Mercurial > repos > galaxyp > translate_bed
changeset 0:038ecf54cbec draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219
| author | galaxyp |
|---|---|
| date | Mon, 22 Jan 2018 13:59:27 -0500 |
| parents | |
| children | |
| files | bedutil.py digest.py ensembl_rest.py macros.xml test-data/GRCh38.1.2bit test-data/human_transcripts.bed test-data/human_transcripts_seq.bed tool-data/twobit.loc.sample tool_data_table_conf.xml.sample translate_bed.py translate_bed.xml |
| diffstat | 11 files changed, 1601 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedutil.py Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,515 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2016, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +from __future__ import print_function + +import sys + +from Bio.Seq import reverse_complement, translate + + +def bed_from_line(line, ensembl=False, seq_column=None): + fields = line.rstrip('\r\n').split('\t') + if len(fields) < 12: + return None + (chrom, chromStart, chromEnd, name, score, strand, + thickStart, thickEnd, itemRgb, + blockCount, blockSizes, blockStarts) = fields[0:12] + bed_entry = BedEntry(chrom=chrom, chromStart=chromStart, chromEnd=chromEnd, + name=name, score=score, strand=strand, + thickStart=thickStart, thickEnd=thickEnd, + itemRgb=itemRgb, + blockCount=blockCount, + blockSizes=blockSizes.rstrip(','), + blockStarts=blockStarts.rstrip(',')) + if seq_column is not None and -len(fields) <= seq_column < len(fields): + bed_entry.seq = fields[seq_column] + if ensembl and len(fields) >= 20: + bed_entry.second_name = fields[12] + bed_entry.cds_start_status = fields[13] + bed_entry.cds_end_status = fields[14] + bed_entry.exon_frames = fields[15].rstrip(',') + bed_entry.biotype = fields[16] + bed_entry.gene_name = fields[17] + bed_entry.second_gene_name = fields[18] + bed_entry.gene_type = fields[19] + return bed_entry + + +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 BedEntry(object): + def __init__(self, chrom=None, chromStart=None, chromEnd=None, + name=None, score=None, strand=None, + thickStart=None, thickEnd=None, itemRgb=None, + blockCount=None, blockSizes=None, blockStarts=None): + 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 = int(thickStart) if thickStart else self.chromStart + self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd + self.itemRgb = str(itemRgb) if itemRgb is not None else r'100,100,100' + self.blockCount = int(blockCount) + self.blockSizes = as_int_list(blockSizes) + self.blockStarts = as_int_list(blockStarts) + self.second_name = None + self.cds_start_status = None + self.cds_end_status = None + self.exon_frames = None + self.biotype = None + self.gene_name = None + self.second_gene_name = None + self.gene_type = None + self.seq = None + self.cdna = None + self.pep = None + # T26C + self.aa_change = [] + # p.Trp26Cys g.<pos><ref>><alt> # g.1304573A>G + self.variants = [] + + 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' % ( + self.chrom, self.chromStart, self.chromEnd, + self.name, self.score, self.strand, + self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount, + ','.join([str(x) for x in self.blockSizes]), + ','.join([str(x) for x in self.blockStarts])) + + def get_splice_junctions(self): + splice_juncs = [] + for i in range(self.blockCount - 1): + splice_junc = "%s:%d_%d"\ + % (self.chrom, + self.chromStart + self.blockSizes[i], + self.chromStart + self.blockStarts[i+1]) + splice_juncs.append(splice_junc) + return splice_juncs + + def get_exon_seqs(self): + if not self.seq: + return None + exons = [] + for i in range(self.blockCount): + exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + + self.blockSizes[i]]) + if self.strand == '-': # reverse complement + exons.reverse() + for i, s in enumerate(exons): + exons[i] = reverse_complement(s) + return exons + + def get_spliced_seq(self, strand=None): + if not self.seq: + return None + seq = ''.join(self.get_exon_seqs()) + if strand and self.strand != strand: + seq = reverse_complement(seq) + return seq + + def get_cdna(self): + if not self.cdna: + self.cdna = self.get_spliced_seq() + return self.cdna + + def get_cds(self): + cdna = self.get_cdna() + if cdna: + if self.chromStart == self.thickStart\ + and self.chromEnd == self.thickEnd: + return cdna + pos = [self.cdna_offset_of_pos(self.thickStart), + self.cdna_offset_of_pos(self.thickEnd)] + if 0 <= min(pos) <= max(pos) <= len(cdna): + return cdna[min(pos):max(pos)] + return None + + def set_cds(self, cdna_start, cdna_end): + cdna_len = sum(self.blockSizes) + if 0 <= cdna_start < cdna_end <= cdna_len: + cds_pos = [self.pos_of_cdna_offet(cdna_start), + self.pos_of_cdna_offet(cdna_end)] + if all(cds_pos): + self.thickStart = min(cds_pos) + self.thickEnd = max(cds_pos) + return self + return None + + def trim_cds(self, basepairs): + if self.chromStart <= self.thickStart < self.thickEnd <= self.chromEnd: + cds_pos = [self.cdna_offset_of_pos(self.thickStart), + self.cdna_offset_of_pos(self.thickEnd)] + if basepairs > 0: + return self.set_cds(min(cds_pos) + basepairs, max(cds_pos)) + else: + return self.set_cds(min(cds_pos), max(cds_pos) + basepairs) + return None + + def get_cds_bed(self): + cds_pos = [self.cdna_offset_of_pos(self.thickStart), + self.cdna_offset_of_pos(self.thickEnd)] + return self.trim(min(cds_pos), max(cds_pos)) + + def get_cigar(self): + cigar = '' + r = range(self.blockCount) + xl = None + for x in r: + if xl is not None: + intronSize = abs(self.blockStarts[x] - self.blockSizes[xl] + - self.blockStarts[xl]) + cigar += '%dN' % intronSize + cigar += '%dM' % self.blockSizes[x] + xl = x + return cigar + + def get_cigar_md(self): + cigar = '' + md = '' + r = range(self.blockCount) + xl = None + for x in r: + if xl is not None: + intronSize = abs(self.blockStarts[x] - self.blockSizes[xl] + - self.blockStarts[xl]) + cigar += '%dN' % intronSize + cigar += '%dM' % self.blockSizes[x] + xl = x + md = '%d' % sum(self.blockSizes) + return (cigar, md) + + def get_translation(self, sequence=None): + translation = None + seq = sequence if sequence else self.get_spliced_seq() + if seq: + seqlen = len(seq) / 3 * 3 + if seqlen >= 3: + translation = translate(seq[:seqlen]) + return translation + + def get_translations(self): + translations = [] + seq = self.get_spliced_seq() + if seq: + for i in range(3): + translation = self.get_translation(sequence=seq[i:]) + if translation: + translations.append(translation) + return translations + + def pos_of_cdna_offet(self, offset): + if offset is not None and 0 <= offset < sum(self.blockSizes): + r = list(range(self.blockCount)) + rev = self.strand == '-' + if rev: + r.reverse() + nlen = 0 + for x in r: + if offset < nlen + self.blockSizes[x]: + if rev: + return self.chromStart + self.blockStarts[x]\ + + self.blockSizes[x] - (offset - nlen) + else: + return self.chromStart + self.blockStarts[x]\ + + (offset - nlen) + nlen += self.blockSizes[x] + return None + + def cdna_offset_of_pos(self, pos): + if not self.chromStart <= pos < self.chromEnd: + return -1 + r = list(range(self.blockCount)) + rev = self.strand == '-' + if rev: + r.reverse() + nlen = 0 + for x in r: + bStart = self.chromStart + self.blockStarts[x] + bEnd = bStart + self.blockSizes[x] + if bStart <= pos < bEnd: + return nlen + (bEnd - pos if rev else pos - bStart) + nlen += self.blockSizes[x] + + def apply_variant(self, pos, ref, alt): + pos = int(pos) + if not ref or not alt: + print("variant requires ref and alt sequences", file=sys.stderr) + return + if not self.chromStart <= pos <= self.chromEnd: + print("variant not in entry %s: %s %d < %d < %d" % + (self.name, self.strand, + self.chromStart, pos, self.chromEnd), + file=sys.stderr) + print("%s" % str(self), file=sys.stderr) + return + if len(ref) != len(alt): + print("variant only works for snp: %s %s" % (ref, alt), + file=sys.stderr) + return + if not self.seq: + print("variant entry %s has no seq" % self.name, file=sys.stderr) + return + """ + if self.strand == '-': + ref = reverse_complement(ref) + alt = reverse_complement(alt) + """ + bases = list(self.seq) + offset = pos - self.chromStart + for i in range(len(ref)): + # offset = self.cdna_offset_of_pos(pos+i) + if offset is not None: + bases[offset+i] = alt[i] + else: + print("variant offset %s: %s %d < %d < %d" % + (self.name, self.strand, self.chromStart, + pos+1, self.chromEnd), file=sys.stderr) + print("%s" % str(self), file=sys.stderr) + self.seq = ''.join(bases) + self.variants.append("g.%d%s>%s" % (pos+1, ref, alt)) + + def get_variant_bed(self, pos, ref, alt): + pos = int(pos) + if not ref or not alt: + print("variant requires ref and alt sequences", file=sys.stderr) + return None + if not self.chromStart <= pos <= self.chromEnd: + print("variant not in entry %s: %s %d < %d < %d" % + (self.name, self.strand, + self.chromStart, pos, self.chromEnd), + file=sys.stderr) + print("%s" % str(self), file=sys.stderr) + return None + if not self.seq: + print("variant entry %s has no seq" % self.name, file=sys.stderr) + return None + tbed = BedEntry(chrom=self.chrom, + chromStart=self.chromStart, chromEnd=self.chromEnd, + name=self.name, score=self.score, strand=self.strand, + thickStart=self.chromStart, thickEnd=self.chromEnd, + itemRgb=self.itemRgb, + blockCount=self.blockCount, + blockSizes=self.blockSizes, + blockStarts=self.blockStarts) + bases = list(self.seq) + offset = pos - self.chromStart + tbed.seq = ''.join(bases[:offset] + list(alt) + + bases[offset+len(ref):]) + if len(ref) != len(alt): + diff = len(alt) - len(ref) + rEnd = pos + len(ref) + # need to adjust blocks + # change spans blocks, + for x in range(tbed.blockCount): + bStart = tbed.chromStart + tbed.blockStarts[x] + bEnd = bStart + tbed.blockSizes[x] + # change within a block or extends (last block) + # adjust blocksize + # seq: GGGcatGGG + # ref c alt tag: GGGtagatGGG + # ref cat alt a: GGGaGGG + if bStart <= pos < rEnd < bEnd: + tbed.blockSizes[x] += diff + return tbed + + # (start, end) + def get_subrange(self, tstart, tstop, debug=False): + chromStart = self.chromStart + chromEnd = self.chromEnd + if debug: + print("%s" % (str(self)), file=sys.stderr) + r = list(range(self.blockCount)) + if self.strand == '-': + r.reverse() + bStart = 0 + bEnd = 0 + for x in r: + bEnd = bStart + self.blockSizes[x] + if bStart <= tstart < bEnd: + if self.strand == '+': + chromStart = self.chromStart + self.blockStarts[x] +\ + (tstart - bStart) + else: + chromEnd = self.chromStart + self.blockStarts[x] +\ + self.blockSizes[x] - (tstart - bStart) + if bStart <= tstop < bEnd: + if self.strand == '+': + chromEnd = self.chromStart + self.blockStarts[x] +\ + (tstop - bStart) + else: + chromStart = self.chromStart + self.blockStarts[x] +\ + self.blockSizes[x] - (tstop - bStart) + if debug: + print("%3d %s\t%d\t%d\t%d\t%d\t%d\t%d" % + (x, self.strand, bStart, bEnd, + tstart, tstop, chromStart, chromEnd), file=sys.stderr) + bStart += self.blockSizes[x] + return(chromStart, chromEnd) + + # get the blocks for sub range + def get_blocks(self, chromStart, chromEnd): + tblockCount = 0 + tblockSizes = [] + tblockStarts = [] + for x in range(self.blockCount): + bStart = self.chromStart + self.blockStarts[x] + bEnd = bStart + self.blockSizes[x] + if bStart > chromEnd: + break + if bEnd < chromStart: + continue + cStart = max(chromStart, bStart) + tblockStarts.append(cStart - chromStart) + tblockSizes.append(min(chromEnd, bEnd) - cStart) + tblockCount += 1 + return (tblockCount, tblockSizes, tblockStarts) + + def trim(self, tstart, tstop, debug=False): + (tchromStart, tchromEnd) =\ + self.get_subrange(tstart, tstop, debug=debug) + (tblockCount, tblockSizes, tblockStarts) =\ + self.get_blocks(tchromStart, tchromEnd) + tbed = BedEntry( + chrom=self.chrom, chromStart=tchromStart, chromEnd=tchromEnd, + name=self.name, score=self.score, strand=self.strand, + thickStart=tchromStart, thickEnd=tchromEnd, itemRgb=self.itemRgb, + blockCount=tblockCount, + blockSizes=tblockSizes, blockStarts=tblockStarts) + if self.seq: + ts = tchromStart-self.chromStart + te = tchromEnd - tchromStart + ts + tbed.seq = self.seq[ts:te] + return tbed + + def get_filtered_translations(self, untrimmed=False, filtering=True, + ignore_left_bp=0, ignore_right_bp=0, + debug=False): + translations = [None, None, None] + seq = self.get_spliced_seq() + ignore = (ignore_left_bp if self.strand == '+' + else ignore_right_bp) / 3 + block_sum = sum(self.blockSizes) + exon_sizes = [x for x in self.blockSizes] + if self.strand == '-': + exon_sizes.reverse() + splice_sites = [sum(exon_sizes[:x]) / 3 + for x in range(1, len(exon_sizes))] + if debug: + print("splice_sites: %s" % splice_sites, file=sys.stderr) + junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0] + if seq: + for i in range(3): + translation = self.get_translation(sequence=seq[i:]) + if translation: + tstart = 0 + tstop = len(translation) + offset = (block_sum - i) % 3 + if debug: + print("frame: %d\ttstart: %d tstop: %d " + + "offset: %d\t%s" % + (i, tstart, tstop, offset, translation), + file=sys.stderr) + if not untrimmed: + tstart = translation.rfind('*', 0, junc) + 1 + stop = translation.find('*', junc) + tstop = stop if stop >= 0 else len(translation) + offset = (block_sum - i) % 3 + trimmed = translation[tstart:tstop] + if debug: + print("frame: %d\ttstart: %d tstop: %d " + + "offset: %d\t%s" % + (i, tstart, tstop, offset, trimmed), + file=sys.stderr) + if filtering and tstart > ignore: + continue + # get genomic locations for start and end + if self.strand == '+': + chromStart = self.chromStart + i + (tstart * 3) + chromEnd = self.chromEnd - offset\ + - (len(translation) - tstop) * 3 + else: + chromStart = self.chromStart + offset\ + + (len(translation) - tstop) * 3 + chromEnd = self.chromEnd - i - (tstart * 3) + # get the blocks for this translation + (tblockCount, tblockSizes, tblockStarts) =\ + self.get_blocks(chromStart, chromEnd) + translations[i] = (chromStart, chromEnd, trimmed, + tblockCount, tblockSizes, tblockStarts) + if debug: + print("tblockCount: %d tblockStarts: %s " + + "tblockSizes: %s" % + (tblockCount, tblockStarts, tblockSizes), + file=sys.stderr) + return translations + + def get_seq_id(self, seqtype='unk:unk', reference='', frame=None): + # Ensembl fasta ID format + # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT + # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1\ + # gene:ENSG00000158815:transcript:ENST00000328693\ + # gene_biotype:protein_coding transcript_biotype:protein_coding + frame_name = '' + chromStart = self.chromStart + chromEnd = self.chromEnd + strand = 1 if self.strand == '+' else -1 + if frame is not None: + block_sum = sum(self.blockSizes) + offset = (block_sum - frame) % 3 + frame_name = '_' + str(frame + 1) + if self.strand == '+': + chromStart += frame + chromEnd -= offset + else: + chromStart += offset + chromEnd -= frame + location = "chromosome:%s:%s:%s:%s:%s"\ + % (reference, self.chrom, chromStart, chromEnd, strand) + seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location) + return seq_id + + def get_line(self, start_offset=0, end_offset=0): + if start_offset or end_offset: + s_offset = start_offset if start_offset else 0 + e_offset = end_offset if end_offset else 0 + if s_offset > self.chromStart: + s_offset = self.chromStart + chrStart = self.chromStart - s_offset + chrEnd = self.chromEnd + e_offset + blkSizes = self.blockSizes + blkSizes[0] += s_offset + blkSizes[-1] += e_offset + blkStarts = self.blockStarts + for i in range(1, self.blockCount): + blkStarts[i] += s_offset + items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name, + self.score, self.strand, self.thickStart, + self.thickEnd, self.itemRgb, + self.blockCount, + ','.join([str(x) for x in blkSizes]), + ','.join([str(x) for x in blkStarts])]] + return '\t'.join(items) + '\n' + return self.line
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/digest.py Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,162 @@ +# Copyright 2012 Anton Goloborodko, Lev Levitsky +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import itertools as it +import re +from collections import deque + + +def cleave(sequence, rule, missed_cleavages=0, min_length=None): + """Cleaves a polypeptide sequence using a given rule. + + Parameters + ---------- + sequence : str + The sequence of a polypeptide. + + .. note:: + The sequence is expected to be in one-letter uppercase notation. + Otherwise, some of the cleavage rules in :py:data:`expasy_rules` + will not work as expected. + + rule : str or compiled regex + A regular expression describing the site of cleavage. It is recommended + to design the regex so that it matches only the residue whose + C-terminal bond is to be cleaved. All additional requirements should be + specified using `lookaround assertions + <http://www.regular-expressions.info/lookaround.html>`_. + :py:data:`expasy_rules` contains cleavage rules + for popular cleavage agents. + missed_cleavages : int, optional + Maximum number of allowed missed cleavages. Defaults to 0. + min_length : int or None, optional + Minimum peptide length. Defaults to :py:const:`None`. + + ..note :: + This checks for string length, which is only correct for one-letter + notation and not for full *modX*. Use :py:func:`length` manually if + you know what you are doing and apply :py:func:`cleave` to *modX* + sequences. + + Returns + ------- + out : set + A set of unique (!) peptides. + + Examples + -------- + >>> cleave('AKAKBK', expasy_rules['trypsin'], 0) == {'AK', 'BK'} + True + >>> cleave('GKGKYKCK', expasy_rules['trypsin'], 2) == \ + {'CK', 'GKYK', 'YKCK', 'GKGK', 'GKYKCK', 'GK', 'GKGKYK', 'YK'} + True + + """ + return set(_cleave(sequence, rule, missed_cleavages, min_length)) + + +def _cleave(sequence, rule, missed_cleavages=0, min_length=None): + """Like :py:func:`cleave`, but the result is a list. Refer to + :py:func:`cleave` for explanation of parameters. + """ + peptides = [] + ml = missed_cleavages+2 + trange = range(ml) + cleavage_sites = deque([0], maxlen=ml) + cl = 1 + for i in it.chain([x.end() for x in re.finditer(rule, sequence)], + [None]): + cleavage_sites.append(i) + if cl < ml: + cl += 1 + for j in trange[:cl-1]: + seq = sequence[cleavage_sites[j]:cleavage_sites[-1]] + if seq: + if min_length is None or len(seq) >= min_length: + peptides.append(seq) + return peptides + + +def num_sites(sequence, rule, **kwargs): + """Count the number of sites where `sequence` can be cleaved using + the given `rule` (e.g. number of miscleavages for a peptide). + + Parameters + ---------- + sequence : str + The sequence of a polypeptide. + rule : str or compiled regex + A regular expression describing the site of cleavage. It is recommended + to design the regex so that it matches only the residue whose + C-terminal bond is to be cleaved. All additional requirements should be + specified using `lookaround assertions + <http://www.regular-expressions.info/lookaround.html>`_. + labels : list, optional + A list of allowed labels for amino acids and terminal modifications. + + Returns + ------- + out : int + Number of cleavage sites. + """ + return len(_cleave(sequence, rule, **kwargs)) - 1 + + +expasy_rules = { + 'arg-c': r'R', + 'asp-n': r'\w(?=D)', + 'bnps-skatole': r'W', + 'caspase 1': r'(?<=[FWYL]\w[HAT])D(?=[^PEDQKR])', + 'caspase 2': r'(?<=DVA)D(?=[^PEDQKR])', + 'caspase 3': r'(?<=DMQ)D(?=[^PEDQKR])', + 'caspase 4': r'(?<=LEV)D(?=[^PEDQKR])', + 'caspase 5': r'(?<=[LW]EH)D', + 'caspase 6': r'(?<=VE[HI])D(?=[^PEDQKR])', + 'caspase 7': r'(?<=DEV)D(?=[^PEDQKR])', + 'caspase 8': r'(?<=[IL]ET)D(?=[^PEDQKR])', + 'caspase 9': r'(?<=LEH)D', + 'caspase 10': r'(?<=IEA)D', + 'chymotrypsin high specificity': r'([FY](?=[^P]))|(W(?=[^MP]))', + 'chymotrypsin low specificity': + r'([FLY](?=[^P]))|(W(?=[^MP]))|(M(?=[^PY]))|(H(?=[^DMPW]))', + 'clostripain': r'R', + 'cnbr': r'M', + 'enterokinase': r'(?<=[DE]{3})K', + 'factor xa': r'(?<=[AFGILTVM][DE]G)R', + 'formic acid': r'D', + 'glutamyl endopeptidase': r'E', + 'granzyme b': r'(?<=IEP)D', + 'hydroxylamine': r'N(?=G)', + 'iodosobenzoic acid': r'W', + 'lysc': r'K', + 'ntcb': r'\w(?=C)', + 'pepsin ph1.3': r'((?<=[^HKR][^P])[^R](?=[FLWY][^P]))|' + r'((?<=[^HKR][^P])[FLWY](?=\w[^P]))', + 'pepsin ph2.0': r'((?<=[^HKR][^P])[^R](?=[FL][^P]))|' + r'((?<=[^HKR][^P])[FL](?=\w[^P]))', + 'proline endopeptidase': r'(?<=[HKR])P(?=[^P])', + 'proteinase k': r'[AEFILTVWY]', + 'staphylococcal peptidase i': r'(?<=[^E])E', + 'thermolysin': r'[^DE](?=[AFILMV])', + 'thrombin': r'((?<=G)R(?=G))|' + r'((?<=[AFGILTVM][AFGILTVWA]P)R(?=[^DE][^DE]))', + 'trypsin': r'([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))' + } +""" +This dict contains regular expressions for cleavage rules of the most +popular proteolytic enzymes. The rules were taken from the +`PeptideCutter tool +<http://ca.expasy.org/tools/peptidecutter/peptidecutter_enzymes.html>`_ +at Expasy. +"""
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensembl_rest.py Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,129 @@ +#!/usr/bin/env python +""" +# +#------------------------------------------------------------------------------ +# University of Minnesota +# Copyright 2017, Regents of the University of Minnesota +#------------------------------------------------------------------------------ +# Author: +# +# James E Johnson +# +#------------------------------------------------------------------------------ +""" + +from __future__ import print_function +from __future__ import unicode_literals + +import sys + +from time import sleep + +import requests + + +server = "https://rest.ensembl.org" +ext = "/info/assembly/homo_sapiens?" +max_region = 4000000 +debug = False + + +def ensembl_rest(ext, headers): + if debug: + print("%s" % ext, file=sys.stderr) + r = requests.get(server+ext, headers=headers) + if r.status_code == 429: + print("response headers: %s\n" % r.headers, file=sys.stderr) + if 'Retry-After' in r.headers: + sleep(r.headers['Retry-After']) + r = requests.get(server+ext, headers=headers) + if not r.ok: + r.raise_for_status() + return r + + +def get_species(): + results = dict() + ext = "/info/species" + req_header = {"Content-Type": "application/json"} + r = ensembl_rest(ext, req_header) + for species in r.json()['species']: + results[species['name']] = species + print("%s\t%s\t%s\t%s\t%s" % + (species['name'], species['common_name'], + species['display_name'], + species['strain'], + species['taxon_id']), file=sys.stdout) + return results + + +def get_biotypes(species): + biotypes = [] + ext = "/info/biotypes/%s?" % species + req_header = {"Content-Type": "application/json"} + r = ensembl_rest(ext, req_header) + for entry in r.json(): + if 'biotype' in entry: + biotypes.append(entry['biotype']) + return biotypes + + +def get_toplevel(species): + coord_systems = dict() + ext = "/info/assembly/%s?" % species + req_header = {"Content-Type": "application/json"} + r = ensembl_rest(ext, req_header) + toplevel = r.json() + for seq in toplevel['top_level_region']: + if seq['coord_system'] not in coord_systems: + coord_systems[seq['coord_system']] = dict() + coord_system = coord_systems[seq['coord_system']] + coord_system[seq['name']] = int(seq['length']) + return coord_systems + + +def get_transcripts_bed(species, refseq, start, length, strand='', + params=None): + bed = [] + param = params if params else '' + req_header = {"Content-Type": "text/x-bed"} + regions = list(range(start, length, max_region)) + if not regions or regions[-1] < length: + regions.append(length) + for end in regions[1:]: + ext = "/overlap/region/%s/%s:%d-%d%s?feature=transcript;%s"\ + % (species, refseq, start, end, strand, param) + start = end + 1 + r = ensembl_rest(ext, req_header) + if r.text: + bed += r.text.splitlines() + return bed + + +def get_seq(id, seqtype, params=None): + param = params if params else '' + ext = "/sequence/id/%s?type=%s;%s" % (id, seqtype, param) + req_header = {"Content-Type": "text/plain"} + r = ensembl_rest(ext, req_header) + return r.text + + +def get_cdna(id, params=None): + return get_seq(id, 'cdna', params=params) + + +def get_cds(id, params=None): + return get_seq(id, 'cds', params=params) + + +def get_genomic(id, params=None): + return get_seq(id, 'genomic', params=params) + + +def get_transcript_haplotypes(species, transcript): + ext = "/transcript_haplotypes/%s/%s?aligned_sequences=1"\ + % (species, transcript) + req_header = {"Content-Type": "application/json"} + r = ensembl_rest(ext, req_header) + decoded = r.json() + return decoded
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,125 @@ +<macros> + <xml name="bedutil_requirements"> + <requirement type="package" version="1.62">biopython</requirement> + </xml> + <xml name="ensembl_requirements"> + <requirement type="package" version="0.4.10">requests-cache</requirement> + </xml> + <xml name="twobit_requirements"> + <requirement type="package" version="3.1.4">twobitreader</requirement> + </xml> + <xml name="species_options"> + <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option> + <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option> + <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option> + <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option> + <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option> + <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option> + <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option> + <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option> + <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option> + <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option> + <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option> + <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option> + <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option> + <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option> + <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option> + <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option> + <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option> + <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option> + <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option> + <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option> + <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option> + <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option> + <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option> + <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option> + <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option> + <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option> + <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option> + <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option> + <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option> + <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option> + <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option> + <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option> + <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option> + <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option> + <option value="heterocephalus_glaber_female">heterocephalus_glaber_female (Naked mole-rat female) taxon_id: 10181</option> + <option value="heterocephalus_glaber_male">heterocephalus_glaber_male (Naked mole-rat male) taxon_id: 10181</option> + <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus (Squirrel) taxon_id: 43179</option> + <option value="jaculus_jaculus">jaculus_jaculus (Lesser Egyptian jerboa) taxon_id: 51337</option> + <option value="latimeria_chalumnae">latimeria_chalumnae (Coelacanth) taxon_id: 7897</option> + <option value="lepisosteus_oculatus">lepisosteus_oculatus (Spotted gar) taxon_id: 7918</option> + <option value="loxodonta_africana">loxodonta_africana (Elephant) taxon_id: 9785</option> + <option value="macaca_mulatta">macaca_mulatta (Macaque) taxon_id: 9544</option> + <option value="meleagris_gallopavo">meleagris_gallopavo (Turkey) taxon_id: 9103</option> + <option value="mesocricetus_auratus">mesocricetus_auratus (Golden Hamster) taxon_id: 10036</option> + <option value="microcebus_murinus">microcebus_murinus (Mouse Lemur) taxon_id: 30608</option> + <option value="microtus_ochrogaster">microtus_ochrogaster (Prairie vole) taxon_id: 79684</option> + <option value="monodelphis_domestica">monodelphis_domestica (Opossum) taxon_id: 13616</option> + <option value="mus_caroli">mus_caroli (Ryukyu mouse) taxon_id: 10089</option> + <option value="mus_musculus_129s1svimj">mus_musculus_129s1svimj (Mouse 129S1/SvImJ) taxon_id: 10090</option> + <option value="mus_musculus_aj">mus_musculus_aj (Mouse A/J) taxon_id: 10090</option> + <option value="mus_musculus_akrj">mus_musculus_akrj (Mouse AKR/J) taxon_id: 10090</option> + <option value="mus_musculus_balbcj">mus_musculus_balbcj (Mouse BALB/cJ) taxon_id: 10090</option> + <option value="mus_musculus_c3hhej">mus_musculus_c3hhej (Mouse C3H/HeJ) taxon_id: 10090</option> + <option value="mus_musculus_c57bl6nj">mus_musculus_c57bl6nj (Mouse C57BL/6NJ) taxon_id: 10090</option> + <option value="mus_musculus_casteij">mus_musculus_casteij (Mouse CAST/EiJ) taxon_id: 10091</option> + <option value="mus_musculus_cbaj">mus_musculus_cbaj (Mouse CBA/J) taxon_id: 10090</option> + <option value="mus_musculus_dba2j">mus_musculus_dba2j (Mouse DBA/2J) taxon_id: 10090</option> + <option value="mus_musculus_fvbnj">mus_musculus_fvbnj (Mouse FVB/NJ) taxon_id: 10090</option> + <option value="mus_musculus_lpj">mus_musculus_lpj (Mouse LP/J) taxon_id: 10090</option> + <option value="mus_musculus_nodshiltj">mus_musculus_nodshiltj (Mouse NOD/ShiLtJ) taxon_id: 10090</option> + <option value="mus_musculus_nzohlltj">mus_musculus_nzohlltj (Mouse NZO/HlLtJ) taxon_id: 10090</option> + <option value="mus_musculus_pwkphj">mus_musculus_pwkphj (Mouse PWK/PhJ) taxon_id: 39442</option> + <option value="mus_musculus_wsbeij">mus_musculus_wsbeij (Mouse WSB/EiJ) taxon_id: 10092</option> + <option value="mus_pahari">mus_pahari (Shrew mouse) taxon_id: 10093</option> + <option value="mus_spretus_spreteij">mus_spretus_spreteij (Algerian mouse) taxon_id: 10096</option> + <option value="mustela_putorius_furo">mustela_putorius_furo (Ferret) taxon_id: 9669</option> + <option value="myotis_lucifugus">myotis_lucifugus (Microbat) taxon_id: 59463</option> + <option value="nannospalax_galili">nannospalax_galili (Upper Galilee mountains blind mole rat) taxon_id: 1026970</option> + <option value="nomascus_leucogenys">nomascus_leucogenys (Gibbon) taxon_id: 61853</option> + <option value="notamacropus_eugenii">notamacropus_eugenii (Wallaby) taxon_id: 9315</option> + <option value="ochotona_princeps">ochotona_princeps (Pika) taxon_id: 9978</option> + <option value="octodon_degus">octodon_degus (Degu) taxon_id: 10160</option> + <option value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option> + <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option> + <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option> + <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option> + <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option> + <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option> + <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option> + <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option> + <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option> + <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option> + <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option> + <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option> + <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option> + <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option> + <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option> + <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option> + <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option> + <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option> + <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option> + <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option> + <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option> + <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option> + <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option> + <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option> + <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option> + <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option> + <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option> + <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option> + </xml> + <xml name="biotypes_help"> + <help><![CDATA[ +Example biotypes: +protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, +translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, +polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, +retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, +LRG_gene, IG_C_gene, IG_D_gene, IG_J_gene, IG_LV_gene IG_V_gene, TR_C_gene, TR_D_gene, TR_J_gene, TR_V_gene, +IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, +ribozyme, RNase_P_RNA, guide_RNA, macro_lncRNA, bidirectional_promoter_lncRNA, 3prime_overlapping_ncRNA, antisense_RNA, vaultRNA, Y_RNA, SRP_RNA, RNase_MRP_RNA, IG_C_pseudogene, lncRNA, lincRNA, miRNA, snRNA, sRNA, telomerase_RNA, Mt_tRNA, Mt_rRNA, scaRNA, misc_RNA, rRNA, tRNA, scRNA, snoRNA, other + ]]></help> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_transcripts.bed Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,19 @@ +chr1 14403 29570 ENST00000488147 1000 - 14402 14402 0,0,0 11 98,34,152,159,198,136,137,147,99,154,37 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130 WASH7P-201 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 unprocessed_pseudogene ENSG00000227232 WASH7P unprocessed_pseudogene +chr1 29553 31097 ENST00000473358 1000 + 29552 29552 0,0,0 3 486,104,122 0,1010,1422 MIR1302-2HG-202 none none -1,-1,-1 lincRNA ENSG00000243485 MIR1302-2HG lincRNA +chr1 30266 31109 ENST00000469289 1000 + 30265 30265 0,0,0 2 401,134 0,709 MIR1302-2HG-201 none none -1,-1 lincRNA ENSG00000243485 MIR1302-2HG lincRNA +chr1 30365 30503 ENST00000607096 1000 + 30364 30364 0,0,0 1 138 0 MIR1302-2-201 none none -1 miRNA ENSG00000284332 MIR1302-2 miRNA +chr1 34553 36081 ENST00000417324 1000 - 34552 34552 0,0,0 3 621,205,361 0,723,1167 FAM138A-201 none none -1,-1,-1 lincRNA ENSG00000237613 FAM138A lincRNA +chr1 35244 36073 ENST00000461467 1000 - 35243 35243 0,0,0 2 237,353 0,476 FAM138A-202 none none -1,-1 lincRNA ENSG00000237613 FAM138A lincRNA +chr1 52472 53312 ENST00000606857 1000 + 52471 52471 0,0,0 1 840 0 AL627309.6-201 none none -1 unprocessed_pseudogene ENSG00000268020 AL627309.6 unprocessed_pseudogene +chr1 57597 64116 ENST00000642116 1000 + 57596 57596 0,0,0 3 56,157,1201 0,1102,5318 OR4G11P-202 none none -1,-1,-1 processed_transcript ENSG00000240361 OR4G11P transcribed_unprocessed_pseudogene +chr1 62948 63887 ENST00000492842 1000 + 62947 62947 0,0,0 1 939 0 OR4G11P-201 none none -1 transcribed_unprocessed_pseudogene ENSG00000240361 OR4G11P transcribed_unprocessed_pseudogene +chr1 65418 71585 ENST00000641515 1000 + 69090 70008 0,0,0 3 15,54,2549 0,101,3618 OR4F5-202 cmpl cmpl -1,-1,0 protein_coding ENSG00000186092 OR4F5 protein_coding +chr1 69054 70108 ENST00000335137 1000 + 69090 70008 0,0,0 1 1054 0 OR4F5-201 cmpl cmpl 0 protein_coding ENSG00000186092 OR4F5 protein_coding +chr1 131024 134836 ENST00000442987 1000 + 131023 131023 0,0,0 1 3812 0 CICP27-201 none none -1 processed_pseudogene ENSG00000233750 CICP27 processed_pseudogene +chr1 139789 140339 ENST00000493797 1000 - 139788 139788 0,0,0 2 58,265 0,285 AL627309.2-201 none none -1,-1 antisense_RNA ENSG00000239906 AL627309.2 antisense_RNA +chr1 157783 157887 ENST00000410691 1000 - 157782 157782 0,0,0 1 104 0 RNU6-1100P-201 none none -1 snRNA ENSG00000222623 RNU6-1100P snRNA +chr1 187890 187958 ENST00000612080 1000 - 187889 187889 0,0,0 1 68 0 MIR6859-2-201 none none -1 miRNA ENSG00000273874 MIR6859-2 miRNA +chr1 263014 297502 ENST00000424587 1000 - 263013 263013 0,0,0 4 5190,150,105,158 0,5652,26251,34330 AP006222.1-206 none none -1,-1,-1,-1 processed_transcript ENSG00000228463 AP006222.1 transcribed_processed_pseudogene +chr1 347981 348366 ENST00000458203 1000 - 347980 347980 0,0,0 1 385 0 RPL23AP24-201 none none -1 processed_pseudogene ENSG00000236679 RPL23AP24 processed_pseudogene +chr1 439869 440232 ENST00000437905 1000 + 439868 439868 0,0,0 1 363 0 WBP1LP7-201 none none -1 processed_pseudogene ENSG00000269732 WBP1LP7 processed_pseudogene +chr1 450702 451697 ENST00000426406 1000 - 450739 451678 0,0,0 1 995 0 OR4F29-201 cmpl cmpl 0 protein_coding ENSG00000284733 OR4F29 protein_coding
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_transcripts_seq.bed Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,12 @@ +1 14403 29570 ENST00000488147 1000 - 14402 14402 0,0,0 11 98,34,152,159,198,136,137,147,99,154,37 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130 WASH7P-201 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 unprocessed_pseudogene ENSG00000227232 WASH7P unprocessed_pseudogene ATGGGAGCCGTGTGCACGTCGGGAGCTCGGAGTGAGCGTGAGTTCCGTGCCCAGGCCCGCGACTCGGCCCGACAGGACAGCGCTCCGGGTCGACGGGGTCCTGGAGCCGCGCTCGGGGAGGGCGCAGTGGAGGGCGAGCGGCGGCGTTAGGACCCGGAGGCGCGGGCGGACTGGGGGCGGCGGGGCTAGGACCCAGCGGCTCCGGCAGAGCGGAAGCGGCGGCGGGAGCTTCCGGGAGGGCGGCTCGCAGGTGAGGAGGCGTCCGGGGCCGCGGGAAGTAGGGTCGTGGGGGCCTGGCGGGGCGAAGTAGGGGACCCGGAGGGGCTGGAGGGAGGCGGGCGGGAGGCCCGGGACCGTTCCTGACCGAGAAGCCTGCGCCAAGCTGGTGTTCCGCGGCCGCTGCCCGGTGCCCGGCTCCACTGCGAACGCCGCCGCTGGGCCCCGACCGCCCGGGAGGCGTCTTGGGCTCGCCCCGGAGCTTCCTCCCTGGAGCCGCGCCCTGCACCCGGCCTTGCCCGGCCCTAGCAGGGAAGCCAAGGCTTGTGGGGCGCAGGGACCCGGGCTCTGCGGGGTCCCGGTTCCGCCTCCCCACTCCTGCGTCTTCCCGCCCCTGCCGGGTTCTGGGAAGCCTCGCGCGGCTCTTCCGCAGCTGCTGCCCGCCCGGAGCTCCTGGTCCCTCGTAGGGGACCCCACTTCTCTGACACCGCGTTGGGTTCCCGGGGCCTACAGCGAGGCTTGTAACTCCGGGAGAGACCCTGGAGCGGGGTGTGGGAGAACGGTCTGGAGGAAGGGCTCCGAGCACTTCGAAAGTATAAACCGCGGTCCCAAAGAGGCGTGCTGTGTCTGCATTTTCCTGGGAGTGCACGGTTTACATTCTCGAAAGCAGTGCTGTCGACTAGAAATATTGAGCGATACACATGTACAAGTTTTGTCACTTAAAAAGAATTTGAAAAAACTTCATAGATGCAAAAAAAAAAAAAAACCACCATTATTAAAGAATACTTAGGTATTTGTGGAATGCATTGAAGAGTTAACAAAATGGATAGGCAGGAAATATCGCAGACCTAGAATGAATTACAGTTACCCACTGTGGAACTGAGGAGCTAGGGTTTCTCATAAAACTCCCTGATAGAAGACGACTTTTGATAAATTTTTTTTTCCGCCAACAAAATCCCCTGTCTTCTCAACTAGTTACTGTCTGTCCACTAAATAAGAGGTGGTCCGTCACTTCTTCAGATGAGCAACTACAGGCTTTTCAAAAGATAATTGCTAATCAACCCCTTTGTGCCTGGGTTTTCTTATTTGTAAAAATAGATACTACTACCTAACTCCAAAGTGTGTGGTGAAGACAAACAATTGGGGTGATGTATACTAAAGTAACGAAAGTGTTGACCACACACTACGGGCTGGTTAGTGTTAGATTCCCTTGTTTTTCCCTCAGTATCAAAAACAGATCTAATTTAGGTTTACATAAAGACAAAGTATGAAGATAAGGTGACTTACAGTTGGTACTACTAACAAAATGTTTGGGCTAAGATTTGCATTATTGCATGAAAACAACAAAACATATCAATAAATAACAAAAAGCTTGGAATTCAGACGACAGATCCAAGTCTGGGCTTGATCTCAAGCTAGTGTTTTGATGTTGAAAAAATGTTATTTGGTCTTTCTAACCCCATTTCCTTATGTAAAATAGGGGATGATGATAAATTCACTGATAATAAGAGTTAAATGAGATTCTTGAGGAGTCAGAATGGTTCTAACATGTGTAGGTATTATTAGCAGTCATACTGTAGCATAAGAAAATACCGTCTGCTGAAAGAGGGACAATAAAGATTATCTACATGGTCATCATTTAAAAGCTACCAGATATAGGAAGAAGGGGCCATAAAATGATAACGTTATGATGATTAATTTTGATGCTTAGGTCAGAGTCCATTCTAGGATATCTGCTGCCCAAAAACAGCAGAGACTCATTTCTTTGGAATCACAGGACGCTGAGTGAGAGGAAAGAAAAAGAAAAGAAATATTTAAGTCACATATGTGATTTCTAAAAGTAAAAAGAAACAGATGAAATTAGTGATATATTTTTAAAATCCAGTATATCCCAAATATGGTTATTTTAGCACGTAATCAATATAAAATAATAAGATATTTTACATTCTTTTTTTCTAGCCTTTGAAATTTGGTGCATATTTTACACTTATGGCACATCTCAATTCAGACTATCCACATTTCAAGTGCTCAGTGGCTGCATGTGCCTGGTGGCTACCATATTGGACAGCACAGGTCTAAGGATTTCATTCCTGCCACAAGTCCAAACTCCTAGCTTTAATTTTGAGTGTTTTTAACAAACTGGCCTCTGTTTATCATTCTTTCTTCTAGTACTTCCCCAAGGATGATTGTACCCTCAGCACTCAAGACCGCTTGCGGTTCCCCTACACACTTTTTGTTCAAGCTGTTTCTTTTACCTGGAATGCTGTCTTTGCACCTTCTTCCTGGACCTGGTTCACCCTCGTTGCCTAGGCTGGAGTGCCATGGCGCGATCTTGGCACACTGCAACCTCCACCTTCCTGGTTCAAGTGATTCTCCTTCCTCAGCCTCCCGAGTAGCGGGGATTACAGGCATGCACCACCACGCCTGGCTAATTTTGTATTTTTAGTAGAGATGGAGTTTCACCATGTTGGTCAGACTGGTCTCGAACTCCCGACCTCAGGTGATCTGCCTGCCTTCGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCGCTGCGCCCGGCCGAGAGGCACACATTCTGCTAAGAGCTTTTTCCTGACTCCCCTAACTCCAAGAGGGATTTGTCACTCCTTAGCTTTGTACCCATGACTGGAGTAGAATGAATTTAATTTGAGTTTAGTTGTTTTTGAGACTCTCCCTGGCTAGTGTAGTGTCTTATTCGTCTTTGTTGTGATCATGGCCTGCACCTAACAGATGATCAGTAGATGTTTGCAGACAGAAAGTAAACCACTCATCAGGTGTATTCAGTCCCATTCTTGAACGGGCTTGCTGCCTCCTTTTTGAGGAGATCTGTGTATGTACTCTTCTTTCACGCATATGTGTGAGCAAACACACACACACTAACAAGAAATTCATCTGAAGATGTGCACAGGAAATATCTTGCATCTTTACCCCCTTTGTGATCTTACATATGGGAGAACTGAGGCACAGAAATAAGTTAGGACAGCCAGCAAACTTGCATCAGTATAAATACAAAGAAGGGGAGGGAGGAACATGCTTGAAAGGGGTGTGCTGGTCTCAGAGGGTTGGGTTTCTCAGTTGGCTGGGCATCAGCTGGCCATGCTTTAGTTATTTGATGGGAGGAAAAATAAGTGGGAGGTGAGGAGTAACTCCTGGGCTCTGATGAGTATTCAAGGCAAGTACAGATCTGGAAAGCCTGTATGCAAAGGAGGAACTCACTGAAAAGTGCTGGCCTGAGGAGGGCAGAAGGGAGGGCTGGGGAAGCCAGCAGCGGGAGCAAAGGAGTAGGCTCCAACTGGGTGAAGATGTTGGTGTGGTGCGTTATGTAAAATATACAAATTATTATTGGAAATAACCACGTCTCAGCAGTGCTAGTTCTCAGTTTGGAGAATGGGAAATCGAAAGGATCAGATTCAGAGACGGCAACTTACTCAAGGTCACAGCATTTTAAACCCAAGTGAAATCTCCTAGGCCCTTCATGCCACACTCATCCATCCCTACCTACTTGTGTTGCAACCAAGGGCCCCACTGTAGTGCCTAGGGGAGCAGGTCTAGGGCACAGTGCCAGGCCTGATTAATGTCTTCCTTACCATTTTCCAGTGAGGGGCTGTGATTAGGCCTATTTATAGGGGCCTGGTCCCTTAATATTCTGCCTGGTGCATCTCTTGCCAATCAAATCAGTGCTGTCTGCAGTGTGATTGCTGCTTTAGTGGCACCAGGGAGAGGAGTTAATTAAACCCAATATAAATAGACTCTGCCCTCACTTTGCAATTCCAGGAGTGTTTTTCCTTCCTGTCCTCCACCCCCACAGGCACCTCTTTCCTCTTGTCCCCCTAAGCTCTAGCCTGGGTGAGCAGGGCTGGATACTCCTATACCTAGAGTCACTAGCCACTGCCCAGTCTGTTTCAGGAGCAGGCCTCAGATTCCTCAGGGGTTAAAGTGGGAAGAACCCGTGTGTGCACATTTTTTGTGCTTTTCCAGAACTGTGTACCATTTGGCAGTTGATCAGGCAATCTCCCCTGCTACCCCATTTCTACCCCTTTGTTTCCAGCCTCTTTTTTCCTCTGCAACCAAGGTTTCTTGTTTATCCAAGGTGGGGAGCTGAACTGAGACAAGGTATGGAAAGGGTGCCTGGCAGGTAGCAAGCACCTTGTAGGGGGTCAGAAATGTTGCACCTTCTCTGAACTCCTCCATTGACCCTACAGATTCCCCAGTCCCGGGCCCTGCCCTTTCCCTCATTCACTCAGCAGGCATCAGCAGAGTCCCATCTATGCGCTCCTGGCCTCTCAGCAAATGCTCTGTCCCCTACTCCCCTATCTGTGCAGGCTGAAGCTATGTGCATAGTTGGGATGAGGGCTGTGTTGTCTCAACACCACGCTGCCCTGTGGTGGGGGCGTGCCGGTGGTCGTGGGTGGCTCTGACGCTCCGGCTCCGACCCACAGGCACCATGACTCCTGTGAGGATGCAGCACTCCCTGGCAGGTCAGACCTATGCCGTGCCCTTCATCCAGCCAGACCTGCGGCGAGAGGAGGCCGTCCAGCAGATGGCGGATGCCCTGCAGTACCTGCAGAAGGTCTCTGGAGACATCTTCAGCAGGTGGGTGCTGCCACTCACCCCCACCTGATGAGAGGGCCATCCCTGTCCTGGGCAATCCCAGCAACACACCCTCTGGGAGCAGCCCCCTTGGGGAATCCCGGTCCTGGGGAACCCATCTGGCTTCCCTGTGTGGGAGGGGCTGAAGTGAGAGCCCAACTTGGAAGCTTTTACTCCTGGGAGTCCGAGAGCTCACTCCCTTCCACCCCACTTAGCCTCCTGGTTTCCTGTGGTGGCTCTGCTCTCACAACTCATGCTTTTCCTCCCATTGGAGGGCCTATTCCTTCACGTTTTCCTGCAGCCAACAAATATTTACCCAGCAGTGCTCGTGTGCAAGGCAGTGTGGGAATCTCTATATATCCAGCCACGGATAAGGCAACATACCTCTCCACCTGGAGCGCACATTCTGGCAGGAGAGAAAGACCTAAATAAGCAATAGATGATTAGTTCTTCAATAACAGTTGTGACAAGGTCTATTGATAATATTTTGTAATCACTAATATTCATATAAACCGTGCACAACCATTGATTTGAGTGCATTAACTCACACTTCATGAGCAGGCACTGCCGTCATCTCATTTTATAGATGAGGAAACTGAGGCACAGAAGGGCTGAGAGACCTGGCCTAGTGACAGAGCCAGGATTCAAAGCCATAGATCATGGCCCCGGGTTATGTAGGTTATTACTGCATCTGTTCAGGGGAGATGGGGTACTGTGAGGCTCGTCATGGGAAGCCTGGCTTGGTCTCAGGTCAGGGAAGGCAGACGTGAGGAAATGACATTTATGGTAAAGTCTGAGGGTTGAGTGGGTAGGTTGGGAAGAACATTCCAGAAAGAAGCACATGAACTACAGCCTGGAGGTGGAGGACCTAAAAGGAAGCCAGCATGGCTGGAGCACGGAGTGGCCATTGAGGGAGGCGAGCTGGAGGGCTGCAGCTTCTTGTATTGGCAGTGCTGACCTCGCACAGTCCTTGGGCTCCAGTGACTTCACTCAGTGTTTATCTAACATGAGTGAGTGAATGGTGTTTGCTCTTTTTTTGGTAAAGGTCCCAGGGGTTGTCGGGTACACAGGTCCTGTCTTTGGCCATAAGCAAACTGAAATGAGGCTTGGTCTCCTTCCCAGGATCCCACACCATGCCTCACATGGTAGACCCCAGTGGGAAGTATGTGACTGCCTGACTCAGGTGCCTCTCGTGGTCCAAGCCATCCCTGCCCTGTCCCTTCCCTGGTTGTCGCCAGACCTGGAGCCCCTGCTCCTTCACTTTGCAGCCTCCTCTTCTGTCACCAACTGGGAACCCACCTCTTCCTGAAAGTCCTCCCCCACTGACTCACCGGCTTGCCCCGAGTTTGTCAAGAATGTCCCAGTAACCAGGGGACACACAGTGAAGTGACTGAGGGGTTACCTTGGAGTTGATGCCTTGGCTCAGATCCAGCTCCCCTGTTTTCTTCCTCTGTAACCTTGGGCAACCCAACCCCTCTAAGCCTCGGTGTTCTCATTTGTGAAGTTGTGGTAATAATGGTAGCTTCCTGGTAGAATTATTTTAAATATTAAATTAATCAAAACATGCAAAGGAATGGAACAGTGCCTGGCACCTAGGAAGCCTTCAGGAAATGCTATCTCTTCCCTGTTGATAATCTTGACCCGTACACTGCCTTTGGTTGCCATTCATAAACCTGCCACCAATAGTAACAAAGTGCTGGATGCACCTTTTGTGCTTATCTTTGTGCTAAATGTGCCCGAGGGACACCTAGGGAAGAGGATGCAGGTCTTTAAGAGCCATCAGCTCCAGATTATGGCCACCCCATGTCCAGCACTTAGAATGGAGGCCAAAACCATTCCCTCGGAAATTGTGTTTCCTTGCCAAGATGGGGACTGCGTGGTTGCCCTTCTCTGAGGGCAGCGCTGGATTTTTGGCGTCTTTCCTTTCCTGTCCTGGTACTTGGCACCTTGTAGACAGTTGCATGTCCCCTGCCCAGGGATGGGATGAGGAGAGGGCAGGAAGGCATTTCCTGGGTAGTGGAGTGCTGCGTTCATTGAGTGTGGGTTCTCCAAGCTGCTGGCACAGCGCAGGGAGGGCCAGATGCCTCTCAGGAGCCTTGGGCCTGAGTCCTGGCTCCCTCACTCCTGGGTTCCAGGTCACTGCATCTGTCTCTCCACCATGTGCTCCACCTCGTGCTGGACCTTAAGAGATACCAATTATGTGGCTGCCACTGTGTCCTAGAGGCTGGAATGGGAACACATAGGGCGAGATTGATTGTTAATTGCTAGCATGAACCGCGTGGGCTTCTCAGGGTCTAGAGTGGAGAGAAATCGGTAAGAATTGGTGGCACGCCTGTCAGAACTCCCCAGACCAAGCTAAGCAAAAATTAACCAATCAGTAGAGCAGCCTTCGGAGTAAGGGCTAAAATGATGTCCTCAGGGCCTGGTTTTGCTTTCCTTCCATGTCAGTTTGCTTCTTTGGGTCTGGCTGCATTCCCAGACAGGCCATGCTCTCGTGGTAGCAAGGTGACATGACACAGGGTCAGGTCCAGCAGGAAAGAATGCTGTCCTGTGTCCCCACTTCCTCCAGAAGCCACACTCACTCATCCCACCTGGCTTGGTCCTCATGTCTATCCCAGAATCCATTAATGGGGCCAGGGGACTATGACACACCACTTGGCTTAGACTGAGGAGCTCTGTGGGCAGCCCCACCTGAAGCTCTGGGACTAAGCCTGCGAGAGAGATGGATTCCCCAAGGGAAATGGGGCCATTGCTTGAGTAAAAAGGAAATAGTTGCTGAAGAGGAAAACCACGTGCTTACTCCACATAGGGCAGACTCCTGGAAGAGGGGGGCAGGGTAGGGAGGTGGATATGCAGGTTGCCCTGGCAGGGTCTGGAAATGGGGGCTGCAGGCTTGGAGGGAGGCCTCAGTGTGGCTTGGAACGTGGTGTATGGTGGTCTGCCGCGAAGGCCGGCCTGCACAGGGGTGGGAGGGGGGTGCTTCTGCATGGGAAGCACAGACAGCGCTGCCTCTCCCTTGCACTCAGCTCTCGGGGCATGAGAGGCTGACTTTCCGTGAGCCTGTGGGCCAGGCCTCTTTGAATGGGGCTGAGGGAGCTTTGCCCTGGTTCCTTTGTGTCCCCACGGTGCCACGGGAGGCTCCCTGGCAGGGTGTGGGGCAGGGCAGTGAGTGAAGAGTTGGGATGAGTGAGTTAGGGCCCACGGATTACTCAAGACAGGACTTCAAGTTGATTCAGGCGTGTTAGGGAGCTGTGATTGGATTTTGAGCAGGGCAGGGATGGGACAGAAGAGTTTGGGGAAGGTTCCTCAGGCATCCGTCACGGAAGGGACAAGAAGGGAGAGAGAGTGGATGCCAGGGACACCCAGAAGCTGTTATTGTAGTCAGGATACGACAGGGGTGAGGCTACAGACAGGGGACTTGCAAGCAGGGAGGGCAGGGTGAGACATTCAGAGGAAACGACGACAGGAAATGGTGACAGATAGGGAACGAGGATGAAGGGAAGGGAGAGCCAGTGACGACTGGCAGTGGAGTGGGGAGCACCGCCACCTCTCCTCCTCCACTTGCCCCTCCTGTGGCACTGGACAAGCTAGTGGGCTTTTCGTTGTCCATGGGCTTTTTCGGTGGGGATGTGACCAGCTTTGAACCCGTCCCCTTAAACATGCTCCTCCTGCACGGAAGAGACAGGGGCAGGGGAGAGACTCTCTCCCCACCACCCGGCTCAGGCCCCAGCACAGCCCGGCCTCTGGCCTCACTGGCGTCTGTGCCCAGTGACGCAGGCAGGTGAGCTCCTGGCAAATTAGCATTGCAGGCTGTGCTCTCTCCTCCTGCTCTGCTGCAGCTGGGAGTGTGCAGAGACTGGAGGGGATGACAGTCACCCTCTGTTTTCTGTGGTGGCTCTGTTTTCTGTGGTGCTGGATGCACCTCTGTTTTCTGTGGTGGCTCCAAGAGAGTGCACGGTCCCTGCTGATTGAAAGAAGGATGAAGGGCAGAAGAGGGGCGGGGAGCTGTGTGCCCTAAGATCTCATTGCCTTTTTATGCCGATTAACATGCTTTTAGCCCCTACTGAGCTTATAGTTAACAGAAGTTTCCAGGTCTTTCTTCACCTGAACTGTGTCTAAAGCAAGTTCCCTCCACCTTCTGTATTTATACGCTTGATTTTTAAAACCTAAATGTTGGGCTTCACATTTGTTCCTTGTAAATTTCATCTTGGTGATTGCAGTCTACCCTCTGGCCTTTAAAAATTGTCTGAGCCTTGATTCGATCATGAAACCAGCTTACCCTTCCCCTGTGTGCTGGCCCCAGTTTTCTAACCAGGTGTTGAATGAACTGGATGGACTCTGCCAGATCCCTCCGTGCAAGGCTGGAATCAGTCCATTGTTCAACTGTGCCCTTTGGGGCTGTGGTTCATTTGGCTCTGATTTTTCCTATATGTTCTCTCCTCCAACCCCCATAGCTCCATCTTGTCTACAAGATTTTGTTAGAAGCCGTCAAAATCCTGCTGACTCGAGATGCACTGTGCTGCATGTTTTCCCCGGGCACAGCAGGCTAATAATCCTGTTACAAAGAGAAATGCTGTACATTTCGAGCAGTGCTGGCCCCTGGGACTCACCGCGGCCTTTTCTAAGTGCTTACAGACTCTCTGTTTAATAATCCATTCCAGAAATTTTCCAGGGCTCATTGTTGAGCTTGGTGTTCGCAACTTTGAGTGATCAGCCCTTCTCCTTTGTGGGAGCACCAGGACAGAGCAGCCTTTGTCCCTCCCCAGTCTCAGTTCCCTCCCACTGCCCCTGTGGACCTCGAATGCAGAGCTTATGCACCTACCGAAGGTCGTGTCAGCACCCAAGGCAGAACGAGGCTGCCCTGGGAACTAGGGTCAATTAAGACAGCTTGTGCTGGAGGACCCTTTACAGCAGATGAAGGCCTCTCCCCAGCCAGAAAAGATGGAGCACACGCTGGGTGGTGGTCCCGCTTCCTCACTGGAAGGAGATGGTGCTCTTCTTTTTTCTTTCTGAATTGTGGCCACCTTCATACCAGTCTGTCATGGAACACTTAAGCCGCTTGAGTGCCTGCTGGTACTCCCAGCCCTGCCATGCCTGAGCCCCCTGCACACAAGGAGCCAGGAGTAATCAGGGCAGACCCTTTAGGGCACGGGGACTTCTGGATTGTGAAATTGGCTCTCTGGGGGCCAAGGCCTTCTAACGTTGGTGGAAGTGGCTTTGGCTTATTGGGTCGGATTCTAGGCCATTCATTCCAACCTTTAGAGACATCCCAGCTTTCCCTAGCCCAGAGTCTGCAGCCCCTCCACCATCCCACATCCTCCCCCTCCCTTTCCTCATGAACCCCAGTCGCGCCTCTGCCTTCTCAAACCCCTCCACCATCCCACACCCTCCTCCTGCCCTTCCTCATGAACCCCAGTCGCGCCTCTGCCTTCTCATCCCTGCGCACCACACAGGCTCGCTCGTGCCCGGTGAGTGCTGAGGCTGCTCTGCACGTGGAGTGTGGCCCTGTGGGCAAGGGCTGGGCTCTTGGAGGTAGGGGAGCTACAGGGGCGACTGGGAGGAGGATGTTGTGTTACACACGCATCAGAGTTAACTTTGCAGTGAGAGCGGCCTTGCTGCGGCCAAAGAACATGGAAAAGCATGAGTGGGGTGATGTGCCTTAAAGCATCAGACACTTGGGCCTCGGGCATCAGGAGCCAGCCACAGGGATGTCTGGGGAAATGGCGTTCCATGAGATGCAAGCACACAAGAATGCACTTGGCACATCTGGGGAACAGCAGGCAGCTGATATCACTGGGCCCACCCCGCACCAGGGAGGATGGAAGCAGGTGAGGAGCTAGACCACACTGAGGCGGTGGTCGGGACTCGGGGTTTGCTCAGTGAGCCGTTCAGTATGTGCAGGGGCAGTTCCCCGTCTGAATTTAGGTGACGACACTCAGGTCCAGCCTTGCCAGTCTCAGCCTCCGGTCTCCGTTCCCCCTCTGCAGAGGCCACATTGTCTGCTGCACGTGATCATGAGGGGTTGTGAAGTGCTTGCCCCATCAGTAGCCATGTGTGCATGTGTAAATACCATCCTCTGTGTGCCCTGGAGGCTGTCCTTCAGATAGCATGTACAGGTGGCAGCATAGGGCCTGTCCCTACTGAGAGTGCAGGGAACTCAGCACCGTCAACTCCTCGACCCTGCAGGTCAGATTATCCTTGTAGAGGCCCCCTGGATGGCACCAAGATCGGCCCTGGCAAGTAGGTGACCCTGACTTCAGAGCCCTTGCCTGAGGGCCTGGCCTGGCAGCTCTGCTGTTAGAAGCAGGAGGTGTGCAGAGGGTGGGGAGCAGCCCAGCCTCTGTGATCTTCTCCATGGCAGGATCTCCCAGCAGGTAGAGCAGAGCCGGAGCCAGGTGCAGGCCATTGGAGAGAAGGTCTCCTTGGCCCAGGCCAAGATTGAGAAGATCAAGGGCAGCAAGAAGGCCATCAAGGTAGTCCCCATACCCCTGTGTCCTGAGGCTACTGGGCAGTCCCTCCATTTCCCCGTGCCTCTGAGGCTGCCCAGTCTCTGCCCTGCTGCCCACCTGTACCTTGAGCTTTCTTCTCGCCCAGGCTTCCAACTCCACCCTCTCCTGCCAAGCAATCCTAGCCCTCTGAGCCTCTTGGGGCCCCCTCAGACTTGTCCCTGTGTCCACAGGTGTTCTCCAGTGCCAAGTACCCTGCTCCAGGGCGCCTGCAGGAATATGGCTCCATCTTCACGGGCGCCCAGGACCCTGGCCTGCAGAGACGCCCCCGCCACAGGATCCAGAGCAAGCACCGCCCCCTGGACGAGCGGGCCCTGCAGGTCTGCTGGCCGCGCATATAGCCTGTCACACACCAGGAGGACTGGATACTGGGGAGGAGCCGGGGCCACCATAGGGTTCTGTCCCCCAGAGGAGGCTGACTGGGATGGGATGGCAGCTGATTAGGCCCAGCACCAAATATTCACCATCCCTTGGCCATCCTGGCCCTCTCAGGAGAAGCTGAAGGACTTTCCTGTGTGCGTGAGCACCAAGCCGGAGCCCGAGGACGATGCAGAAGAGGGACTTGGGGGTCTTCCCAGCAACATCAGCTCTGTCAGCTCCTTGCTGCTCTTCAACACCACCGAGAACCTGTATGGCCAGAGGGCAGGGCCGAGGGGTGTGGGCGGGAGGCCCGGCCTGGCTTAGTGGGGACCCAGGGCATCAGACACAGGTACAGCACATAGGCCAGGAGCCAGGGGGTGACGGGTGGCTCGGCTCGGGAGGCCTGGGACCCCACAGTGCACGCTGTGCCCCTGATGATGTGGGAGAGGAACATGGGCTCAGGACAGCGGGTGTCAGCTTGCCTGACCCCCATGTCGCCTCTGTAGGTAGAAGAAGTATGTCTTCCTGGACCCCCTGGCTGGTGCTGTAACAAAGACCCATGTGATGCTGGGGGCAGAGACAGAGGAGAAGCTGTTTGATGCCCCCTTGTCCATCAGCAAGAGAGAGCAGCTGGAACAGCAGGTGGGAGGGGTGGGACAGAGGTGGAGACAGGTGCAGTGGCCCAGGGCCTTGCCAGAGCTCCTCTCCAGTCAAGGCTGTTGGGCCCCTTATTCCACCCATGGGAGGTGCACACAAGGTCTTGTTGGCTGCCCCTGCAGGTCCCTGTCACCTCTCACATGTCCCTGCCTAATCTTGCAGGTCCCAGAGAACTACTTCTATGTGCCAGACCTGGGCCAGGTGCCTGAGATTGATGTTCCATCCTACCTGCCTGACCTGCCCGGCATTGCCAACGACCTCATGTACATTGCCGACCTGGGCCCCGGCATTGCCCCCTCTGCCCCTGGCACCATTCCAGAACTGCCCACCTTCCACACTGAGGTAGCCGAGCCTCTCAAGGTAGGTGAGCTGGGTTCTGGGATGGGAGCTGGGCCGGGGACCTCCCTGGTCACACACCTTCTTCCCTAGACACCCCACACTTTGTGTTTCAGACCTACAAGATGGGGTACTAACACCACCCCCACCGCCCCCACCACCACCCCCAGCTCCTGAGGTGCTGGCCAGTGCACCCCCACTCCCACCCTCAACCGCGGCCCCTGTAGGCCAAGGCGCCAGGCAGGACGACAGCAGCAGCAGCGCGTCTCCTTCAGGTGGGAGCAGCTCTTTGAGGCCACCTGATTTCTGGCGTGCTCAGTGCACTCGGGTGGATTTTCTGTGGGTTTGTTAAGTGGTCAGAAATTCTCAATTTTTTGAATAGTTTCCATTTCAAATATCTTGTTCTACTTGGTTCATAAAATAGTGGTTTTCAAACTGTAGAGCTCTGGACTTCTCACTTCTAGGGCAGAGGGAGCCTGAACAAGTGAGGCTCTGGGTTCCCCATTCCTAATTAAACCAATGGAAAGAAGGGGTCTAATAACAAACTACAGCAACACATTTTTCATTTCAGCTTCACTGCTGTGTCTCCCAGTGTAACCCTAGCATCCAGAAGTGGCACAAAACCCCTCTGCTGGCTCGTGTGTGCAACTGAGACTGTCAGAGCATGGCTAGCTCAGGGGTCCAGCTCTGCAGGGTGGGGGCTAGAGAGGAAGCAGGGAGTATCTGCACACAGGATGCCCGCGCTCAGGTGGTTGCAGAAGTCAGTGCCCAGGCCCCCACACACAGTCTCCAAAGGTCCGGCCTCCCCAGCGCAGGGCTCCTCGTTTGAGGGGAGGTGACTTCCCTCCCAGCAGGCTCTTGGACACAGTAAGCTTCCCCAGCCCTGCCTGAGCAGCCTTTCCTCCTTGCCCTGTTCCCCACCTCCCGGCTCCAGTCCAGGGAGCTCCCAGGGAAGTGGTTGACCCCTCCGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCGGCAAGGCCAAGCTGCGCAGCATGAAGGAGCGAAAGCTGGAGAAGCAGCAGCAGAAGGAGCAGGAGCAAGGTGAGCGGGCCCTGGAGCTTGCAGTCGGAGGGCCTTGGGCAAGATCGCCTCCTCCCCTCCAGCCCTGAGTCCACCGGGTGCTTTCTGCCCACCCCCTGCTCTTGCCAGCTGGCCCCTGCTTCCCCTAGGGCACATGCTGGAAGCCCTGGGCCGCCACCAGAGGTCCTCAGCCCTCCTGCCTGGGCTATGGCTCCTTCCTGGTTTGGGAGCCATAGTGGAGCTTTCCTCTCTAAGCTCACCCAGCTCAAACTGACAGGAGAATCTTCTTCGACTGCCAAGAGCGGTCCAAGGCAATGGTCAGCCACTGCAGCCTCCTGAGATATTTTTAGAGACTGGACCTGAGGCCTCTGGAGGCTACTGATGATGCCTGCTGTGAACGCAGACACTGGTGTGATGCGATGCCTGCGCCTGCAGCGGCAGTGCCCTGGGCACTATGGTTTTGAGCTTGTACCCAGCGCTGCTTTTGCCTTGCTCTGTGACCCCAGGCAAGCTGCCTCACCTCTCTGGGCCAGTTTCCCCATTGTACAGTGGTGCTGCACACCCTGGCCCTGGCCCCGAGGTGGCTGGGAGGTGGCTCCTCAAACAGCCGCTGTCTCATCAGTGCCCGGTGCTGGGTCAGGGATCGACTGAGGCTCTGAGCTAACTGGGAAACACAGTGGCCTTGGAGGGCTGGGGAGTGTCATGGGGGTGGGGACAGGGAGTCACCGGTCGCATGTGACTGAACTCTTCACCCCAGTCTGTGGCTTTCCCGTTGCAGTGAGAGCCACGAGCCAAGGTGGGCACTTGATGTCGGATCTCTTCAACAAGCTGGTCATGAGGCGCAAGGGTAGGAGGCAGGGCCGCTGCCCGCCCTGGGCCAGCACCTTGTAATTCTGTCCTGCCTTTTTCTTCCTGTATTTAAGTCTCCGGGGGCTGGGGGAACCAGGGTTTCCCACCAACCACCCTCACTCAGCCTTTTCCCTCCAGGCATCTCTGGGAAAGGACCTGGGGCTGGTGAGGGGCCCGGAGGAGCCTTTGCCCGCGTGTCAGACTCCATCCCTCCTCTGCCGCCACCGCAGCAGCCACAGGCAGAGGAGGACGAGGACGACTGGGAATCGTAGGGGGCTCCATGACACCTTCCCCCCCAGACCCAGACTTGGGCCGTTGCTCTGACATGGACACAGCCAGGACAAGCTGCTCAGACCTACTTCCTTGGGAGGGGGTGACGGAACCAGCACTGTGTGGAGACCAGCTTCAAGGAGCGGAAGGCTGGCTTGAGGCCACACAGCTGGGGCGGGGACTTCTGTCTGCCTGTGCTCCATGGGGGGACGGCTCCACCCAGCCTGCGCCACTGTGTTCTTAAGAGGCTTCCAGAGAAAACGGCACACCAATCAATAAAGAACTGAGCAGAAA +1 29553 31097 ENST00000473358 1000 + 29552 29552 0,0,0 3 486,104,122 0,1010,1422 MIR1302-2HG-202 none none -1,-1,-1 lincRNA ENSG00000243485 MIR1302-2HG lincRNA GTGCACACGGCTCCCATGCGTTGTCTTCCGAGCGTCAGGCCGCCCCTACCCGTGCTTTCTGCTCTGCAGACCCTCTTCCTAGACCTCCGTCCTTTGTCCCATCGCTGCCTTCCCCTCAAGCTCAGGGCCAAGCTGTCCGCCAACCTCGGCTCCTCCGGGCAGCCCTCGCCCGGGGTGCGCCCCGGGGCAGGACCCCCAGCCCACGCCCAGGGCCCGCCCCTGCCCTCCAGCCCTACGCCTTGACCCGCTTTCCTGCGTCTCTCAGCCTACCTGACCTTGTCTTTACCTCTGTGGGCAGCTCCCTTGTGATCTGCTTAGTTCCCACCCCCCTTTAAGAATTCAATAGAGAAGCCAGACGCAAAACTACAGATATCGTATGAGTCCAGTTTTGTGAAGTGCCTAGAATAGTCAAAATTCACAGAGACAGAAGCAGTGGTCGCCAGGAATGGGGAAGCAAGGCGGAGTTGGGCAGCTCGTGTTCAATGGGTAGAGTTTCAGGCTGGGGTGATGGAAGGGTGCTGGAAATGAGTGGTAGTGATGGCGGCACAACAGTGTGAATCTACTTAATCCCACTGAACTGTATGCTGAAAAATGGTTTAGACGGTGAATTTTAGGTTATGTATGTTTTACCACAATTTTTAAAAAGCTAGTGAAAAGCTGGTAAAAAGAAAGAAAAGAGGCTTTTTTAAAAAGTTAAATATATAAAAAGAGCATCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTTAGGGTTGCCAGATTAAAAGACAGGATGCCCAGCTAGTTTGAATTTTAGATAAACAACGAATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTTGTTTATCTGAGATTCAGAATTAAGCATTTTATATTTTATTTGCTGCCTCTGGCCACCCTACTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCATGTTGTAGACAGAATGTTTATGTCCTCTCCAAATGCTTATGTTGAAACCCTAACCCCTAATGTGATGGTATGTGGAGATGGGCCTTTGGTAGGTAATTACGGTTAGATGAGGTCATGGGGTGGGGCCCTCATTATAGATCTGGTAAGAAAAGAGAGCATTGTCTCTGTGTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCATTTCTCTCTATCTCATTTCTCTCTCTCTCGCTATCTCATTTTTCTCTCTCTCTCTTTCTCTCCTCTGTCTTTTCCCACCAAGTGAGGATGCGAAGAGAAGGTGGCTGTCTGCAAACCAGGAAGAGAGCCCTCACCGGGAACCCGTCCAGCTGCCACCTTGAACTTGGACTTCCAAGCCTCCAGAACTGTGAGGGATAAATGTAT +1 30266 31109 ENST00000469289 1000 + 30265 30265 0,0,0 2 401,134 0,709 MIR1302-2HG-201 none none -1,-1 lincRNA ENSG00000243485 MIR1302-2HG lincRNA TCATCAGTCCAAAGTCCAGCAGTTGTCCCTCCTGGAATCCGTTGGCTTGCCTCCGGCATTTTTGGCCCTTGCCTTTTAGGGTTGCCAGATTAAAAGACAGGATGCCCAGCTAGTTTGAATTTTAGATAAACAACGAATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTTGTTTATCTGAGATTCAGAATTAAGCATTTTATATTTTATTTGCTGCCTCTGGCCACCCTACTCTCTTCCTAACACTCTCTCCCTCTCCCAGTTTTGTCCGCCTTCCCTGCCTCCTCTTCTGGGGGAGTTAGATCGAGTTGTAACAAGAACATGCCACTGTCTCGCTGGCTGCAGCGTGTGGTCCCCTTACCAGAGGTAAAGAAGAGATGGATCTCCACTCATGTTGTAGACAGAATGTTTATGTCCTCTCCAAATGCTTATGTTGAAACCCTAACCCCTAATGTGATGGTATGTGGAGATGGGCCTTTGGTAGGTAATTACGGTTAGATGAGGTCATGGGGTGGGGCCCTCATTATAGATCTGGTAAGAAAAGAGAGCATTGTCTCTGTGTCTCCCTCTCTCTCTCTCTCTCTCTCTCTCATTTCTCTCTATCTCATTTCTCTCTCTCTCGCTATCTCATTTTTCTCTCTCTCTCTTTCTCTCCTCTGTCTTTTCCCACCAAGTGAGGATGCGAAGAGAAGGTGGCTGTCTGCAAACCAGGAAGAGAGCCCTCACCGGGAACCCGTCCAGCTGCCACCTTGAACTTGGACTTCCAAGCCTCCAGAACTGTGAGGGATAAATGTATGATTTTAAAGTC +1 30365 30503 ENST00000607096 1000 + 30364 30364 0,0,0 1 138 0 MIR1302-2-201 none none -1 miRNA ENSG00000284332 MIR1302-2 miRNA GGATGCCCAGCTAGTTTGAATTTTAGATAAACAACGAATAATTTCGTAGCATAAATATGTCCCAAGCTTAGTTTGGGACATACTTATGCTAAAAAACATTATTGGTTGTTTATCTGAGATTCAGAATTAAGCATTTTA +1 34553 36081 ENST00000417324 1000 - 34552 34552 0,0,0 3 621,205,361 0,723,1167 FAM138A-201 none none -1,-1,-1 lincRNA ENSG00000237613 FAM138A lincRNA CACACAACGGGGTTTCGGGGCTGTGGACCCTGTGCCAGGAAAGGAAGGGCGCAGCTCCTGCAATGCGGAGCAGCCAGGGCAGTGGGCACCAGGCTTTAGCCTCCCTTTCTCACCCTACAGAGGGCAGGCCCTTCAGCTCCATTCTCCTCCAAGGCTGCAGAGGGGGCAGGAATTGGGGGTGACAGGAGAGCTGTAAGGTCTCCAGTGGGTCATTCTGGGCCCAGAGATGGGTGCTGAAGCTCCCACGCCTGCCTGTGAAAATGGAGTCCTCTCTCACCTGGGAGAGCCAGGTGCTGCCCCGAGAAGGATGCATTTATGGCTTCGTGAAGTCTTTCCTGACCCCCGATGCTGCTGACTATAGGTAAGTCTGAGCAAATCTGGGGGAGCCTCATCTTGGCATGAGAAAGAGATGGCTTCTTCTAAGCCCACTGGCCGTGATCCCAGGATTATAACACATTCTGGCTCAAGTCCAGACTATTTGTAGAACACAGGAGATCCTCCATGAGAGGTAGTATAATATAGAGGATATGTGTGCTTACTAAGAGGCTGCCTGTCTGACCTTGGACAAGTTGTTTTTATTTATTTATTTATTTTTTATAGAGACAAAGTCTCACTATGTTGCTCAGGCTGGTCTTGAACTCCTGGCCTCAAGCGATCCTCCCACCTCAGCCTCCCAAAGTGTTGGGATTATAGACATGAGCCACTGCACCTGGCCGACCTTGGGCAAGTTCTTAAACCCTTCAAAGCCTCATTTTTCTCCAATCACAAAAGGGAAAGATGGTAATATTTTCCCCACCAAATTCTTGTAAGTATTAAACATTGTATATGTATTTTGAACACGATTAAGCTCTAAACACTTGTTAGGAAGCAGGACTGGCATTTGAAACAAACAGCTCTTTTCCCACAGGTCGGATGCCCTCACAGAATTGAGATTATGTACGTAAAACACCAGGTGCCTAACCCGGCACAGAGCAGGAGGGCTAAGCGTGACATCCAGCACGTGGTCAGTGGAATCCAGTATTCCTACCCACCTCTCTAGTCTCCCCTCCACCCCTCTCCCTTTCAGAGGCACCAAGCTGCTTGTGGTCTTGTCTATTCCCACTCCCTGCCTGACTGAACATTTTCTCCACCTCCTGATCATCAGCAGCAGAAACTGGCTGCTCTTCCTCCTGGGTAGACAGCCAGACTGTATTTCCCAGCTGCCCCTGCAGTGAGATGTGGCCATCGGAGCCAGCATTGGCCAATGGACTCTGCATGGGAGTGACGCATGCTGCCTCCAGGCTTGTCCCTAAAACCTCCCACGTGTCCTCCGCCTGCTCTTCCCACCTCCAAGGAGCACGGCAATTGTGGAAGACCCAGATTAGTGATGGCAGAACCATAGATGGGAGGAACCTGGGTCCCTGACTTAAAGTATCATGGATTTGGATGTTCCCTTAGTGAGAAATAAACTTCCATTGTGTTTAAGCCTTTATTTGTTTATAGTTGGTTACAGCAACTGCCTTCTTTTAATTAAAACACTCCTGCTGCT +1 35244 36073 ENST00000461467 1000 - 35243 35243 0,0,0 2 237,353 0,476 FAM138A-202 none none -1,-1 lincRNA ENSG00000237613 FAM138A lincRNA GGGGTTTCGGGGCTGTGGACCCTGTGCCAGGAAAGGAAGGGCGCAGCTCCTGCAATGCGGAGCAGCCAGGGCAGTGGGCACCAGGCTTTAGCCTCCCTTTCTCACCCTACAGAGGGCAGGCCCTTCAGCTCCATTCTCCTCCAAGGCTGCAGAGGGGGCAGGAATTGGGGGTGACAGGAGAGCTGTAAGGTCTCCAGTGGGTCATTCTGGGCCCAGAGATGGGTGCTGAAGCTCCCACGCCTGCCTGTGAAAATGGAGTCCTCTCTCACCTGGGAGAGCCAGGTGCTGCCCCGAGAAGGATGCATTTATGGCTTCGTGAAGTCTTTCCTGACCCCCGATGCTGCTGACTATAGGTAAGTCTGAGCAAATCTGGGGGAGCCTCATCTTGGCATGAGAAAGAGATGGCTTCTTCTAAGCCCACTGGCCGTGATCCCAGGATTATAACACATTCTGGCTCAAGTCCAGACTATTTGTAGAACACAGGAGATCCTCCATGAGAGGTAGTATAATATAGAGGATATGTGTGCTTACTAAGAGGCTGCCTGTCTGACCTTGGACAAGTTGTTTTTATTTATTTATTTATTTTTTATAGAGACAAAGTCTCACTATGTTGCTCAGGCTGGTCTTGAACTCCTGGCCTCAAGCGATCCTCCCACCTCAGCCTCCCAAAGTGTTGGGATTATAGACATGAGCCACTGCACCTGGCCGACCTTGGGCAAGTTCTTAAACCCTTCAAAGCCTCATTTTTCTCCAATCACAAAAGGGAAAGATGGTAATATTTTCCCCACCAAATTCTTGTAAGTATTAAACATTGTATATGTATTTTGAA +1 52472 53312 ENST00000606857 1000 + 52471 52471 0,0,0 1 840 0 AL627309.6-201 none none -1 unprocessed_pseudogene ENSG00000268020 AL627309.6 unprocessed_pseudogene GCGGTATCTAAATTTGTATTGATTGGACTTTCAAGCTCTTGGGAGATGCATCTTTTTCTTTTTTGGTTCTTCTCTGTGTTCTACATGGGAATTATCCTGGAAAATCTCTTCATTGTGTTCACAGTAATTATTGACTCTCATTTAAATTCCCCAGGTACTGCCTACTGGCCAACATTTATCTTCTTGATCTGGGTCTTCTCCTACAGTTCTGACTTTTTCACTAACTGCAGCATCATTTCTTTTCCAAGATGCATCATACAGATATTTTTCATTTGTGTCATGCGTAAAAATTGAGATGGTGCTGCTCATAACCATGGCATAGAGCAGGTACACTGCCAATCTGTAAGCCTCCCCATTACCTGACCACAATGAACCCCAAAATGTGTGTTTCCTTTGTTGGAGGCATCCTGGATAGTCAGGATAATCCATGCTGTATCTCAGTTTGTTTTTGCCATAAACTTGCCTTTTTGTGGCCCTAATAGAGTAGGTAGTTTTCACTGTGATTTTCCTTATGTCATGAAACTTGCTTGTGTAGACACTTACAAACTAGAGGTTGTAGTCACTGCTAACAGTGGGCTTATATCCATAGCTACCTGTTTCTTATTAATAATATCCTATATTTTCATTTCGGTAACCGTCTAGAATCCTTCTTCAGGAGACTTATCTAAAGCATTTGTGTCATGTTAGATCACATCACAGTAGGGATTTTGTTTTTTATGCCATGTATATTTCTGTATGTGTAGCCTTTGCCTAAAACAACACATGATTAATATTTGTTCATTGTTCCTTTTGCTATCACCCCTGTCTAGGATCTACACATTAAGAAACAAAGACATGAAC +1 57597 64116 ENST00000642116 1000 + 57596 57596 0,0,0 3 56,157,1201 0,1102,5318 OR4G11P-202 none none -1,-1,-1 processed_transcript ENSG00000240361 OR4G11P transcribed_unprocessed_pseudogene AGCTATCTGAATTTCTCCTTCTCCTAAAAATGCACATCCTATGACTGAAAAGACAGGTAAAAGAGATGCTTTTAATTACAAAACTTTCCCTGTCGTGGTTGCTTCTCTCTATCCTTCTAAACTCCCTTTCAATTTCTTCTCTTCTGTAACATATTTGTGCCCAAAATCTTCTGCTTTCTGAAATATTTTATCTTTTTCTTCCACACTATCTCTTATTTTCCAATTTTAATCATTAAATTATATTATGTCTTATAAAACTAATCCCACATATAAACCCCTATGATAATTTCAGTTTGTCCCTAGTATGAAGTTCTTTAAAGATGTGTAGTTTTCTAACTTTCATGCTCTCCAATTAATTATAAACTTCATTTTCCACTCTGAAAAGGAGATGTCTGATCTCAGCTATTTCCATCCTATTTGAAAACCAGATTTAGTTTTAAACCAGAGGAAGGGAATCTCAAGTCTTTACCTCCCACAGTCTGGTGTGATTCTCTCTCTTTTGGTATTACCTTCCTCCACATTGGAACACTCCAGCCAATGCATAGGCTGAGAGGCTATCTCAGATTCAGAAAGATTTGGCCTCATCCCAGGGGAGGGTACAGAGGAGCTGATGACTATGAATTCTGAAATGGAACTGTTCCAGGTTGAAGAAATAAGAAAGGGAATTGGGAAGAGCAATGCCCAGTGAAAAAGAAGAAATAATATTTTAGGAAGTGAATGCTAATTTTATTTTAAACAAAATAAGAACTCAAGGAATAAGAGGGTTCTTCCAATAGGTTAGAGTGATCCTGTCAAACATATATGCTTCTAGATTTTTTTAAAGACTGTTTCTACTAAGAAAGCATAGACCGCTATTGAGAAAGATCATTAAACTGGAATTTAGGAGGTCTGCCTTCTGATTCTGACTTCTTGAATGTATTGTTAGCCATTTAACCACACTGTGTTGTTTCTCATTCTACCTGTAGAATCTCAAAGTTCTTTCCCACTTCTATACAAAACTATAATTCTGAACATCCTTTTTGTTTAATATAAGTCTGCATTTCCTGTTTGAAGATATGTGTCCCAGACCCTAAATGACTGACAAATTTTAAATCTCCAATAGGAAAGATGACAAACTCTATGGAAACTTGGCTTCTGAAGAACTCCTAGAAGCTTTCCAAAGTCATCAGTGTTTCCTAAGAAGGCAGAGAAATCAAACACATGGTCTTTTCCTCCAGACAAGCTCCTTTGGGTCATCAGGATTTCTTCAACAATAAAATGTAATAATTCCAAATGTTTGTAACAGAATGGGTAGGACTTTCTTCACTTATTTAAATACTCCCTTTTTTATGCAACTGAGTTTTCATCAACAAGTACAAGCTTGTGAAGGAGTACTTTAAAATGCAATTTCTCTCTATTTTTGTGGGGGCTAATATTTTATTTCTCATATTGACAATTTATTATGCTGTTTTTAAAAAGTTCATTCATCAAGTATTTCTTGAGCTTTTTCTATGAGACAGGCACTGTTTTAGGCAAGTAATTATGCACTGAACAATGCAAAAAGTTTCCCTGCACTCATGGACTTTAATTTTACATTTATGAAAAGCTACAAATATTAGAATAAGTAAAATACTGCCTGGAGGCTAAAGCATATTTTGATCACTTATTCCCTAATTCTTTTAGAAGAGAACTCACCTGTCGGTTAGCTGAACCACTGCCAGTGATATCCAACTATACATTCAATCCCACCATACCTCATTATCACACCTATTCACTCACAAGCTTAAACTCTTAACTTTTCTCCACATATCAGTGACTATTTCCTACAGCTTTTCTTTTACTTTCCATGTTTGCAGTGACAATATACATAAACAGTGTATGAAAACTCAAGTAAAATCTACTCTCTCAGGTGTTCATAATGTATCAATGTATATTGCTTTAAGCCTGAAGGTAACCTAAGTAAAGATGTACCATGTTCCACCAATGCTTCTTTTGATCATCATTTTATCCTGTTTTTTCTTTAGGATTCTTTCTTATTCCTTCCCCTGACCCTTCTTTTATTCTCCAAATTTCTTTCCAATTCATCTTTGTTCTTCCCTTTCCTTTTTACTCTCTTTAAACATTCTATGGACTCTGCCTCCTTCACACTGATATTGAACGCCCATAGTTTCATATTTTGGATTGCGATTGTTTTATTTTAAAATGGCAAATGTTCATGTTATAAAGAGAATTTTTCAGTCTTTAGACTAATAGGTTCATGTAGTTTGGGATTTTCCTCTTTAAGAAAATTAATTATCACTCACACTCCAAGACAAACACCATTTCAGTAGCAATATGAATTTCAGTAGTAATAGGAATCTCCAAATATGACAAAGTAATTCAGACATTAATTGCTTTTGTTTTGGAATTGCTCTTATAAGATGAAATATCACTTTCATGATGAGAGTCCTAGAGTGCTTGGTTTATATATTGTATCTTAGTTTTAACAGGATAAAACACTTGATCCTAAGCAGTAAACATGATTCTTCAGCTTCAACTTCATTTCTTTATAAATAACTATTTATGAATTGGTGTTGAGCTTAGTAAGTCACCAAACACCTTCTGCTCAGCAGCATAAAGGACATTTCCATGAAACCTCCCAGGGATAATCTTATTTACTCTATAATGTTTCCCGGGTTCAATTCCTCTCCCAAAATTCTTTGTTCTTAAGCCCCTATGATCTGGGTGATCTAAATATGGGTAAGAAGTCCAGGGATAGCACTATGAATGAAGTGAAAATAGTAAAACATAGTTAAAAATGTACAGATGCTCTCTGACTTATAATAGGGTTACGTCCTGATAAATCCATCATAAGTCAAAAATGCATTTAATATTCCTAATGTACCTCACATCATAGTTTGGCCTAGCCTACCTTAAATGTGCTCAGAACACTTTCATTAGCTTATATAAGATCACCTAATACAAAGCCTATTTTATAATAAAATATTGAATAGCTCACGTAATATACTGACTACTATACTCAAGTACAGTTTCTTCTGAATGCATGTCACTTTCTCACCATTGTAAAGTCAAACAATTATAAGTCAAACTATCACAAGCCAGGGACCATCCATATGTATTTCATTCAGAAAATGCTGGAAAGAGCATTTCGGAGAATATCTAGATGAGAGAAGGTAGAAAGCCATGCACAAATTCACTGAGAGTTTAAAAAAATACATGCATATTGTGGAGATAGAAATCAAATCTATTTGTCTCCATCTGCTGTATTCTTCCCAAAATATTATCTCTTCTTATCCCATTGTACTATATTGCATTTCTTTGACCATTTATTGTGTATCTCTTAATATTTCCCACTTCATCATTACTAACCTCACTCACTCTGAACTTGATGAGAGCACCTGAGCATTAATTTTTCTTATAATTATTTAATGATTACCAGAATTCGTTCAGTATGGCCAGCTCTGGTCAAAGTGAGGCAGGCAAGATGCTTTGTCAACTGCCTGGATGGAATGTCTCAAAAGGTTTCCATTTCATGGTAGCATTATGCAAAGTTCAAGACGTTTAATCAAGACCCTTCACTTACTTAACTATACCTCCTTGAGAATCCCATCTATGAAAAAATTCTAGTCATTATAAAAATGATTGATTAAATGAGGGAAGTAGTAGAGTTCTTCATTTCTTTAGTTGGTTTAGTCTCCTATGAGTCAATCCTATTTTCAAAATTCTTAATAAACCATTTATTCCTTCAACTTTCTATGCCATTTGATGTTTTGTAAAAAAAAAAATATAATATGTATACAAAAAGATATTTCAAAATCTAGAAAGAGAGCTTTAGAGCTTTGTAAAGCTCTTTTAAAAATCAAAAACAACTACTGTTAATTAACATGTTGTACTATGCAATTTGTTTACCATTATTACTCTTGGTATTTTTAAGAAAAGTCTTTCCATTGTTATTATAAATGCTTCTATTGATATTTATTTTAATAACTGTTATTACAGTCCGTCATGTACATACACTATACTTAAACCTAATGTTTGGTATTTAAATCGTTTCAAGATTTTATCACTGTCAACAAAGTATGATGAATATTTTTATGCTGAAAACTTCTGTAAAAATAGAATTCCAAGAGTATTATTGCACCAAAAGGCATGGACTTAAAATTCTTGATACATGATTTCAAAATATTTTCTTTAAGGTTTGAATCAGTCTATATTCCCTCCAGCAGCGTATAAAAGTGCCAATTTCTCTGATCCTTAGCCAGTTTGGGTAATAATAATTGTAAAACTTTTTTTTCTTTTTTTTTGAGACAGAGTCTCCCTCTGTCGCCAGGCTGAAGTGCAGTGGCGCAATCTCGGCTCACTGCAACCTCCGCCTCCCGGGGTCAAGCTATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTACAGGCATGCACCACCATGCCCAGCTAATTTTTGTTATTTTTAGTAGAGATGGAGTTTCCCCATGTTGGACAGGATGGTCTCGATCTCTTGACCTCGTGATCCACCCTCCTCGGCCTCCCAAAGTGCTGGGATAACAGGCGTGAACAACCATGCCCGGCCTGTAAAACTTTTTCCTAATTTAACAGAAAAATAATAGTATTATATTTTATCATATTTCTTTGATTTCTAAGACACACATACACACACACACACACATATCTGTATATACAAATACACGTATAGCTTACATTTTAATTCTTCATTTCATTTGTTCATTTATTAGGTCTTGGAGATTTTGTGAAACTGTTTAAATTCTTTTTTATACTATGAAGATATCAACCTTTTGTCTCTACAGCATTTCAAATTCAAGTATGATTCACGTGTTGGTTTGGGGTAGATCATTATAGGCACATGTAGGAAACAGCTTTCAGAGATGCCTTAACCGTAATTATGCATTTGTATTCTAATTTTTATTTAATGTTATTATTGATTGCATTTTTAAAGATTCTGTATTTTTTAAACCATTTATTTGTATATGTTGGTATACAATCTTGCCATTTTCTGGGATTTCATATTTCCTTATTTTTGTTTTTTACCTTTTTTGGCTTGAATTTTTTGAGTTTTTATGCATTCTTTTCCAGTTTCTTAAGATGCTAATAAGTTCATGTATTTGAGCAATTGAGAACATTTAAAGCAATAGACTGCCTCTGAGCACAGCTTTGTCCATATTACATTAACCTTTTATACCCTGGGTTCCCACTAGTTTTTAAATAATCTACTATCAAATAAAAGATTTGTTAATAATAAATTTTAAATCATTAACACTTAACGCATTATTTTCAGTCACACTAAGTTGATTCCTTCGTTTCTTTCAGGTTGCTTCAGAGTCTTCCCTTCTATCTGATTCAGTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAACACATTTGGTTGATGAGAGCACAGGATAAATGCCATGGACCATCAAGACTCCTGTGATCACCATGATCACTATGGAACGCGCACATTTTTAGTATTGCCTGAAAAAACTGAAAAATCTGCAAAAAGGATGCATTAAATCTAAGAATTGTATTTCAGATAAAGTTGCAACATTTTTTGTTAATCATAAAAAGTATATATTTCTATCTAATGTGTGTATCTAATTAACAGC +1 62948 63887 ENST00000492842 1000 + 62947 62947 0,0,0 1 939 0 OR4G11P-201 none none -1 transcribed_unprocessed_pseudogene ENSG00000240361 OR4G11P transcribed_unprocessed_pseudogene GTGGACCAAGTAAATGACTCTCTGGTAACAGAATTTGTATTACTTGGACTTGCACAATCCTTGGAAATGCAGTTTTTCCTTTTTCTCTTCTTCTCTTTATTCTATGTGGGAATTATCCTGGGAAAACTCTTCATTGTGTTCACAGTGATCTTTGATCCTCACTTACACTCCCCCATGTATATTCTGCTGGCCAACCTATCGCTCATTGACTTGAGCCTTTCATCTACCACAGTTCCTAGGTTGATCTACGATCTTTTTACTGATTGTAAAGTTATTTCCTTCCATAATTGCATGATACAAAAGTTCTTTATCCATGTTATGGGAGGAGTTGAAATGGTGCTGCTGATAGTCATGGCATATGATAGGTACACTGCGATCTGCAAGCCTCTCCACTATCCAACTATTATGAATCCCAAAATGTGCATGTTTTTGGTAGCAGCAGCTTGGGTCATTGGGGTGATTCATGCTATGTCTCAGTTTGTTTTTGTCATAAATTTACCCTTCTGTGGCCCTAATAATGTGGGGAGCTTTTATTGTGATTTTCCTCGGGTTATTAAACTTGCATGCATGGACACTTATGGGCTAGAATTTGTGGTCACTGCCAACAGTGGATTCATATCGATGGGCACCTTCTTTTTCTTAATTGTATCATACATTTTTATTCTGGTCACTGTCCAACGACATTCCTCAAATGATTTATCCAAAGCATTCTTCACTTCGTCGGCTCACATCACCGTAGTGGTTTTGTTTTTTGCTCCATGCATGTTTCTCTACGTGTGGCCTTTCCCTACTAAGTCATTGGATAAATTTTTTGCCATCATGAACTTTGTTGTCACCCCTGTCGTAAATCCTGCCATCTATACTTTAAGGAACAAAGATATGAAGTTTGCAATGAGAAGGCTGAATCAACATATTTTAAATTCTATGGAGACGACATAA +1 65418 71585 ENST00000641515 1000 + 69090 70008 0,0,0 3 15,54,2549 0,101,3618 OR4F5-202 cmpl cmpl -1,-1,0 protein_coding ENSG00000186092 OR4F5 protein_coding CCCAGATCTCTTCAGGTACATCTAGTCCATTCATAAAGGGCTTTTAATTAACCAAGTGGTTTACTAAAAAGGACAATTCACTACATATTATTCTCTTACAGTTTTTATGCCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTTATGAAGAAGGTAGGTGGAAACAAAGACAAAACACATATATTAGAAGAATGAATGAAATTGTAGCATTTTATTGACAATGAGATGGTTCTATTAGTAGGAATCTATTCTGCATAATTCCATTTTGTGTTTACCTTCTGGAAAAATGAAAGGATTCTGTATGGTTAACTTAAATACTTAGAGAAATTAATATGAATAATGTTAGCAAGAATAACCCTTGTTATAAGTATTATGCTGGCAACAATTGTCGAGTCCTCCTCCTCACTCTTCTGGGCTAATTTGTTCTTTTCTCCCCATTTAATAGTCCTTTTCCCCATCTTTCCCCAGGTCCGGTGTTTTCTTACCCACCTCCTTCCCTCCTTTTTATAATACCAGTGAAACTTGGTTTGGAGCATTTCTTTCACATAAAGGTACAAATCATACTGCTAGAGTTGTGAGGATTTTTACAGCTTTTGAAAGAATAAACTCATTTTAAAAACAGGAAAGCTAAGGCCCAGAGATTTTTAAATGATATTCCCATGATCACACTGTGAATTTGTGCCAGAACCCAAATGCCTACTCCCATCTCACTGAGACTTACTATAAGGACATAAGGCATTTATATATATATATATTATATATACTATATATTTATATATATTACATATTATATATATAATATATATTATATAATATATATTATATTATATAATATATAATATAAATATAATATAAATTATATTATATAATATATAATATAAATATAATATAAATTATATAAATATAATATATATTTTATTATATAATATAATATATATTATATAAATATAATATATAAATTATATAATATAATATATATTATATAATATAATATATTTTATTATATAAATATATATTATATTATATAATATATATTTTATTATATAATATATATTATATATTTATAGAATATAATATATATTTTATTATATAATATATATTATATAATATATATTATATTTATATATAACATATATTATTATATAAAATATGTATAATATATATTATATAAATATATTTATATATTATATAAATATATATATTATATATAATTCTAATGGTTGAATTCCAAGAATAATCTATGGCATGAAAGATTTTACCTGTCAACAGTGGCTGGCTCTTCATGGTTGCTACAATGAGTGTGTAAGATTCTGAAGGACTCCTTTAATAAGCCTAAACTTAATGTTCAACTTAGAATAAATACAATTCTTCTAATTTTTTTTGAATAATTTTTAAAAAGTCAGAAATGAGCTTTGAAAGAATTATGGTGGTGAAGGATCCCCTCAGCAGCACAAATTCAGGAGAGAGATGTCTTAACTACGTTAGCAAGAAATTCCTTTTGCTAAAGAATAGCATTCCTGAATTCTTACTAACAGCCATGATAGAAAGTCTTTTGCTACAGATGAGAACCCTCGGGTCAACCTCATCCTTGGCATATTTCATGTGAAGATATAACTTCAAGATTGTCCTTGCCTATCAATGAAATGAATTAATTTTATGTCAATGCATATTTAAGGTCTATTCTAAATTGCACACTTTGATTCAAAAGAAACAGTCCAACCAACCAGTCAGGACAGAAATTATCTCACAATAAAAATCCTATCGTTTGTACTGTCAATGATTAGTATGATTATATTTATTACCGTGCTAAGCAGAAGAGAAATGAAGTGAATGTTCATGATTTATTCCACTATTAGACTTCTCTTTATTCTTAAAAATATTTAAGATCACTAAATTTTTATAGGACTTTAAAAACAGTAATGTGCTGCTTTGAGTGTGTAGGACTAAGAAATGGGATTCAGAGTAGTAAAGAGAAAAGTGGAATTTCCAAGCACTATGAATTACTGTTCTTTAAAAAACAGCAAAAATCAAATAACAGTATTCCTCCAAAAAAGATGGCAAGTGTAAACTCTATACCTTCATGTCTCCCGTGGAATGTTAGTGATCAATTTCCACTTCTCTCTTTTACATCTTACTTGCCCATTAACTCTTATACCTAATCCAAAGATTGTTAATATGGCTATGTCTCACTTTCAGGACACCTTTTATTTGTTACTTCTCTTCACTGCAAAACTTCTTGAAACAGTACTTATTTTCTCTCCTCCATACACAATTGAAATGGCTCTCAACTCATGCCCAGAAGTCAGTGTTCAGTCTCTCACCTGGCAGATAGCAACTTACAAAGATGCCCCAACAATACCTCCTTGTGTCTAGACAGTCATCATTATCCTTTACCTTTTTCTGTATTTATTTCTGCTCCTAAAAGGGATCTCTATGTAAAGTATTGTTATACTAGTGCTTGTTATAATTATTATCAGAGTTAAAGCCATCACAATGTTCCCAATTACTTAAAGACATTGGAATAACATTTTTTTTATTTTCCACATCTTGCCAAAAAATATTTTGTTATCAGTACCTTAATAATGGCTATTATATATTGACCATTACTATTTGCTAGAAAATTTATATACCTGGTCGTATCCAATCCTCACAGAACTTCTATAAAGTTGTGCTATTATCACCTATATTTTCCAGATGTGGCCGTAAGACTGAAATCACTTAGGTGACTTGTCTAAGGTCATTCAGATACATAGTAGATAACCCAGGATTTGAACACAGGCCTCCTAGCACACAAGCTCATATCTTAACTACTTTAATACGTTGCTCGATGGGATCTTACAGGTCTTCATTCACCCCTTTCCTGCTCACACAACCACAACCTGCAGCTATTACCTATTGTTAGGCTTAAAATAATTACTTGGCTTCATTTCCAAGCTCCCTCCCTTCCAATTCACATTGAGTCCAGAGCTAAATTAAACAATCATTCAAAATTTTTCAGTAGTTCTTGTCTCTATAATAAAACAGAAATGCTTTAGAAAGCATTCCAAAATCTCTTACCAGTTTTATCTCCTATGAAAGTCCTTCACACTTTCTCTCATTTAAACTTTATTGCATTTTCCTCACTTTTTCTCACTTCACTTTTGAATTCCCTATTCTTTTATCCTCTGTTAATTTTTAAGTATTATATTTGTGATATTATTTTTTCTTTTTTTCTATTTTTTATCTTTCATTTCATTTTGGCCTATTTTTTTCTCTTAAGAACTTTAATATCACCAAATAACATGTGTGCTACAAACTGTTTTGTAGTTCAAAGAAAAAGGAGATAAACATAGAGTTATGGCATAGACTTAATCTGGCAGAGAGACAAGCATAAATAATGGTATTTTATATTAGGAATAAACCTAACATTAATGGAGACACTGAGAAGCCGAGATAACTGAATTATAAGGCATAGCCAGGGAAGTAGTGCGAGATAGAATTATGATCTTGTTGAATTCTGAATGTCTTTAAGTAATAGATTATAGAAAGTCACTGTAAGAGTGAGCAGAATGATATAAAATGAGGCTTTGAATTTGAATATAATAATTCTGACTTCCTTCTCCTTCTCTTCTTCAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCCTCCATTCCCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAACAACTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCTTTTGCTAATTCTTAGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTTCCTTCCTGTGTGACCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCTTATAAATTTAAAAAAAAATTTATTTGGTCCATTTTGTGAAAAACATAAAAAAAGAACTGTCACATCTTAATTTAAAAAATATATGCTTAGTGGTAAGGAGATATATGTCAACTTTTAAGAGGTTGAAAAACAAACGCCTCCCATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAGAATCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGCCTTCTAGGTCCTAGACGTCTGTGGTATAACTGCTCATAAGCAGTAGAAAGAATTTAGAGGGATCCAGGCTCTCATCACGTTGGCACAAAGTATATTACTTGGATCCATCTATGTCATTTTCCATGGTTAATGTTTAAAAGCACAGGCTTTAAAGTAAAAAACAAAGAGCTGGATTCAACTCTACTGACTCTTATTAATCATGATTTTGGGCACATTACGTAGCTTTCATGAGCTTTAGTTTCTACATTTATAAACAGGAGATTATACCTATTATGCATGGTTATTATGAAGGAAAATGACAAAATAGATATAAATCAAATAGCCCACTTCGAGACATATTAAGCATGAATAAACATTAGATACTATTAAAATCCTATATATTAACAAAGCCAAAAGTTTCAAACTTTACTTTTTCCCAACATTCTTGTGAAATATGACACATCCCAATCTTAACAGATGCTCATTTGGGATACTGTACTTGTGAGTGGAAGTGTGTATATTTGTGTGCAAGTGTGTACTCATATACTTCCACCTTACCACCCTAGAAAGGCATGATGAAAATTTAAGATAGAAGGAAAATATAAATTGAAAAAAAAAAACCTTAACAAATGATTCTGACAAATATCTTCTCTTTCCAGGGAGAATCACTGAGCCAGAATAAAATTGAACACTAAATATTCTAAGAAAAAAGGAATCTAGTTTGTCAAAATGTGACTTGAATTAATAGATAAGGAGAGTCAGATGATAAGAGGGTCAAAATTATGTTTATCTTAGGAAAAGTAGAATAGAAAATTTATAAGCAGATTAAAAACACATAATAAAAGTAGTAAATAATAATGACAGTATCTCAAATCAGTGCAGGGGGGAAAGGCCTACTAATGTGATGGTGGGATAATTGGATAGCAATATGGGAAAAGATATATTTAATTTATTTGCTACACCAAATGCCAGGACAATCTCTAAGTGAATTCAAGACATAACTCTTTTTTCAAAAAAAC +1 69054 70108 ENST00000335137 1000 + 69090 70008 0,0,0 1 1054 0 OR4F5-201 cmpl cmpl 0 protein_coding ENSG00000186092 OR4F5 protein_coding TCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACACAAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCCTCCATTCC +1 131024 134836 ENST00000442987 1000 + 131023 131023 0,0,0 1 3812 0 CICP27-201 none none -1 processed_pseudogene ENSG00000233750 CICP27 processed_pseudogene CCCCTTCTCTGGGCCCAAGCCACCTTGGCTGAGGAGGGGGCGAGGAGGTGTGAGCCCCTGCCAGGAACCCCCTGCCCGGACCAAGTGCTCGGCCCCCAGGCCTGCGTTCAGTGAGGCCTCCCGTGGCGTCAGCATGTTCGTGTGGAGGAATGTGGAAGGTCACTCTGCGGCCGTGTTCTCCTGGTACTCCATCCCCTTCCTGACCCCTCCCTGCAGCCACACGAGGCCCAGCAACCTGCCAGTCACTCAGTGGCCTCCAACCAGAGAAAACAACCTGCCAAGTTGGCAGCTGTTGCTCATGAGCGTCCACCAGGTGGGACAGGGAGTGTTGACCCTGGGCGGCCCCCTGGAGCCACCTGCCCTGAAAGCCCAGGGCCCGCAACCCCACACACTTTGGGGTTGGTGGAACCTGGTAAAAGCTCACCTCCCACCATGGAGGAGGAGCCCTGGGCCCCTCAGGGGAGTCCCTGCTGGACAGTGAGACAGAGAATGACCATGATGATGCTTTCCTCTCCATCATGTCTCCTGACACCCAGTTGCCTCTACCACTCAGATGATGTCAGGCCCAGTCCCTCAGTGCCCTGCGCAAGGAACAGGACTCATCTTCTGAGAAGGATGGACGCAGCCCCAACAAATCAGACAAGGACCACATCCGGTGGCCCATGAGTGGCGCTCATGATCTTCAGCAGGCGGCACCAGGCCCTGGCGGGGCGCACCAGGGTCACCCCAACCAGGATAACCGGACCGTCAGCCAGATGCTGAGCGAGCGGTGGTACACCCTGGGGCCCAATGAGATGCAGAAATACAACCTGGCCTTCCAGGTGAAGGTGGCCCACTTGCAACAAGGACCGAAAGAAGTCCAGCTCAGAGGCCAAGCCCACAAGCCAGGGGCTAGCAGGAGTGTAACAAGGGCTCGTGGGAGCGGAGCATATCAGAGACGGGCACTGCCACTGCCCCTGGGGTGTCCTCTGAACTCCTGTCAGTTGCAGCCCAAACACTCCAGAGCTCGGATACCAAGGAGCAGCTTCTGTGGGGCAGAACGGCTGCACACAGTCAGGGAACCTGGCTCAGCCTGGCCCAAGCCTTCTCCCACAGCGGGGTACACAGCCTGGACGGCAGGGAAATAGACCGTCAGGCACTACGGGAACTGACACAGGTGGTGTCTGGCACTGCATCATACTCTGGCCCAAAGCCTTCTACTCAGCATGGAGCTCCAGGCCACTTTGCAGCCCCTGGTGAGGGAGGTGACCCGTGGGCAGCCCTGCTGCCGCCCACGTGAGCTGCTCATTCCCAGCACATGGCCAGCGAGGTCATAGCGAGTGACGAAGAGCACACGGTCATCCATGAGGAGGAGGGGGTGATGATGTCATTGCTGATGATGGCTTTAGCACCACCGACACCGATCTCAAGTTCAAGGAGTGGGTGACCGACTGAGAGTGGGGACAACTCTGGGGAGGAGCCAGAGGGCAACAAGGGCTTTGGTGGGAAGGTATTTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCGCCCCTTGCTGGATCCTGAGCCCCCAGGGTCCCCCGATCCACCTGCAGCTTTTGGCAGTCTATGGTCACACCCTGTCCTCCTCCTACACATACTCGGATGCTTCCTCCTCAACCTTGGCACCCACCTCCTTCTTACTGGGCCCAGGAGCCTTCAAAGCCCAGGAGTCTGGTCAACGCAGCAGAGCGGGCCCCCTACGGCCCCAACCCCTGGGGATGGGGGCCCAGGGACGCCTTCCAAGGTGGCCTGTTTCCTCCCAATGGATCCTGCCACCTTCTGGTGCAAGAGACCTGAAAGTGTGGGCGACCTGGAGCTACCAGGCTCCTCAGTCATCAGGGTCCCTCCCAACACTAAGGCTTTCCTAGGCAGGAGCTGGGCTGAGCCACCCGGGGGGCAGAGCCTGAAGAGAAACTGACTGGGCTTTCGGGGTCGGGGCAGAGGGAACCCCACGGACATGGACCCCACACTGGAGGACCCCACCGCGCCCAAATGCAAGATGAGAAGATGCTCCAGCTGCAGTCCAAAGCCCAACACCCCCAAGTGTGCCATGTGTGATGGGGACAGCTTCCCCTTTGCCTGTACAGGTGGAGAAGCCGAGGACAGGCTCAGGGAACCGGAGACCAAGAAGGCGCTGTCCTCTTCACTGCATGTACCCTGGACCAGTGCCGGCCCTGATCATGCAGCTCTTCCAGGCCCACTGCTTCTTCCTGTCCACTAGGCCACAGCCGCCCTCCAGGCCCACTATGCACACATCTTCCCCTCCAAGGTTTGTTCTGCCCCTGCCCTGACTCCCAGCCCTGTGGGGGTCCTGACCGCACCTCACCTGGCTCAGACTCTTGACGCTGCCCTGGCTGCCCCACCAGTGCTTCTGCCCGAGAGTCACGTGAGGCTGAGAGTAGGGGCAGGGGCAGCAGTGGTGCCAGTTGGGGGGCGGTCCAGTGGGAGGAGCCTCAGCCTCGCAGGCTGCTCCGTGGGACTGATGACTGCATGATCTTCTGGGCACCTCACGGATCTTCAACTGCAGGTGAAACGGATGCTGGTGGTGGGTGCAGGGCCGCTGGGAGCTGCTGCATGGTTCCCAGAGGCTGGACTGAGGCAGGTGCCAACTGAAGCTGCTGGGGCAGCATGGGCAGGATGTTCTGCACACAAACCTTGGAGAAGAAGATGTGTGCATAGCAGGTCCACTGCTGCTGCCCCTGCCCTGACTCCCAGCCCTGCCTGACCCCACCTCAACCTGCTCAGGCTCTGGCACAACCCTGGCTGCCCTGCCACTGCCTCTGCCCCAGAGTTGGTGCCTTGACAGCCTGGTTGGAAGGGGACACCCCAGCCCTGCCTCAACACCTGGGGGTCTCCATAACTAGCACAGGCAGGTGGGCAACCCCAAAGATCCCAGGACTCACAGTACCCCCTGAGAACATGGACAGTATGTGGGGGTAGCAATGGAGGGCAGGATGGTTATCTTCTCCCAGGTGAAGCCATTTAATCCTTTCAGTTTGGGACGGAGTAAGGCCTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACCGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAACCTCTTCCCGCTGGGTTCACGCCATTCTCCTGCCTCAGCCTTCCGGGTAGCTAGGATTACAGGTGGACGCTACCACGTCCGGCTAATTTTTGTATTTTTAGTACAGACGGGGCTTCATCATCTTGGCCAGGCTGATTTCGATCTCCTGACATCGTGATCTGCCTGCCTCCCCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCAAGGCCTGCTCCTCTTATCTATACCCCCTACCCCTGCAGCTGTGCCGGGGGAAAGCTGGGCAGTTTCCCTCCTCCGAGCCCCTGTACATACCATGAATTGTGGGACCTTCAGAGCTTTTCACTTTTCGGAAAATAGCTCCTGCTGGGGCTACAAGATGGAGTGTGAAGAGGGCCTTGGGCCACAGGGAGGCGCCTGTGGACTAGGGGGAGTTCATGCACCCCTTCTTTCCCCAGAGGGGCTGGACTCAGGTGAGTATGGGGGTGGGGGCTCCTGCACTTCGACACAGGCAGCAGGAGGGTTTTCTCCCCATTCCCTCTGCACTCCCAACTTGAGCTATACTTTTTAAGAAAGTGATTCACCCTGCCTTTGCCCCCTTCCCCAGAACAGAACACGTTGATCGTGGGCGATATTTTTCATTGTGCCAAAAAGTTGCCATGACCGTCATTAAACCTGTTTAACAC
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/twobit.loc.sample Mon Jan 22 13:59:27 2018 -0500 @@ -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...
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,6 @@ +<tables> + <table name="twobit" comment_char="#"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table> +</tables>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/translate_bed.py Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,303 @@ +#!/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 + +from Bio.Seq import translate + +from bedutil import bed_from_line + +import digest + +from ensembl_rest import get_cdna + +from twobitreader import TwoBitFile + + +def __main__(): + parser = argparse.ArgumentParser( + description='Translate from BED') + parser.add_argument( + 'input_bed', default=None, + help="BED to translate, '-' for stdin") + pg_seq = parser.add_argument_group('Genomic sequence source') + pg_seq.add_argument( + '-t', '--twobit', default=None, + help='Genome reference sequence in 2bit format') + pg_seq.add_argument( + '-c', '--column', type=int, default=None, + help='Column offset containing genomic sequence' + + 'between start and stop (-1) for last column') + pg_out = parser.add_argument_group('Output options') + pg_out.add_argument( + '-f', '--fasta', default=None, + help='Path to output translations.fasta') + pg_out.add_argument( + '-b', '--bed', default=None, + help='Path to output translations.bed') + pg_bed = parser.add_argument_group('BED filter options') + pg_bed.add_argument( + '-E', '--ensembl', action='store_true', default=False, + help='Input BED is in 20 column Ensembl format') + pg_bed.add_argument( + '-R', '--regions', action='append', default=[], + help='Filter input by regions e.g.:' + + ' X,2:20000-25000,3:100-500+') + pg_bed.add_argument( + '-B', '--biotypes', action='append', default=[], + help='For Ensembl BED restrict translations to Ensembl biotypes') + pg_trans = parser.add_argument_group('Translation filter options') + pg_trans.add_argument( + '-m', '--min_length', type=int, default=10, + help='Minimum length of protein translation to report') + pg_trans.add_argument( + '-e', '--enzyme', default=None, + help='Digest translation with enzyme') + pg_trans.add_argument( + '-M', '--start_codon', action='store_true', default=False, + help='Trim translations to methionine start_codon') + pg_trans.add_argument( + '-C', '--cds', action='store_true', default=False, + help='Only translate CDS') + pg_trans.add_argument( + '-A', '--all', action='store_true', + help='Include CDS protein translations ') + pg_fmt = parser.add_argument_group('ID format options') + pg_fmt.add_argument( + '-r', '--reference', default='', + help='Genome Reference Name') + pg_fmt.add_argument( + '-D', '--fa_db', dest='fa_db', default=None, + help='Prefix DB identifier for fasta ID line, e.g. generic') + pg_fmt.add_argument( + '-s', '--fa_sep', dest='fa_sep', default='|', + help='fasta ID separator defaults to pipe char, ' + + 'e.g. generic|ProtID|description') + pg_fmt.add_argument( + '-P', '--id_prefix', default='', + help='prefix for the sequence ID') + parser.add_argument('-v', '--verbose', action='store_true', help='Verbose') + parser.add_argument('-d', '--debug', action='store_true', help='Debug') + args = parser.parse_args() + + input_rdr = open(args.input_bed, 'r')\ + if args.input_bed != '-' else sys.stdin + fa_wtr = open(args.fasta, 'w')\ + if args.fasta is not None and args.fasta != '-' else sys.stdout + bed_wtr = open(args.bed, 'w') if args.bed is not None else None + + enzyme = digest.expasy_rules.get(args.enzyme, None) + + biotypea = [bt.strip() for biotype in args.biotypes + for bt in biotype.split(',')] + + twobit = TwoBitFile(args.twobit) if args.twobit else None + + selected_regions = dict() # chrom:(start, end) + region_pat = '^(?:chr)?([^:]+)(?::(\d*)(?:-(\d+)([+-])?)?)?' + if args.regions: + for entry in args.regions: + if not entry: + continue + regs = [x.strip() for x in entry.split(',') if x.strip()] + for reg in regs: + m = re.match(region_pat, reg) + if m: + (chrom, start, end, strand) = m.groups() + if chrom: + if chrom not in selected_regions: + selected_regions[chrom] = [] + selected_regions[chrom].append([start, end, strand]) + if args.debug: + print("selected_regions: %s" % selected_regions, file=sys.stderr) + + def filter_by_regions(bed): + if not selected_regions: + return True + ref = re.sub('^(?i)chr', '', bed.chrom) + if ref not in selected_regions: + return False + for reg in selected_regions[ref]: + (_start, _stop, _strand) = reg + start = int(_start) if _start else 0 + stop = int(_stop) if _stop else sys.maxint + if _strand and bed.strand != _strand: + continue + if bed.chromEnd >= start and bed.chromStart <= stop: + return True + return False + + translations = dict() # start : end : seq + + def unique_prot(tbed, seq): + if tbed.chromStart not in translations: + translations[tbed.chromStart] = dict() + translations[tbed.chromStart][tbed.chromEnd] = [] + translations[tbed.chromStart][tbed.chromEnd].append(seq) + elif tbed.chromEnd not in translations[tbed.chromStart]: + translations[tbed.chromStart][tbed.chromEnd] = [] + translations[tbed.chromStart][tbed.chromEnd].append(seq) + elif seq not in translations[tbed.chromStart][tbed.chromEnd]: + translations[tbed.chromStart][tbed.chromEnd].append(seq) + else: + return False + return True + + 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 None + + def write_translation(tbed, accession, peptide): + if args.id_prefix: + tbed.name = "%s%s" % (args.id_prefix, tbed.name) + probed = "%s\t%s\t%s\t%s%s" % (accession, peptide, + 'unique', args.reference, + '\t.' * 9) + if bed_wtr: + bed_wtr.write("%s\t%s\n" % (str(tbed), probed)) + bed_wtr.flush() + location = "chromosome:%s:%s:%s:%s:%s"\ + % (args.reference, tbed.chrom, + tbed.thickStart, tbed.thickEnd, tbed.strand) + fa_desc = '%s%s' % (args.fa_sep, location) + fa_db = '%s%s' % (args.fa_db, args.fa_sep) if args.fa_db else '' + fa_id = ">%s%s%s\n" % (fa_db, tbed.name, fa_desc) + fa_wtr.write(fa_id) + fa_wtr.write(peptide) + fa_wtr.write("\n") + fa_wtr.flush() + + def translate_bed(bed): + translate_count = 0 + transcript_id = bed.name + refprot = None + if not bed.seq: + if twobit: + bed.seq = get_sequence(bed.chrom, bed.chromStart, bed.chromEnd) + else: + bed.cdna = get_cdna(transcript_id) + cdna = bed.get_cdna() + if cdna is not None: + cdna_len = len(cdna) + if args.cds or args.all: + try: + cds = bed.get_cds() + if cds: + if args.debug: + print("cdna:%s" % str(cdna), file=sys.stderr) + print("cds: %s" % str(cds), file=sys.stderr) + if len(cds) % 3 != 0: + cds = cds[:-(len(cds) % 3)] + refprot = translate(cds) if cds else None + except: + refprot = None + if args.cds: + if refprot: + tbed = bed.get_cds_bed() + if args.start_codon: + m = refprot.find('M') + if m < 0: + return 0 + elif m > 0: + bed.trim_cds(m*3) + refprot = refprot[m:] + stop = refprot.find('*') + if stop >= 0: + bed.trim_cds((stop - len(refprot)) * 3) + refprot = refprot[:stop] + if len(refprot) >= args.min_length: + write_translation(tbed, bed.name, refprot) + return 1 + return 0 + if args.debug: + print("%s\n" % (str(bed)), file=sys.stderr) + print("CDS: %s %d %d" % + (bed.strand, bed.cdna_offset_of_pos(bed.thickStart), + bed.cdna_offset_of_pos(bed.thickEnd)), + file=sys.stderr) + print("refprot: %s" % str(refprot), file=sys.stderr) + for offset in range(3): + seqend = cdna_len - (cdna_len - offset) % 3 + aaseq = translate(cdna[offset:seqend]) + aa_start = 0 + while aa_start < len(aaseq): + aa_end = aaseq.find('*', aa_start) + if aa_end < 0: + aa_end = len(aaseq) + prot = aaseq[aa_start:aa_end] + if args.start_codon: + m = prot.find('M') + aa_start += m if m >= 0 else aa_end + prot = aaseq[aa_start:aa_end] + if enzyme and refprot: + frags = digest._cleave(prot, enzyme) + for frag in reversed(frags): + if frag in refprot: + prot = prot[:prot.rfind(frag)] + else: + break + is_cds = refprot and prot in refprot + if args.debug: + print("is_cds: %s %s" % (str(is_cds), str(prot)), + file=sys.stderr) + if len(prot) < args.min_length: + pass + elif not args.all and is_cds: + pass + else: + tstart = aa_start*3+offset + tend = aa_end*3+offset + prot_acc = "%s_%d_%d" % (transcript_id, tstart, tend) + tbed = bed.trim(tstart, tend) + if args.all or unique_prot(tbed, prot): + translate_count += 1 + tbed.name = prot_acc + write_translation(tbed, bed.name, prot) + aa_start = aa_end + 1 + return translate_count + + if input_rdr: + translation_count = 0 + transcript_count = 0 + for i, bedline in enumerate(input_rdr): + try: + bed = bed_from_line(bedline, ensembl=args.ensembl, + seq_column=args.column) + if bed is None: + continue + transcript_count += 1 + if bed.biotype and biotypea and bed.biotype not in biotypea: + continue + if filter_by_regions(bed): + translation_count += translate_bed(bed) + except Exception as e: + print("BED format Error: line %d: %s\n%s" + % (i, bedline, e), file=sys.stderr) + break + if args.debug or args.verbose: + print("transcripts: %d\ttranslations: %d" + % (transcript_count, translation_count), file=sys.stderr) + + +if __name__ == "__main__": + __main__()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/translate_bed.xml Mon Jan 22 13:59:27 2018 -0500 @@ -0,0 +1,304 @@ +<tool id="translate_bed" name="Translate BED transcripts" version="0.1.0"> + <description>cDNA in 3frames or CDS</description> + <macros> + <import>macros.xml</import> + </macros> + <requirements> + <expand macro="ensembl_requirements" /> + <expand macro="bedutil_requirements" /> + <expand macro="twobit_requirements" /> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command detect_errors="aggressive"><![CDATA[ + python '$__tool_directory__/translate_bed.py' + #if $ref.ref_source == 'cached': + --twobit='$ref.ref_loc.fields.path' + #elif $ref.ref_source == 'history': + --twobit='$ref.ref_file' + #elif $ref.ref_source == 'last_column': + --column '-1' + #elif $ref.ref_source == 'select_column': + --column ${int(str($ref.seq_column)) - 1} + #elif $ref.ref_source == 'ensembl_rest': + --ensembl + #end if + #if $translations.translate == 'CDS': + --cds + #elif $translations.translate == 'cDNA': + --all + #end if + $translations.start_codon + #if $bed_filters.biotypes: + --biotypes '$bed_filters.biotypes' + --ensembl + #end if + #if $bed_filters.regions: + --regions '$bed_filters.regions' + #end if + --min_length $translations.min_length + #if $translations.enzyme: + --enzyme '$translations.enzyme' + #end if + #if $fa_id.fa_db: + --fa_db='$fa_id.fa_db' + #end if + #if $fa_id.fa_sep: + --fa_sep='$fa_id.fa_sep' + #end if + #if $fa_id.reference: + --reference $fa_id.reference + #else: + --reference ${input.metadata.dbkey} + #end if + #if $fa_id.id_prefix: + --id_prefix '$fa_id.id_prefix' + #end if + --bed '$translation_bed' + --fasta '$translation_fasta' + -v + $input + ]]></command> + <inputs> + <param name="input" type="data" format="bed" label="A BED file with 12 columns" + help="thickStart and thickEnd define protein coding region, blocks define exon regions"/> + <conditional name="ref"> + <param name="ref_source" type="select" label="Source for Genomic Sequence Data"> + <option value="cached">Locally cached twobit</option> + <option value="history">History dataset twobit</option> + <option value="last_column">Last Column in the BED file</option> + <option value="select_column">Select Column in the BED file</option> + <option value="ensembl_rest">Retrieve sequences from Ensembl (Slow and only for Ensembl Transcripts)</option> + </param> + <when value="cached"> + <param name="ref_loc" type="select" label="Select reference 2bit file"> + <options from_data_table="twobit" /> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="twobit" label="reference 2bit file" /> + </when> + <when value="last_column"/> + <when value="select_column"> + <param name="seq_column" type="data_column" data_ref="input" label="BED column conatining the genomic sequence" + help="unspliced genomic sequence from chromStart to chromEnd (Extract Genomic DNA)"/> + </when> + <when value="ensembl_rest"/> + </conditional> + <section name="bed_filters" expanded="false" title="BED Filtering Options"> + <param name="regions" type="text" value="" optional="true" label="Restrict to features overlapping a comma-separated list of regions" > + <help>Each region is specifed as: chr or chr:pos or chr:from-to</help> + <validator type="regex" message="">^(\w+(:\d+(-\d+)?)?(,\w+(:\d+(-\d+)?)?)*)?$</validator> + </param> + <param name="biotypes" type="text" value="" optional="true" label="Restrict Feature translation to these biotypes" + help="For 20 column BED from Ensembl REST server"> + <expand macro="biotypes_help" /> + </param> + </section> + <section name="translations" expanded="false" title="Translation Options"> + <param name="translate" type="select" label="Feature translation"> + <option value="cDNA_minus_CDS">cDNA in 3 frames excluding known CDS</option> + <option value="cDNA">cDNA in 3 frames</option> + <option value="CDS">CDS proteins</option> + </param> + <param name="min_length" type="integer" value="10" min="1" label="Minimum length of protein translation to report"/> + <param name="start_codon" type="boolean" truevalue="--start_codon" falsevalue="" checked="false" + label="Require translations to start with Methionine, trim other leading Amino Acids"/> + <param name="enzyme" type="select" optional="true" label="Digest enzyme" + help="Split the protein into peptides according to enzyme digestion"> + <option value="trypsin">trypsin: ([KR](?=[^P]))|((?<=W)K(?=P))|((?<=M)R(?=P))</option> + </param> + </section> + <section name="fa_id" expanded="false" title="Fasta ID Options"> + <param name="reference" type="text" value="" optional="true" label="Genome reference name" + help="By default, the input bed dataset metadata will be used."/> + <param name="fa_db" type="text" value="" optional="true" label="fasta ID source, e.g. generic" + help="Any Compomics application such as PeptideShaker, requires a source for non reference proteins of 'generic' e.g.: generic|pep1|peptide description"> + </param> + <param name="fa_sep" type="text" value="" optional="true" label="fasta ID line separator character" + help="defaults to the pipe character, Ensembl FASTA files usually use a space character"> + </param> + <param name="id_prefix" type="text" value="" optional="true" label="ID prefix for generated IDs" + help="Can be used to distinguish samples"> + <validator type="regex" message="Allowed chars:a-z A-Z 0-9 _ - |">^[a-zA-Z0-9_-|]*$</validator> + </param> + </section> + </inputs> + <outputs> + <!-- update translation_bed format to "probed" when datatype is available --> + <data name="translation_bed" format="bed" label="Translate ${translations.translate} on ${on_string} ${input.name}.proBed"> + <actions> + <action name="column_names" type="metadata" + default="chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts,proteinAccession,peptideSequence,uniqueness,genomeReferenceVersion,psmScore,fdr,modifications,charge,expMassToCharge,calcMassToCharge,psmRank,datasetID,uri"/> + </actions> + </data> + <data name="translation_fasta" format="fasta" label="Translate ${translations.translate} on ${on_string} ${input.name}.fasta"/> + </outputs> + <tests> + <test> + <param name="input" value="human_transcripts.bed" ftype="bed12"/> + <param name="ref_source" value="ensembl_rest"/> + <param name="translate" value="cDNA_minus_CDS"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="ENST00000641515" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text=">ENST00000641515" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/> + <param name="ref_source" value="last_column"/> + <param name="translate" value="cDNA_minus_CDS"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="ENST00000488147" /> + <has_text text="FLLSSLLIGVPFCTSPHSCFSMFFGRSKAALTAKLTLMRV" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text="ENST00000488147" /> + <has_text text="FLLSSLLIGVPFCTSPHSCFSMFFGRSKAALTAKLTLMRV" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/> + <param name="ref_source" value="last_column"/> + <param name="translate" value="CDS"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="ENST00000641515" /> + <has_text text="MVTEFIFLGLSDSQELQTFLFMLFFVFY" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text="ENST00000641515" /> + <has_text text="MVTEFIFLGLSDSQELQTFLFMLFFVFY" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/> + <param name="ref_source" value="last_column"/> + <param name="translate" value="cDNA_minus_CDS"/> + <param name="biotypes" value="protein_coding"/> + <param name="start_codon" value="False"/> + <param name="fa_db" value="generic"/> + <param name="id_prefix" value="test_"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="test_ENST00000641515" /> + <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text="generic|test_ENST00000641515" /> + <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/> + <param name="ref_source" value="last_column"/> + <param name="translate" value="cDNA_minus_CDS"/> + <param name="biotypes" value="protein_coding"/> + <param name="start_codon" value="True"/> + <param name="fa_db" value="generic"/> + <param name="id_prefix" value="test_"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="test_ENST00000641515" /> + <has_text text="MLSKYSFANS" /> + <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text="generic|test_ENST00000641515" /> + <has_text text="MLSKYSFANS" /> + <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" /> + </assert_contents> + </output> + </test> + <test> + <param name="input" value="human_transcripts.bed" ftype="bed12"/> + <param name="ref_source" value="history"/> + <param name="ref_file" value="GRCh38.1.2bit" ftype="twobit"/> + <param name="translate" value="cDNA_minus_CDS"/> + <param name="regions" value="1:0-30000"/> + <param name="start_codon" value="True"/> + <param name="fa_db" value="generic"/> + <param name="id_prefix" value="test_"/> + <output name="translation_bed"> + <assert_contents> + <has_text text="test_ENST00000488147" /> + <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" /> + <not_has_text text="ENST00000335137" /> + </assert_contents> + </output> + <output name="translation_fasta"> + <assert_contents> + <has_text text="generic|test_ENST00000488147" /> + <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" /> + <not_has_text text="ENST00000335137" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ +Translate transcripts from the input BED file into protein sequences. + +The genomic sequence: + + - may be supplied in an extra column in the BED input file + - retrieved from a twobit genomic reference file + - retrieved from the Ensembl REST API for Ensembl transcripts + + +**INPUTS** + + - BED file with at least the standard 12 columns + - Genome reference in twobit format (optional) + + +**OUTPUTS** + + - FASTA of transcript translations + - BED with the genomic location of the translated protein. The added 13th column contains the protein sequence. + + +**OPTIONS** + + - Feature translation + + - cDNA - three frame translations of the cDNA sequences with an output for each sequence between STOP codons + - CDS - three frame translations of CDS (coding sequence defined by thickStart and thickEnd in the BED file) + + - Translation filtering + + - can be trimmed to a Methionine start codon + - can be split into peptides by an enzyme digestion + - must exceed specified minimum length + + + - BED Filtering + + - genomic regions + - ensembl biotype if the BED contains the 20 columns as retrieved from the Ensembl REST API + + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu613</citation> + <citation type="doi">10.1093/nar/gku1010</citation> + </citations> +</tool>