si ON si.spectrum_identification_result_ref = sr.id +JOIN peptide_evidence pe ON si.peptide_ref = pe.peptide_ref +JOIN peptides pep ON pe.peptide_ref = pep.id +WHERE pe.isDecoy = 'false' +AND sr.id = :sr_id +GROUP BY sr.id +""" + + +## number of genomic locations to which the peptide sequence maps +## uniqueness of the peptide mapping +## peptides => peptide_evidence -> db_sequence -> location +## proteins_by_peptide +PEPTIDE_ACC_QUERY = """\ +SELECT + pe.dBSequence_ref, + pe.start, + pe.end +FROM peptide_evidence pe +JOIN peptides pep ON pe.peptide_ref = pep.id +WHERE pe.isDecoy = 'false' +AND pep.sequence = :sequence +""" + + +MAP_QUERY = """\ +SELECT distinct * +FROM feature_cds_map +WHERE name = :acc +AND :p_start < cds_end +AND :p_end >= cds_start +ORDER BY name,cds_start,cds_end +""" + + +GENOMIC_POS_QUERY = """\ +SELECT distinct chrom, CASE WHEN strand = '+' THEN start + :cds_offset - cds_start ELSE end - :cds_offset - cds_start END as "pos" +FROM feature_cds_map +WHERE name = :acc +AND :cds_offset >= cds_start +AND :cds_offset < cds_end +""" + + +FEATURE_QUERY = """\ +SELECT distinct seqid,start,end,featuretype,strand, +CAST(frame AS INTEGER) as "frame", CAST(frame AS INTEGER)==:frame as "in_frame", +CASE WHEN :strand = '+' THEN start - :start ELSE end - :end END as "start_pos", +CASE WHEN :strand = '+' THEN end - :end ELSE start - :start END as "end_pos", +parent as "name" +FROM features JOIN relations ON features.id = relations.child +WHERE seqid = :seqid +AND parent in ( +SELECT id +FROM features +WHERE seqid = :seqid +AND featuretype = 'transcript' +AND start <= :tstart AND :tend <= end +) +AND :end >= start AND :start <= end +AND featuretype in ('CDS','five_prime_utr','three_prime_utr','transcript') +ORDER BY strand = :strand DESC, featuretype +""" + +## Use order by to get best matches +## one_exon strand, featuretype, contained, inframe, +## first_exon strand, featuretype, contained, end_pos, +## middle_exon strand, featuretype, contained, start_pos, end_pos, +## last_exon strand, featuretype, contained, start_pos, + +ONLY_EXON_QUERY = FEATURE_QUERY + """,\ +start <= :start AND end >= :end DESC, +in_frame DESC, end - start DESC, start DESC, end +""" + +FIRST_EXON_QUERY = FEATURE_QUERY + """,\ +start <= :start AND end >= :end DESC, +in_frame DESC, abs(end_pos), start DESC, end +""" + +MIDDLE_EXON_QUERY = FEATURE_QUERY + """,\ +start <= :start AND end >= :end DESC, +in_frame DESC, abs(start_pos), abs(end_pos), start DESC, end +""" + +LAST_EXON_QUERY = FEATURE_QUERY + """,\ +start <= :start AND end >= :end DESC, +in_frame DESC, abs(start_pos), start DESC, end +""" + + +def __main__(): + parser = argparse.ArgumentParser( + description='Generate proBED and proBAM from mz.sqlite') + parser.add_argument('mzsqlite', help="mz.sqlite converted from mzIdentML") + parser.add_argument('genomic_mapping_sqlite', help="genomic_mapping.sqlite with feature_cds_map table") + parser.add_argument( + '-R', '--genomeReference', default='Unknown', + help='Genome reference sequence in 2bit format') + parser.add_argument( + '-t', '--twobit', default=None, + help='Genome reference sequence in 2bit format') + parser.add_argument( + '-r', '--reads_bam', default=None, + help='reads alignment bam path') + parser.add_argument( + '-g', '--gffutils_sqlite', default=None, + help='gffutils GTF sqlite DB') + parser.add_argument( + '-B', '--probed', default=None, + help='proBed path') + parser.add_argument( + '-s', '--prosam', default=None, + help='proSAM path') + parser.add_argument( + '-b', '--probam', default=None, + help='proBAM path') + parser.add_argument( + '-l', '--limit', type=int, default=None, + help='limit numbers of PSMs for testing') + parser.add_argument('-v', '--verbose', action='store_true', help='Verbose') + parser.add_argument('-d', '--debug', action='store_true', help='Debug') + args = parser.parse_args() + + def get_sequence(chrom, start, end): + if twobit: + if chrom in twobit and 0 <= start < end < len(twobit[chrom]): + return twobit[chrom][start:end] + contig = chrom[3:] if chrom.startswith('chr') else 'chr%s' % chrom + if contig in twobit and 0 <= start < end < len(twobit[contig]): + return twobit[contig][start:end] + return '' + return None + + twobit = TwoBitFile(args.twobit) if args.twobit else None + samfile = pysam.AlignmentFile(args.reads_bam, "rb" ) if args.reads_bam else None + seqlens = twobit.sequence_sizes() + + probed = open(args.probed,'w') if args.probed else sys.stdout + + gff_cursor = get_connection(args.gffutils_sqlite).cursor() if args.gffutils_sqlite else None + map_cursor = get_connection(args.genomic_mapping_sqlite).cursor() + mz_cursor = get_connection(args.mzsqlite).cursor() + + unmapped_accs = set() + timings = dict() + def add_time(name,elapsed): + if name in timings: + timings[name] += elapsed + else: + timings[name] = elapsed + + XG_TYPES = ['N','V','W','J','A','M','C','E','B','O','T','R','I','G','D','U','X','*'] + FT_TYPES = ['CDS','five_prime_utr','three_prime_utr','transcript'] + def get_exon_features(exons): + efeatures = None + transcript_features = dict() + t_start = min(exons[0][2],exons[-1][2]) + t_end = max(exons[0][3],exons[-1][3]) + if gff_cursor: + ts = time() + (acc,gc,gs,ge,st,cs,ce) = exons[0] + ft_params = {"seqid" : str(gc).replace('chr',''), 'strand' : st, 'tstart': t_start, 'tend': t_end} + efeatures = [None] * len(exons) + for i,exon in enumerate(exons): + (acc,gc,gs,ge,st,cs,ce) = exon + fr = cs % 3 + if args.debug: + 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) + ft_params = {"seqid" : str(gc).replace('chr',''), "start" : gs + 1, "end" : ge, 'strand' : st, 'frame' : fr, 'tstart': t_start, 'tend': t_end} + if len(exons) == 1: + q = ONLY_EXON_QUERY + elif i == 0: + q = FIRST_EXON_QUERY + elif len(exons) - i == 1: + q = LAST_EXON_QUERY + else: + q = MIDDLE_EXON_QUERY + features = [f for f in gff_cursor.execute(q,ft_params)] + transcripts = [] + efeatures[i] = [] + for j,f in enumerate(features): + transcript = f[-1] + ftype = f[3] + if ftype == 'transcript': + if i > 0 or efeatures[i]: + continue + if i == 0: + if transcript not in transcript_features: + transcript_features[transcript] = [[] for _ in range(len(exons))] + transcript_features[transcript][i].append(f) + efeatures[i].append(f) + else: + if transcript in transcript_features: + transcript_features[transcript][i].append(f) + efeatures[i].append(f) + else: + del transcript_features[transcript] + if not efeatures[i]: + + efeatures[i] = transcripts + for f in efeatures[i]: + (seqid,start,end,featuretype,strand,frame,in_frame,start_offset,end_offset,parent) = f + if args.debug: + print('feat%d:\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s' % \ + (i,seqid,start,end,featuretype,strand,frame,str(in_frame) == '1',start_offset,end_offset,parent),file=sys.stderr) + if args.debug: + print('fmap:\t%s' % transcript_features,file=sys.stderr) + return (efeatures,transcript_features) + + def is_structural_variant(exons): + if len(exons) > 1: + (acc,gc,gs,ge,st,cs,ce) = exons[0] + for i in range(1,len(exons)): + if gc != exons[i][1] or st != exons[i][4]: + return True + return False + + XG_TYPES = ['N','V','W','J','A','M','C','E','B','O','T','R','I','G','D','U','X','*'] + FT_TYPES = ['CDS','five_prime_utr','three_prime_utr','transcript'] + def classify_transcript(exons,transcript_features,ref_prot,peptide): + etypes = ['*'] * len(exons) + features = transcript_features[0] + (acc,gc,gs,ge,st,cs,ce) = exons[0] + if len(features) == 1: + (seqid,start,end,featuretype,strand,frame,in_frame,start_offset,end_offset,parent) = features[0] + if strand == st: + if featuretype == 'CDS': + if start <= gs and ge <= end: + if in_frame: + if ref_prot == peptide: + if len(exons) > 1: + pass + return 'N' + elif len(ref_prot) != len(peptide): + return 'W' + else: + return 'V' + else: + return 'O' + elif strand == '+' and start <= gs or ge > end: + return 'C' + elif strand == '-' and start <= gs and ge <= end: + return 'C' + elif featuretype == 'five_prime_utr': + return 'E' + elif featuretype == 'three_prime_utr': + return 'B' + elif featuretype == 'transcript': + return 'I' + else: + return 'R' + elif len(features) > 1: + ftypes = [f[3] for f in features] + if 'five_prime_utr' in ftypes: + return 'E' + elif 'three_prime_utr' in ftypes: + return 'B' + else: + return 'C' + return '*' + + def classify_peptide(exons,ref_prot,peptide,pep_cds,probam_dict): + if ref_prot != peptide and samfile: + try: + if args.debug: + print('name: %s \nref: %s\npep: %s\n' % (scan_name,ref_prot,peptide), file=sys.stderr) + ts = time() + for exon in exons: + (acc,chrom,start,end,strand,c_start,c_end) = exon + a_start = c_start / 3 * 3 + a_end = c_end / 3 * 3 + if ref_prot[a_start:a_end] != peptide[a_start:a_end]: + pileup = get_exon_pileup(chrom,start,end) + for i, (bi,ai,ao) in enumerate([(i,i / 3, i % 3) for i in range(c_start, c_end)]): + if ao == 0 or i == 0: + if ref_prot[ai] != peptide[ai]: + codon = get_pep_codon(pileup, bi - c_start, peptide[ai], ao) + if args.debug: + 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) + if codon: + pep_cds = pep_cds[:bi] + codon + pep_cds[bi+3:] + te = time() + add_time('var_cds',te - ts) + except Exception as e: + print('name: %s \nref: %s\npep: %s\n%s\n' % (scan_name,ref_prot,peptide,e), file=sys.stderr) + probam_dict['XG'] = '*' + if is_structural_variant(exons): + probam_dict['XG'] = 'G' + else: + (efeatures,transcript_features) = get_exon_features(exons) + n = len(exons) + if efeatures and efeatures[0]: + for f in efeatures[0]: + transcript = f[9] + features = transcript_features[transcript] + xg = classify_transcript(exons,features,ref_prot,peptide) + if xg != '*': + probam_dict['XG'] = xg + break + return pep_cds + + def get_variant_cds(exons,ref_prot,peptide,pep_cds): + if ref_prot != peptide and samfile: + try: + if args.debug: + print('name: %s \nref: %s\npep: %s\n' % (scan_name,ref_prot,peptide), file=sys.stderr) + ts = time() + for exon in exons: + (acc,chrom,start,end,strand,c_start,c_end) = exon + a_start = c_start / 3 * 3 + a_end = c_end / 3 * 3 + if ref_prot[a_start:a_end] != peptide[a_start:a_end]: + pileup = get_exon_pileup(chrom,start,end) + for i, (bi,ai,ao) in enumerate([(i,i / 3, i % 3) for i in range(c_start, c_end)]): + if ao == 0 or i == 0: + if ref_prot[ai] != peptide[ai]: + codon = get_pep_codon(pileup, bi - c_start, peptide[ai], ao) + if args.debug: + 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) + if codon: + pep_cds = pep_cds[:bi] + codon + pep_cds[bi+3:] + te = time() + add_time('var_cds',te - ts) + except Exception as e: + print('name: %s \nref: %s\npep: %s\n%s\n' % (scan_name,ref_prot,peptide,e), file=sys.stderr) + return pep_cds + + def get_mapping(acc,pep_start,pep_end): + ts = time() + p_start = (pep_start - 1) * 3 + p_end = pep_end * 3 + map_params = {"acc" : acc, "p_start" : p_start, "p_end" : p_end} + if args.debug: + print('%s' % map_params, file=sys.stderr) + locs = [l for l in map_cursor.execute(MAP_QUERY,map_params)] + exons = [] + ## ========= pep + ## --- continue + ## --- trim + ## --- copy + ## --- trim + ## --- break + c_end = 0 + for i, (acc,chrom,start,end,strand,cds_start,cds_end) in enumerate(locs): + if args.debug: + 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) + c_start = c_end + if cds_end < p_start: + continue + if cds_start >= p_end: + break + if strand == '+': + if cds_start < p_start: + start += p_start - cds_start + if cds_end > p_end: + end -= cds_end - p_end + else: + if cds_start < p_start: + end -= p_start - cds_start + if cds_end > p_end: + start += cds_end - p_end + c_end = c_start + abs(end - start) + if args.debug: + 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) + exons.append([acc,chrom,start,end,strand,c_start,c_end]) + te = time() + add_time('get_mapping',te - ts) + return exons + + def get_cds(exons): + ts = time() + seqs = [] + for i, (acc,chrom,start,end,strand,cds_start,cds_end) in enumerate(exons): + seq = get_sequence(chrom, min(start,end), max(start,end)) + if strand == '-': + seq = reverse_complement(seq) + seqs.append(seq) + te = time() + add_time('get_cds',te - ts) + if args.debug: + print('CDS: %s' % str(seqs),file=sys.stderr) + return ''.join(seqs) if seqs else '' + + def genomic_mapping_count(peptide): + ts = time() + params = {"sequence" : peptide} + acc_locs = [l for l in mz_cursor.execute(PEPTIDE_ACC_QUERY,params)] + te = time() + add_time('PEPTIDE_ACC_QUERY',te - ts) + if acc_locs: + if len(acc_locs) == 1: + return 1 + locations = set() + for i,acc_loc in enumerate(acc_locs): + (acc,pep_start,pep_end) = acc_loc + if acc in unmapped_accs: + continue + try: + add_time('GENOMIC_POS_QUERY_COUNT',1) + ts = time() + p_start = pep_start * 3 + p_end = pep_end * 3 + params = {"acc" : acc, "cds_offset" : p_start} + (start_chrom,start_pos) = map_cursor.execute(GENOMIC_POS_QUERY, params).fetchone() + params = {"acc" : acc, "cds_offset" : p_end} + (end_chrom,end_pos) = map_cursor.execute(GENOMIC_POS_QUERY, params).fetchone() + locations.add('%s:%s-%s:%s' % (start_chrom,start_pos,end_chrom,end_pos)) + te = time() + add_time('GENOMIC_POS_QUERY',te - ts) + except: + unmapped_accs.add(acc) + if args.debug: + print('Unmapped: %s' % acc, file=sys.stderr) + return len(locations) + return -1 + + def spectrum_peptide_count(spectrum_id): + ts = time() + params = {"sr_id" : spectrum_id} + pep_count = mz_cursor.execute(SPECTRUM_PEPTIDES_QUERY, params).fetchone()[0] + te = time() + add_time('SPECTRUM_PEPTIDES_QUERY',te - ts) + return pep_count + + def get_exon_pileup(chrom,chromStart,chromEnd): + cols = [] + for pileupcolumn in samfile.pileup(chrom, chromStart, chromEnd): + if chromStart <= pileupcolumn.reference_pos <= chromEnd: + bases = dict() + col = {'depth' : 0, 'cov' : pileupcolumn.nsegments, 'pos': pileupcolumn.reference_pos, 'bases' : bases} + for pileupread in pileupcolumn.pileups: + if not pileupread.is_del and not pileupread.is_refskip: + col['depth'] += 1 + base = pileupread.alignment.query_sequence[pileupread.query_position] + if base not in bases: + bases[base] = 1 + else: + bases[base] += 1 + cols.append(col) + return cols + + codon_map = {"TTT":"F", "TTC":"F", "TTA":"L", "TTG":"L", + "TCT":"S", "TCC":"S", "TCA":"S", "TCG":"S", + "TAT":"Y", "TAC":"Y", "TAA":"*", "TAG":"*", + "TGT":"C", "TGC":"C", "TGA":"*", "TGG":"W", + "CTT":"L", "CTC":"L", "CTA":"L", "CTG":"L", + "CCT":"P", "CCC":"P", "CCA":"P", "CCG":"P", + "CAT":"H", "CAC":"H", "CAA":"Q", "CAG":"Q", + "CGT":"R", "CGC":"R", "CGA":"R", "CGG":"R", + "ATT":"I", "ATC":"I", "ATA":"I", "ATG":"M", + "ACT":"T", "ACC":"T", "ACA":"T", "ACG":"T", + "AAT":"N", "AAC":"N", "AAA":"K", "AAG":"K", + "AGT":"S", "AGC":"S", "AGA":"R", "AGG":"R", + "GTT":"V", "GTC":"V", "GTA":"V", "GTG":"V", + "GCT":"A", "GCC":"A", "GCA":"A", "GCG":"A", + "GAT":"D", "GAC":"D", "GAA":"E", "GAG":"E", + "GGT":"G", "GGC":"G", "GGA":"G", "GGG":"G",} + + aa_codon_map = dict() + for c,a in codon_map.items(): + aa_codon_map[a] = [c] if a not in aa_codon_map else aa_codon_map[a] + [c] + + aa_na_map = dict() # m[aa]{bo : {b1 : [b3] + for c,a in codon_map.items(): + if a not in aa_na_map: + aa_na_map[a] = dict() + d = aa_na_map[a] + for i in range(3): + b = c[i] + if i < 2: + if b not in d: + d[b] = dict() if i < 1 else set() + d = d[b] + else: + d.add(b) + + def get_pep_codon(pileup, idx, aa, ao): + try: + ts = time() + bases = [] + for i in range(3): + if i < ao: + bases.append(list(set([c[i] for c in aa_codon_map[aa]]))) + else: + bases.append([b for b, cnt in reversed(sorted(pileup[idx + i]['bases'].iteritems(), key=lambda (k,v): (v,k)))]) + if args.debug: + print('%s' % bases,file=sys.stderr) + for b0 in bases[0]: + if b0 not in aa_na_map[aa]: + continue + for b1 in bases[1]: + if b1 not in aa_na_map[aa][b0]: + continue + for b2 in bases[2]: + if b2 in aa_na_map[aa][b0][b1]: + return '%s%s%s' % (b0,b1,b2) + te = time() + add_time('pep_codon',te - ts) + except Exception as e: + print("get_pep_codon: %s %s %s %s" + % (aa, ao, idx, pileup), file=sys.stderr) + raise e + return None + + def write_probed(chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts, + spectrum,protacc,peptide,uniqueness,genomeReference,score=1000, + psmScore='.', fdr='.', mods='.', charge='.', + expMassToCharge='.', calcMassToCharge='.', + psmRank='.', datasetID='.', uri='.'): + 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' % \ + (chrom,chromStart,chromEnd,spectrum,score,strand,chromStart,chromEnd,'0',blockCount, + ','.join([str(v) for v in blockSizes]), + ','.join([str(v) for v in blockStarts]), + protacc,peptide,uniqueness, genomeReference, + psmScore, fdr, mods, charge, expMassToCharge, calcMassToCharge, psmRank, datasetID, uri)) + + def get_genomic_location(exons): + chrom = exons[0][1] + strand = exons[0][4] + pos = [exon[2] for exon in exons] + [exon[3] for exon in exons] + chromStart = min(pos) + chromEnd = max(pos) + blockCount = len(exons) + blockSizes = [abs(exon[3] - exon[2]) for exon in exons] + blockStarts = [min(exon[2],exon[3]) - chromStart for exon in exons] + return (chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts) + + def get_psm_modifications(peptide_ref): + mods = [] + ts = time() + params = {"peptide_ref" : peptide_ref} + pepmods = [m for m in mz_cursor.execute(PEP_MODS_QUERY, params)] + if pepmods: + for (location, residue, name, modType, unimod) in pepmods: + mods.append('%s-%s' % (location, unimod if unimod else '%s%s' % (name,residue))) + te = time() + add_time('PEP_MODS_QUERY',te - ts) + return ';'.join(mods) + + ## iterate through PSMs + psm_cursor = get_connection(args.mzsqlite).cursor() + ts = time() + psms = psm_cursor.execute(PSM_QUERY) + te = time() + add_time('PSM_QUERY',te - ts) + proBAM = ProBAM(species=None,assembly=args.genomeReference,seqlens=seqlens,comments=[]) if args.prosam or args.probam else None + proBED = ProBED(species=None,assembly=args.genomeReference,comments=[]) if args.probed else None + for i, psm in enumerate(psms): + probam_dict = PROBAM_DEFAULTS.copy() + (acc,pep_start,pep_end,aa_pre,aa_post,peptide,spectrum_id,spectrum_title,rank,charge,calcmass,exprmass,pepref) = psm + scan_name = spectrum_title if spectrum_title else spectrum_id + if args.debug: + 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) + exons = get_mapping(acc,pep_start,pep_end) + if args.debug: + print('%s' % exons, file=sys.stderr) + if not exons: + continue + mods = get_psm_modifications(pepref) + (chrom,chromStart,chromEnd,strand,blockCount,blockSizes,blockStarts) = get_genomic_location(exons) + ref_cds = get_cds(exons) + if args.debug: + print('%s' % ref_cds, file=sys.stderr) + ref_prot = translate(ref_cds) + if args.debug: + print('%s' % ref_prot, file=sys.stderr) + print('%s' % peptide, file=sys.stderr) + spectrum_peptides = spectrum_peptide_count(spectrum_id) + peptide_locations = genomic_mapping_count(peptide) + if args.debug: + print('spectrum_peptide_count: %d\tpeptide_location_count: %d' % (spectrum_peptides,peptide_locations), file=sys.stderr) + uniqueness = 'unique' if peptide_locations == 1 else 'not-unique[unknown]' + if proBED is not None: + ts = time() + proBEDEntry = ProBEDEntry(chrom,chromStart,chromEnd, + '%s_%s' % (acc,scan_name), + 1000,strand, + blockCount,blockSizes,blockStarts, + acc,peptide,uniqueness,args.genomeReference, + charge=charge,expMassToCharge=exprmass,calcMassToCharge=calcmass, + mods=mods if mods else '.', psmRank=rank) + proBED.add_entry(proBEDEntry) + te = time() + add_time('add_probed',te - ts) + if proBAM is not None: + if len(ref_prot) != len(peptide): + pass + # continue + ts = time() + probam_dict['NH'] = peptide_locations + probam_dict['XO'] = uniqueness + probam_dict['XL'] = peptide_locations + probam_dict['XP'] = peptide + probam_dict['YP'] = acc + probam_dict['XC'] = charge + probam_dict['XB'] = '%f;%f;%f' % (exprmass - calcmass, exprmass, calcmass) + probam_dict['XR'] = ref_prot # ? dbSequence + probam_dict['YA'] = aa_post + probam_dict['YB'] = aa_pre + probam_dict['XM'] = mods if mods else '*' + flag = 16 if strand == '-' else 0 + if str(rank)!=str(1) and rank!='*' and rank!=[] and rank!="": + flag += 256 + probam_dict['XF'] = ','.join([str(e[2] % 3) for e in exons]) + ## what if structural variant, need to split into multiple entries + ## probam_dict['XG'] = peptide_type + pep_cds = classify_peptide(exons,ref_prot,peptide,ref_cds,probam_dict) + ## probam_dict['MD'] = peptide + + ## FIX SAM sequence is forward strand + seq = pep_cds if strand == '+' else reverse_complement(pep_cds) + ## cigar based on plus strand + cigar = '' + if strand == '+': + blkStarts = blockStarts + blkSizes = blockSizes + else: + blkStarts = [x for x in reversed(blockStarts)] + blkSizes = [x for x in reversed(blockSizes)] + for j in range(blockCount): + if j > 0: + intron = blkStarts[j] - (blkStarts[j-1] + blkSizes[j-1]) + if intron > 0: + cigar += '%dN' % intron + cigar += '%dM' % blkSizes[j] + proBAMEntry = ProBAMEntry(qname=scan_name, flag=flag, rname=chrom, pos=chromStart+1, + cigar=cigar,seq=seq,optional=probam_dict) + proBAM.add_entry(proBAMEntry) + te = time() + add_time('add_probam',te - ts) + if args.debug: + print('%s' % probam_dict, file=sys.stderr) + if args.limit and i >= args.limit: + break + if args.probed: + ts = time() + with open(args.probed,'w') as fh: + proBED.write(fh) + te = time() + add_time('write_probed',te - ts) + if args.prosam or args.probam: + samfile = args.prosam if args.prosam else 'temp.sam' + ts = time() + with open(samfile,'w') as fh: + proBAM.write(fh) + te = time() + add_time('write_prosam',te - ts) + if args.probam: + ts = time() + bamfile = args.prosam.replace('.sam','.bam') + pysam.view(samfile, '-b', '-o', args.probam, catch_stdout=False) + te = time() + add_time('write_probam',te - ts) + pysam.index(args.probam) + + if args.verbose: + print('\n%s\n' % str(timings), file=sys.stderr) + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mzsqlite_psm_align.xml Mon Apr 16 18:00:53 2018 -0400 @@ -0,0 +1,113 @@ +<tool id="mzsqlite_psm_align" name="MzSQLite ProBED ProBAM" version="0.1.0"> + <description>from mz.sqlite aand genomic mapping</description> + <requirements> + <requirement type="package">biopython</requirement> + <requirement type="package">twobitreader</requirement> + <requirement type="package">pysam</requirement> + <requirement type="package">gffutils</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $readlignments: + ln -s -f '${$readlignments}' 'input.bam' && + ln -s -f '${$readlignments.metadata.bam_index}' 'input.bam.bai' && + #end if + python '$__tool_directory__/mzsqlite_psm_align.py' + #if $ref.ref_source == 'cached': + --twobit='$ref.ref_loc.fields.path' + #elif $ref.ref_source == 'history': + --twobit='$ref.ref_file' + #end if + #if $gffutilsdb: + --gffutils_sqlite '$gffutilsdb' + #end if + #if $readlignments: + --reads_bam 'input.bam' + #end if + #if 'probed' in str($output_formats).split(','): + --probed '$probed' + #end if + #if 'prosam' in str($output_formats).split(','): + --prosam '$prosam' + #end if + #if 'probam' in str($output_formats).split(','): + --probam '$probam' + #end if + #if $genomicref: + --genomeReference $genomicref + #else + --genomeReference $genomicdb.metadata.dbkey + #end if + -v + '$mzsqlitedb' '$genomicdb' + ]]></command> + <inputs> + <param name="mzsqlitedb" type="data" format="mz.sqlite" label="mz.sqlite databse"/> + <param name="genomicdb" type="data" format="sqlite" label="genomic mapping sqlite databse"/> + <conditional name="ref"> + <param name="ref_source" type="select" label="Source for Genomic Sequence Data"> + <option value="cached">Locally cached twobit</option> + <option value="history">History dataset twobit</option> + </param> + <when value="cached"> + <param name="ref_loc" type="select" label="Select reference 2bit file"> + <options from_data_table="twobit" /> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="twobit" label="reference 2bit file" /> + </when> + </conditional> + <param name="gffutilsdb" type="data" format="sqlite" label="gffutils sqlite database" optional="true"/> + <param name="readlignments" type="data" format="bam" label="read alignments bam" optional="true"/> + <param name="genomicref" type="text" value="" label="Genome Reference name" optional="true"/> + <param name="output_formats" type="select" display="checkboxes" label="outputs" multiple="true"> + <option value="probam">pro.bam</option> + <option value="prosam">pro.sam</option> + <option value="probed">pro.bed</option> + </param> + </inputs> + <outputs> + <data name="prosam" format="sam" label="pro.SAM on ${on_string}"> + <filter>'prosam' in output_formats</filter> + </data> + <data name="probam" format="bam" label="pro.Bam on ${on_string}"> + <filter>'probam' in output_formats</filter> + </data> + <data name="probed" format="bed" label="pro.Bed on ${on_string}"> + <filter>'probed' in output_formats</filter> + </data> + </outputs> + <help><![CDATA[ + +Generates proBAM or proBED feature alignment files for peptides identified from a mass spectrometry protein search analysis. + +The tool mz_to_sqlite generates the a SQLite database for a mzIdentML file, +along with the fasta search database and the spectrum files used in the search. + +The genomic mapping sqlite database has this schema: + + CREATE TABLE feature_cds_map ( /* One row for each exon in the search protein */ + name TEXT, /* Accession name of search protein in mzIdentML */ + chrom TEXT, /* Reference genome chromosome for this exon */ + start INTEGER, /* genomic start of the exon (zero-based like BED) */ + end INTEGER, /* genomic end of the exon (non-incluse like BED) */ + strand TEXT, /* genomic strand: '+' or '-' */ + cds_start INTEGER, /* The CDS coding start for this exon (zero-based) */ + cds_end INTEGER /* The CDS coding start end this exon (non-inclusive) */ + ); + +Example: + sqlite> select * from feature_cds_map WHERE name like 'ENSMUSP00000000001%'; + ENSMUSP00000000001 chr3 108145887 108146005 - 0 118 + ENSMUSP00000000001 chr3 108123794 108123837 - 118 161 + ENSMUSP00000000001 chr3 108123541 108123683 - 161 303 + ENSMUSP00000000001 chr3 108118300 108118458 - 303 461 + ENSMUSP00000000001 chr3 108115762 108115891 - 461 590 + ENSMUSP00000000001 chr3 108112472 108112602 - 590 720 + ENSMUSP00000000001 chr3 108111934 108112088 - 720 874 + ENSMUSP00000000001 chr3 108109421 108109612 - 874 1065 + +This schema can describe structural variants as well as canonical transcripts. + + ]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/profmt.py Mon Apr 16 18:00:53 2018 -0400 @@ -0,0 +1,247 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2018, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +import sys,re +from operator import itemgetter, attrgetter +from twobitreader import TwoBitFile + + +PROBAM_TAGS = ['NH', 'XO', 'XL', 'XP', 'YP', 'XF', 'XI', 'XB', 'XR', 'YB', 'YA', 'XS', 'XQ', 'XC', 'XA', 'XM', 'XN', 'XT', 'XE', 'XG', 'XU'] + + +PROBAM_TYTPES = { + 'NH' : 'i', #number of genomic locations to which the peptide sequence maps + 'XO' : 'Z', #uniqueness of the peptide mapping + 'XL' : 'i', #number of peptides to which the spectrum maps + 'XP' : 'Z', #peptide sequence + 'YP' : 'Z', #Protein accession ID from the original search result + 'XF' : 'Z', #Reading frame of the peptide (0, 1, 2) + 'XI' : 'f', #Peptide intensity + 'XB' : 'Z', #massdiff; experimental mass; calculated mass massdiff can be calculated by experimental mass - calculated mass. If any number is unavailable, the value should be left blank (such as 0.01;;). + 'XR' : 'Z', #reference peptide sequence + 'YB' : 'Z', #Preceding amino acids (2 AA, B stands for before). + 'YA' : 'Z', #Following amino acids (2 AA, A stands for after). + 'XS' : 'f', #PSM score + 'XQ' : 'f', #PSM FDR (i.e. q-value or 1-PEP). + 'XC' : 'i', #peptide charge + 'XA' : 'i', #Whether the peptide is annotated 0:yes; 1:parially unknown; 2:totally unknown; + 'XM' : 'Z', #Modifications + 'XN' : 'i', #Number of missed cleavages in the peptide (XP) + 'XT' : 'i', #Enzyme specificity + 'XE' : 'i', #Enzyme used in the experiment + 'XG' : 'A', #Peptide type + 'XU' : 'Z', #URI +} + + +PROBAM_DEFAULTS = { + 'NH' : -1, #number of genomic locations to which the peptide sequence maps + 'XO' : '*', #uniqueness of the peptide mapping + 'XL' : -1, #number of peptides to which the spectrum maps + 'XP' : '*', #peptide sequence + 'YP' : '*', #Protein accession ID from the original search result + 'XF' : '*', #Reading frame of the peptide (0, 1, 2) + 'XI' : -1, #Peptide intensity + 'XB' : '*', #massdiff; experimental mass; calculated mass massdiff can be calculated by experimental mass - calculated mass. If any number is unavailable, the value should be left blank (such as 0.01;;). + 'XR' : '*', #reference peptide sequence + 'YB' : '*', #Preceding amino acids (2 AA, B stands for before). + 'YA' : '*', #Following amino acids (2 AA, A stands for after). + 'XS' : -1, #PSM score + 'XQ' : -1, #PSM FDR (i.e. q-value or 1-PEP). + 'XC' : -1, #peptide charge + 'XA' : -1, #Whether the peptide is annotated 0:yes; 1:parially unknown; 2:totally unknown; + 'XM' : '*', #Modifications + 'XN' : -1, #Number of missed cleavages in the peptide (XP) + 'XT' : -1, #Enzyme specificity + 'XE' : -1, #Enzyme used in the experiment + 'XG' : '*', #Peptide type + 'XU' : '*', #URI +} + +def cmp_alphanumeric(s1,s2): + if s1 == s2: + return 0 + a1 = re.findall("\d+|[a-zA-Z]+",s1) + a2 = re.findall("\d+|[a-zA-Z]+",s2) + for i in range(min(len(a1),len(a2))): + if a1[i] == a2[i]: + continue + if a1[i].isdigit() and a2[i].isdigit(): + return int(a1[i]) - int(a2[i]) + return 1 if a1[i] > a2[i] else -1 + return len(a1) - len(a2) + + +def sort_chrom_names(names): + rnames = sorted(names,cmp=cmp_alphanumeric) + if 'chrM' in rnames: + rnames.remove('chrM') + rnames.insert(0,'chrM') + if 'MT' in rnames: + rnames.remove('MT') + rnames.append('MT') + return rnames + + +def as_int_list(obj): + if obj is None: + return None + if isinstance(obj, list): + return [int(x) for x in obj] + elif isinstance(obj, str): + return [int(x) for x in obj.split(',')] + else: # python2 unicode? + return [int(x) for x in str(obj).split(',')] + + +class ProBEDEntry (object): + def __init__(self, chrom, chromStart, chromEnd, name, score, strand, + blockCount, blockSizes, blockStarts, + protacc, peptide, uniqueness, genomeReference, + psmScore='.', fdr='.', mods='.', charge='.', + expMassToCharge='.', calcMassToCharge='.', + psmRank='.', datasetID='.', uri='.'): + self.chrom = chrom + self.chromStart = int(chromStart) + self.chromEnd = int(chromEnd) + self.name = name + self.score = int(score) if score is not None else 0 + self.strand = '-' if str(strand).startswith('-') else '+' + self.thickStart = self.chromStart + self.thickEnd = self.chromEnd + self.itemRgb = '0' + self.blockCount = int(blockCount) + self.blockSizes = as_int_list(blockSizes) + self.blockStarts = as_int_list(blockStarts) + self.protacc = protacc + self.peptide = peptide + self.uniqueness = uniqueness + self.genomeReference = genomeReference + self.psmScore = psmScore + self.fdr = fdr + self.mods = mods + self.charge = charge + self.expMassToCharge = expMassToCharge + self.calcMassToCharge = calcMassToCharge + self.psmRank = psmRank + self.datasetID = datasetID + self.uri = uri + + def __str__(self): + return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % \ + (self.chrom, self.chromStart, self.chromEnd, + self.name, self.score, self.strand, + self.thickStart, self.thickEnd, self.itemRgb, + self.blockCount, + ','.join([str(x) for x in self.blockSizes]), + ','.join([str(x) for x in self.blockStarts]), + self.protacc, self.peptide, self.uniqueness, + self.genomeReference, + self.psmScore, self.fdr, self.mods, + self.charge, self.expMassToCharge, self.calcMassToCharge, + self.psmRank, self.datasetID, self.uri) + + +class ProBED ( object ): + def __init__(self,species=None,assembly=None,comments=[]): + self.species = species + self.assembly = assembly + self.comments = comments + self.entries = dict() + + def add_entry(self,entry): + if not entry.chrom in self.entries: + self.entries[entry.chrom] = [] + self.entries[entry.chrom].append(entry) + + def write(self,fh): + rnames = sort_chrom_names(self.entries.keys()) + for sn in rnames: + if sn not in self.entries: + continue + for pbe in sorted(self.entries[sn], key=attrgetter('chromStart','chromEnd')): + fh.write(str(pbe)) + + +class ProBAMEntry (object): + def __init__(self, qname='', flag=0, rname='', pos=0, mapq=255, cigar='', rnext='*', pnext='0', tlen='0', seq='*', qual='*', optional=PROBAM_DEFAULTS): + self.qname = qname + self.flag = flag + self.rname = rname + self.pos = pos + self.mapq = mapq + self.cigar = cigar + self.rnext = rnext + self.pnext = pnext + self.tlen = tlen + self.seq = seq + self.qual = qual + self.optional = optional + def __str__(self): + opt_cols = '\t%s' % '\t'.join(['%s:%s:%s' % (t,PROBAM_TYTPES[t],self.optional[t]) for t in PROBAM_TAGS]) if self.optional else '' + return '%s\t%d\t%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s%s' % ( + self.qname,self.flag,self.rname,self.pos,self.mapq,self.cigar, + str(self.rnext) if self.rnext else '', + str(self.pnext) if self.pnext else '', + str(self.tlen) if self.tlen else '', + self.seq, + self.qual, opt_cols) + def add_optional(self,tag,value): + self.optional[tag] = value + + +class ProBAM ( object ): + def __init__(self,species=None,assembly=None,seqlens={},comments=[]): + self.species = species + self.assembly = assembly + self.seqlens = seqlens + self.comments = comments + self.entries = dict() + self.opt_columns = set() + self.rg = [] + + def add_entry(self,pb_entry): + if not pb_entry.rname in self.entries: + self.entries[pb_entry.rname] = [] + self.entries[pb_entry.rname].append(pb_entry) + if pb_entry.optional: + self.opt_columns | set(pb_entry.optional.keys()) + + def add_entry_from_bed(self,bed_entry,optional=dict()): + if bed_entry.pep: + optional['XP:Z'] = bed_entry.pep + qname=bed_entry.name + flag = 0 if bed_entry.strand == '+' else 16 + rname = bed_entry.chrom + pos = bed_entry.chromStart + 1 + cigar = bed_entry.get_cigar() + seq = bed_entry.get_spliced_seq(strand='+') if bed_entry.seq else '*' + pb_entry = ProBAMEntry(qname=qname, flag=flag, rname=rname, pos=pos,cigar=cigar,seq=seq,optional=optional) + self.add_entry(pb_entry) + + def write(self,fh): + fh.write('@HD VN:1.0 SO:coordinate\n') + rnames = sort_chrom_names(self.seqlens.keys()) + for sn in rnames: + fh.write('@SQ\tSN:%s\tLN:%d\n' % (sn,self.seqlens[sn])) + for rg in self.rg: + fh.write('@RG\tID:%s\n' % (rg)) + fh.write('@PG\tID:SampleSpecificGenerator\n') + for comment in self.comments: + fh.write('@CO\t%s\n' % comment) + for sn in rnames: + if sn not in self.entries: + continue + for pbe in sorted(self.entries[sn], key=attrgetter('pos')): + fh.write('%s\n' % str(pbe))
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/twobit.loc.sample Mon Apr 16 18:00:53 2018 -0400 @@ -0,0 +1,26 @@ +#This is a sample file distributed with Galaxy that is used by some +#tools. The twobit.loc file has this format (white space characters +#are TAB characters): +# +#<Build> <FullPathToFile> +# +#So, for example, if you had droPer1 twobit files stored in +#/depot/data2/galaxy/droPer1/, then the twobit.loc entry +#would look like this: +# +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +# +#and your /depot/data2/galaxy/droPer1/ directory would +#contain all of your twobit files (e.g.): +# +#-rw-rw-r-- 1 nate galaxy 48972650 2007-05-04 11:27 droPer1.2bit +#...etc... +# +#Your twobit.loc file should include an entry per line for each twobit +#file you have stored. For example: +# +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#...etc...