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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/proteogenomics/translate_bed commit 383bb485120a193bcc14f88364e51356d6ede219 |
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added:
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 |
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| diff -r 000000000000 -r 038ecf54cbec bedutil.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bedutil.py Mon Jan 22 13:59:27 2018 -0500 |
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| b'@@ -0,0 +1,515 @@\n+#!/usr/bin/env python\n+"""\n+#\n+#------------------------------------------------------------------------------\n+# University of Minnesota\n+# Copyright 2016, Regents of the University of Minnesota\n+#------------------------------------------------------------------------------\n+# Author:\n+#\n+# James E Johnson\n+#\n+#------------------------------------------------------------------------------\n+"""\n+\n+from __future__ import print_function\n+\n+import sys\n+\n+from Bio.Seq import reverse_complement, translate\n+\n+\n+def bed_from_line(line, ensembl=False, seq_column=None):\n+ fields = line.rstrip(\'\\r\\n\').split(\'\\t\')\n+ if len(fields) < 12:\n+ return None\n+ (chrom, chromStart, chromEnd, name, score, strand,\n+ thickStart, thickEnd, itemRgb,\n+ blockCount, blockSizes, blockStarts) = fields[0:12]\n+ bed_entry = BedEntry(chrom=chrom, chromStart=chromStart, chromEnd=chromEnd,\n+ name=name, score=score, strand=strand,\n+ thickStart=thickStart, thickEnd=thickEnd,\n+ itemRgb=itemRgb,\n+ blockCount=blockCount,\n+ blockSizes=blockSizes.rstrip(\',\'),\n+ blockStarts=blockStarts.rstrip(\',\'))\n+ if seq_column is not None and -len(fields) <= seq_column < len(fields):\n+ bed_entry.seq = fields[seq_column]\n+ if ensembl and len(fields) >= 20:\n+ bed_entry.second_name = fields[12]\n+ bed_entry.cds_start_status = fields[13]\n+ bed_entry.cds_end_status = fields[14]\n+ bed_entry.exon_frames = fields[15].rstrip(\',\')\n+ bed_entry.biotype = fields[16]\n+ bed_entry.gene_name = fields[17]\n+ bed_entry.second_gene_name = fields[18]\n+ bed_entry.gene_type = fields[19]\n+ return bed_entry\n+\n+\n+def as_int_list(obj):\n+ if obj is None:\n+ return None\n+ if isinstance(obj, list):\n+ return [int(x) for x in obj]\n+ elif isinstance(obj, str):\n+ return [int(x) for x in obj.split(\',\')]\n+ else: # python2 unicode?\n+ return [int(x) for x in str(obj).split(\',\')]\n+\n+\n+class BedEntry(object):\n+ def __init__(self, chrom=None, chromStart=None, chromEnd=None,\n+ name=None, score=None, strand=None,\n+ thickStart=None, thickEnd=None, itemRgb=None,\n+ blockCount=None, blockSizes=None, blockStarts=None):\n+ self.chrom = chrom\n+ self.chromStart = int(chromStart)\n+ self.chromEnd = int(chromEnd)\n+ self.name = name\n+ self.score = int(score) if score is not None else 0\n+ self.strand = \'-\' if str(strand).startswith(\'-\') else \'+\'\n+ self.thickStart = int(thickStart) if thickStart else self.chromStart\n+ self.thickEnd = int(thickEnd) if thickEnd else self.chromEnd\n+ self.itemRgb = str(itemRgb) if itemRgb is not None else r\'100,100,100\'\n+ self.blockCount = int(blockCount)\n+ self.blockSizes = as_int_list(blockSizes)\n+ self.blockStarts = as_int_list(blockStarts)\n+ self.second_name = None\n+ self.cds_start_status = None\n+ self.cds_end_status = None\n+ self.exon_frames = None\n+ self.biotype = None\n+ self.gene_name = None\n+ self.second_gene_name = None\n+ self.gene_type = None\n+ self.seq = None\n+ self.cdna = None\n+ self.pep = None\n+ # T26C\n+ self.aa_change = []\n+ # p.Trp26Cys g.<pos><ref>><alt> # g.1304573A>G\n+ self.variants = []\n+\n+ def __str__(self):\n+ return \'%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%d\\t%d\\t%s\\t%d\\t%s\\t%s\' % (\n+ self.chrom, self.chromStart, self.chromEnd,\n+ self.name, self.score, self.strand,\n+ self.thickStart, self.thickEnd, str(self.itemRgb), self.blockCount,\n+ \',\'.join([str(x) for x in self.blockSizes]),\n+ \',\'.join([str(x) for x in self.blockStarts]))\n+\n+ def get_splice_junctions(self):\n+ spl'..b' translation.find(\'*\', junc)\n+ tstop = stop if stop >= 0 else len(translation)\n+ offset = (block_sum - i) % 3\n+ trimmed = translation[tstart:tstop]\n+ if debug:\n+ print("frame: %d\\ttstart: %d tstop: %d " +\n+ "offset: %d\\t%s" %\n+ (i, tstart, tstop, offset, trimmed),\n+ file=sys.stderr)\n+ if filtering and tstart > ignore:\n+ continue\n+ # get genomic locations for start and end\n+ if self.strand == \'+\':\n+ chromStart = self.chromStart + i + (tstart * 3)\n+ chromEnd = self.chromEnd - offset\\\n+ - (len(translation) - tstop) * 3\n+ else:\n+ chromStart = self.chromStart + offset\\\n+ + (len(translation) - tstop) * 3\n+ chromEnd = self.chromEnd - i - (tstart * 3)\n+ # get the blocks for this translation\n+ (tblockCount, tblockSizes, tblockStarts) =\\\n+ self.get_blocks(chromStart, chromEnd)\n+ translations[i] = (chromStart, chromEnd, trimmed,\n+ tblockCount, tblockSizes, tblockStarts)\n+ if debug:\n+ print("tblockCount: %d tblockStarts: %s " +\n+ "tblockSizes: %s" %\n+ (tblockCount, tblockStarts, tblockSizes),\n+ file=sys.stderr)\n+ return translations\n+\n+ def get_seq_id(self, seqtype=\'unk:unk\', reference=\'\', frame=None):\n+ # Ensembl fasta ID format\n+ # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT\n+ # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1\\\n+ # gene:ENSG00000158815:transcript:ENST00000328693\\\n+ # gene_biotype:protein_coding transcript_biotype:protein_coding\n+ frame_name = \'\'\n+ chromStart = self.chromStart\n+ chromEnd = self.chromEnd\n+ strand = 1 if self.strand == \'+\' else -1\n+ if frame is not None:\n+ block_sum = sum(self.blockSizes)\n+ offset = (block_sum - frame) % 3\n+ frame_name = \'_\' + str(frame + 1)\n+ if self.strand == \'+\':\n+ chromStart += frame\n+ chromEnd -= offset\n+ else:\n+ chromStart += offset\n+ chromEnd -= frame\n+ location = "chromosome:%s:%s:%s:%s:%s"\\\n+ % (reference, self.chrom, chromStart, chromEnd, strand)\n+ seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location)\n+ return seq_id\n+\n+ def get_line(self, start_offset=0, end_offset=0):\n+ if start_offset or end_offset:\n+ s_offset = start_offset if start_offset else 0\n+ e_offset = end_offset if end_offset else 0\n+ if s_offset > self.chromStart:\n+ s_offset = self.chromStart\n+ chrStart = self.chromStart - s_offset\n+ chrEnd = self.chromEnd + e_offset\n+ blkSizes = self.blockSizes\n+ blkSizes[0] += s_offset\n+ blkSizes[-1] += e_offset\n+ blkStarts = self.blockStarts\n+ for i in range(1, self.blockCount):\n+ blkStarts[i] += s_offset\n+ items = [str(x) for x in [self.chrom, chrStart, chrEnd, self.name,\n+ self.score, self.strand, self.thickStart,\n+ self.thickEnd, self.itemRgb,\n+ self.blockCount,\n+ \',\'.join([str(x) for x in blkSizes]),\n+ \',\'.join([str(x) for x in blkStarts])]]\n+ return \'\\t\'.join(items) + \'\\n\'\n+ return self.line\n' |
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| diff -r 000000000000 -r 038ecf54cbec digest.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/digest.py Mon Jan 22 13:59:27 2018 -0500 |
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| @@ -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. +""" |
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| diff -r 000000000000 -r 038ecf54cbec ensembl_rest.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ensembl_rest.py Mon Jan 22 13:59:27 2018 -0500 |
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| @@ -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 |
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| diff -r 000000000000 -r 038ecf54cbec macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jan 22 13:59:27 2018 -0500 |
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| b'@@ -0,0 +1,125 @@\n+<macros>\n+ <xml name="bedutil_requirements">\n+ <requirement type="package" version="1.62">biopython</requirement>\n+ </xml>\n+ <xml name="ensembl_requirements">\n+ <requirement type="package" version="0.4.10">requests-cache</requirement>\n+ </xml>\n+ <xml name="twobit_requirements">\n+ <requirement type="package" version="3.1.4">twobitreader</requirement>\n+ </xml>\n+ <xml name="species_options">\n+ <option value="homo_sapiens">homo_sapiens (Human) taxon_id: 9606</option>\n+ <option value="mus_musculus">mus_musculus (Mouse) taxon_id: 10090</option>\n+ <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca (Panda) taxon_id: 9646</option>\n+ <option value="anas_platyrhynchos">anas_platyrhynchos (Duck) taxon_id: 8839</option>\n+ <option value="anolis_carolinensis">anolis_carolinensis (Anole lizard) taxon_id: 28377</option>\n+ <option value="astyanax_mexicanus">astyanax_mexicanus (Cave fish) taxon_id: 7994</option>\n+ <option value="bos_taurus">bos_taurus (Cow) taxon_id: 9913</option>\n+ <option value="caenorhabditis_elegans">caenorhabditis_elegans (Caenorhabditis elegans) taxon_id: 6239</option>\n+ <option value="callithrix_jacchus">callithrix_jacchus (Marmoset) taxon_id: 9483</option>\n+ <option value="canis_familiaris">canis_familiaris (Dog) taxon_id: 9615</option>\n+ <option value="carlito_syrichta">carlito_syrichta (Tarsier) taxon_id: 1868482</option>\n+ <option value="cavia_aperea">cavia_aperea (Brazilian guinea pig) taxon_id: 37548</option>\n+ <option value="cavia_porcellus">cavia_porcellus (Guinea Pig) taxon_id: 10141</option>\n+ <option value="chinchilla_lanigera">chinchilla_lanigera (Long-tailed chinchilla) taxon_id: 34839</option>\n+ <option value="chlorocebus_sabaeus">chlorocebus_sabaeus (Vervet-AGM) taxon_id: 60711</option>\n+ <option value="choloepus_hoffmanni">choloepus_hoffmanni (Sloth) taxon_id: 9358</option>\n+ <option value="ciona_intestinalis">ciona_intestinalis (C.intestinalis) taxon_id: 7719</option>\n+ <option value="ciona_savignyi">ciona_savignyi (C.savignyi) taxon_id: 51511</option>\n+ <option value="cricetulus_griseus_chok1gshd">cricetulus_griseus_chok1gshd (Chinese hamster CHOK1GS) taxon_id: 10029</option>\n+ <option value="cricetulus_griseus_crigri">cricetulus_griseus_crigri (Chinese hamster CriGri) taxon_id: 10029</option>\n+ <option value="danio_rerio">danio_rerio (Zebrafish) taxon_id: 7955</option>\n+ <option value="dasypus_novemcinctus">dasypus_novemcinctus (Armadillo) taxon_id: 9361</option>\n+ <option value="dipodomys_ordii">dipodomys_ordii (Kangaroo rat) taxon_id: 10020</option>\n+ <option value="drosophila_melanogaster">drosophila_melanogaster (Fruitfly) taxon_id: 7227</option>\n+ <option value="echinops_telfairi">echinops_telfairi (Lesser hedgehog tenrec) taxon_id: 9371</option>\n+ <option value="equus_caballus">equus_caballus (Horse) taxon_id: 9796</option>\n+ <option value="erinaceus_europaeus">erinaceus_europaeus (Hedgehog) taxon_id: 9365</option>\n+ <option value="felis_catus">felis_catus (Cat) taxon_id: 9685</option>\n+ <option value="ficedula_albicollis">ficedula_albicollis (Flycatcher) taxon_id: 59894</option>\n+ <option value="fukomys_damarensis">fukomys_damarensis (Damara mole rat) taxon_id: 885580</option>\n+ <option value="gadus_morhua">gadus_morhua (Cod) taxon_id: 8049</option>\n+ <option value="gallus_gallus">gallus_gallus (Chicken) taxon_id: 9031</option>\n+ <option value="gasterosteus_aculeatus">gasterosteus_aculeatus (Stickleback) taxon_id: 69293</option>\n+ <option value="gorilla_gorilla">gorilla_gorilla (Gorilla) taxon_id: 9595</option>\n+ '..b'n value="oreochromis_niloticus">oreochromis_niloticus (Tilapia) taxon_id: 8128</option>\n+ <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus (Platypus) taxon_id: 9258</option>\n+ <option value="oryctolagus_cuniculus">oryctolagus_cuniculus (Rabbit) taxon_id: 9986</option>\n+ <option value="oryzias_latipes">oryzias_latipes (Medaka) taxon_id: 8090</option>\n+ <option value="otolemur_garnettii">otolemur_garnettii (Bushbaby) taxon_id: 30611</option>\n+ <option value="ovis_aries">ovis_aries (Sheep) taxon_id: 9940</option>\n+ <option value="pan_troglodytes">pan_troglodytes (Chimpanzee) taxon_id: 9598</option>\n+ <option value="papio_anubis">papio_anubis (Olive baboon) taxon_id: 9555</option>\n+ <option value="pelodiscus_sinensis">pelodiscus_sinensis (Chinese softshell turtle) taxon_id: 13735</option>\n+ <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii (Northern American deer mouse) taxon_id: 230844</option>\n+ <option value="petromyzon_marinus">petromyzon_marinus (Lamprey) taxon_id: 7757</option>\n+ <option value="poecilia_formosa">poecilia_formosa (Amazon molly) taxon_id: 48698</option>\n+ <option value="pongo_abelii">pongo_abelii (Orangutan) taxon_id: 9601</option>\n+ <option value="procavia_capensis">procavia_capensis (Hyrax) taxon_id: 9813</option>\n+ <option value="pteropus_vampyrus">pteropus_vampyrus (Megabat) taxon_id: 132908</option>\n+ <option value="rattus_norvegicus">rattus_norvegicus (Rat) taxon_id: 10116</option>\n+ <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae (Saccharomyces cerevisiae) taxon_id: 4932</option>\n+ <option value="sarcophilus_harrisii">sarcophilus_harrisii (Tasmanian devil) taxon_id: 9305</option>\n+ <option value="sorex_araneus">sorex_araneus (Shrew) taxon_id: 42254</option>\n+ <option value="sus_scrofa">sus_scrofa (Pig) taxon_id: 9823</option>\n+ <option value="taeniopygia_guttata">taeniopygia_guttata (Zebra Finch) taxon_id: 59729</option>\n+ <option value="takifugu_rubripes">takifugu_rubripes (Fugu) taxon_id: 31033</option>\n+ <option value="tetraodon_nigroviridis">tetraodon_nigroviridis (Tetraodon) taxon_id: 99883</option>\n+ <option value="tupaia_belangeri">tupaia_belangeri (Tree Shrew) taxon_id: 37347</option>\n+ <option value="tursiops_truncatus">tursiops_truncatus (Dolphin) taxon_id: 9739</option>\n+ <option value="vicugna_pacos">vicugna_pacos (Alpaca) taxon_id: 30538</option>\n+ <option value="xenopus_tropicalis">xenopus_tropicalis (Xenopus) taxon_id: 8364</option>\n+ <option value="xiphophorus_maculatus">xiphophorus_maculatus (Platyfish) taxon_id: 8083</option>\n+ </xml>\n+ <xml name="biotypes_help">\n+ <help><![CDATA[\n+Example biotypes: \n+protein_coding, non_coding, pseudogene, nonsense_mediated_decay, non_stop_decay, \n+translated_processed_pseudogene, transcribed_processed_pseudogene, transcribed_unitary_pseudogene, transcribed_unprocessed_pseudogene, \n+polymorphic_pseudogene, processed_pseudogene, unprocessed_pseudogene, unitary_pseudogene, processed_transcript, \n+retained_intron, ccds_gene, sense_overlapping, sense_intronic, cdna_update, antisense, \n+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, \n+IG_pseudogene, IG_C_pseudogene, IG_D_pseudogene, IG_J_pseudogene, IG_V_pseudogene, TR_J_pseudogene, TR_V_pseudogene, TEC, \n+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\n+ ]]></help>\n+ </xml>\n+</macros>\n' |
| b |
| diff -r 000000000000 -r 038ecf54cbec test-data/GRCh38.1.2bit |
| b |
| Binary file test-data/GRCh38.1.2bit has changed |
| b |
| diff -r 000000000000 -r 038ecf54cbec test-data/human_transcripts.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_transcripts.bed Mon Jan 22 13:59:27 2018 -0500 |
| b |
| @@ -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 |
| b |
| diff -r 000000000000 -r 038ecf54cbec test-data/human_transcripts_seq.bed --- /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 |
| b |
| b'@@ -0,0 +1,12 @@\n+1\t14403\t29570\tENST00000488147\t1000\t-\t14402\t14402\t0,0,0\t11\t98,34,152,159,198,136,137,147,99,154,37\t0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130\tWASH7P-201\tnone\tnone\t-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1\tunprocessed_pseudogene\tENSG00000227232\tWASH7P\tunprocessed_pseudogene\tATGGGAGCCGTGTGCACGTCGGGAGCTCGGAGTGAGCGTGAGTTCCGTGCCCAGGCCCGCGACTCGGCCCGACAGGACAGCGCTCCGGGTCGACGGGGTCCTGGAGCCGCGCTCGGGGAGGGCGCAGTGGAGGGCGAGCGGCGGCGTTAGGACCCGGAGGCGCGGGCGGACTGGGGGCGGCGGGGCTAGGACCCAGCGGCTCCGGCAGAGCGGAAGCGGCGGCGGGAGCTTCCGGGAGGGCGGCTCGCAGGTGAGGAGGCGTCCGGGGCCGCGGGAAGTAGGGTCGTGGGGGCCTGGCGGGGCGAAGTAGGGGACCCGGAGGGGCTGGAGGGAGGCGGGCGGGAGGCCCGGGACCGTTCCTGACCGAGAAGCCTGCGCCAAGCTGGTGTTCCGCGGCCGCTGCCCGGTGCCCGGCTCCACTGCGAACGCCGCCGCTGGGCCCCGACCGCCCGGGAGGCGTCTTGGGCTCGCCCCGGAGCTTCCTCCCTGGAGCCGCGCCCTGCACCCGGCCTTGCCCGGCCCTAGCAGGGAAGCCAAGGCTTGTGGGGCGCAGGGACCCGGGCTCTGCGGGGTCCCGGTTCCGCCTCCCCACTCCTGCGTCTTCCCGCCCCTGCCGGGTTCTGGGAAGCCTCGCGCGGCTCTTCCGCAGCTGCTGCCCGCCCGGAGCTCCTGGTCCCTCGTAGGGGACCCCACTTCTCTGACACCGCGTTGGGTTCCCGGGGCCTACAGCGAGGCTTGTAACTCCGGGAGAGACCCTGGAGCGGGGTGTGGGAGAACGGTCTGGAGGAAGGGCTCCGAGCACTTCGAAAGTATAAACCGCGGTCCCAAAGAGGCGTGCTGTGTCTGCATTTTCCTGGGAGTGCACGGTTTACATTCTCGAAAGCAGTGCTGTCGACTAGAAATATTGAGCGATACACATGTACAAGTTTTGTCACTTAAAAAGAATTTGAAAAAACTTCATAGATGCAAAAAAAAAAAAAAACCACCATTATTAAAGAATACTTAGGTATTTGTGGAATGCATTGAAGAGTTAACAAAATGGATAGGCAGGAAATATCGCAGACCTAGAATGAATTACAGTTACCCACTGTGGAACTGAGGAGCTAGGGTTTCTCATAAAACTCCCTGATAGAAGACGACTTTTGATAAATTTTTTTTTCCGCCAACAAAATCCCCTGTCTTCTCAACTAGTTACTGTCTGTCCACTAAATAAGAGGTGGTCCGTCACTTCTTCAGATGAGCAACTACAGGCTTTTCAAAAGATAATTGCTAATCAACCCCTTTGTGCCTGGGTTTTCTTATTTGTAAAAATAGATACTACTACCTAACTCCAAAGTGTGTGGTGAAGACAAACAATTGGGGTGATGTATACTAAAGTAACGAAAGTGTTGACCACACACTACGGGCTGGTTAGTGTTAGATTCCCTTGTTTTTCCCTCAGTATCAAAAACAGATCTAATTTAGGTTTACATAAAGACAAAGTATGAAGATAAGGTGACTTACAGTTGGTACTACTAACAAAATGTTTGGGCTAAGATTTGCATTATTGCATGAAAACAACAAAACATATCAATAAATAACAAAAAGCTTGGAATTCAGACGACAGATCCAAGTCTGGGCTTGATCTCAAGCTAGTGTTTTGATGTTGAAAAAATGTTATTTGGTCTTTCTAACCCCATTTCCTTATGTAAAATAGGGGATGATGATAAATTCACTGATAATAAGAGTTAAATGAGATTCTTGAGGAGTCAGAATGGTTCTAACATGTGTAGGTATTATTAGCAGTCATACTGTAGCATAAGAAAATACCGTCTGCTGAAAGAGGGACAATAAAGATTATCTACATGGTCATCATTTAAAAGCTACCAGATATAGGAAGAAGGGGCCATAAAATGATAACGTTATGATGATTAATTTTGATGCTTAGGTCAGAGTCCATTCTAGGATATCTGCTGCCCAAAAACAGCAGAGACTCATTTCTTTGGAATCACAGGACGCTGAGTGAGAGGAAAGAAAAAGAAAAGAAATATTTAAGTCACATATGTGATTTCTAAAAGTAAAAAGAAACAGATGAAATTAGTGATATATTTTTAAAATCCAGTATATCCCAAATATGGTTATTTTAGCACGTAATCAATATAAAATAATAAGATATTTTACATTCTTTTTTTCTAGCCTTTGAAATTTGGTGCATATTTTACACTTATGGCACATCTCAATTCAGACTATCCACATTTCAAGTGCTCAGTGGCTGCATGTGCCTGGTGGCTACCATATTGGACAGCACAGGTCTAAGGATTTCATTCCTGCCACAAGTCCAAACTCCTAGCTTTAATTTTGAGTGTTTTTAACAAACTGGCCTCTGTTTATCATTCTTTCTTCTAGTACTTCCCCAAGGATGATTGTACCCTCAGCACTCAAGACCGCTTGCGGTTCCCCTACACACTTTTTGTTCAAGCTGTTTCTTTTACCTGGAATGCTGTCTTTGCACCTTCTTCCTGGACCTGGTTCACCCTCGTTGCCTAGGCTGGAGTGCCATGGCGCGATCTTGGCACACTGCAACCTCCACCTTCCTGGTTCAAGTGATTCTCCTTCCTCAGCCTCCCGAGTAGCGGGGATTACAGGCATGCACCACCACGCCTGGCTAATTTTGTATTTTTAGTAGAGATGGAGTTTCACCATGTTGGTCAGACTGGTCTCGAACTCCCGACCTCAGGTGATCTGCCTGCCTTCGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCGCTGCGCCCGGCCGAGAGGCACACATTCTGCTAAGAGCTTTTTCCTGACTCCCCTAACTCCAAGAGGGATTTGTCACTCCTTAGCTTTGTACCCATGACTGGAGTAGAATGAATTTAATTTGAGTTTAGTTGTTTTTGAGACTCTCCCTGGCTAGTGTAGTGTCTTATTCGTCTTTGTTGTGATCATGGCCTGCACCTAACAGATGATCAGTAGATGTTTGCAGACAGAAAGTAAACCACTCATCAGGTGTATTCAGTCCCATTCTTGAACGGGCTTGCTGCCTCCTTTTTGAGGAGATCTGTGTATGTACTCTTCTTTCACGCATATGTGTGAGCAAACACACACACACTAACAAGAAATTCATCTGAAGATGTGCACAGGAAATATCTTGCATCTTTACCCCCTTTGTGATCTTACATATGGGAGAACTGAGGCACAGAAATAAGTTAGGACAGCCAGCAAACTTGCATCAGTATAAATACAAAGAAGGGGAGGGAGGAACATGCTTGAAAGGGGTGTGCTGGTCTCAGAGGGTTGGGTTTCTCAGTTGGCTGGGCATCAGCTGGCCATGCTTTAGTTATTTGATGGGAGGAAAAATAAGTGGGAGGTGAGGAGTAACTCCTGGGCTCTGATGAGTATTCAAGGCAAGTACAGATCTGGAAAGCCTGTATGCAAAGGAGGAACTCACTGAAAAGTGCTGGCCTGAGGAGGGCAGAAGGGAGGGCTGGGGAAGCCAGCAGCGGGAGCAAAGGAGTAGGCTCCAACTGGGTGAAGATGTTGGTGTGGTGCGTTATGTAAAATATACAAATTATTATTGGAAATAACCACGTCTCAGCAGTGCTAGTTCTCAGTTTGGAGAATGGGAAATCGAAAGGATCAGATTCAGAGACGGCAACTTACTCAAGGTCACAGCATTTTAAACCCAAGTGAAATCTCCTA'..b'GCTCATGAAAATTGTGCCCTCCATTCC\n+1\t131024\t134836\tENST00000442987\t1000\t+\t131023\t131023\t0,0,0\t1\t3812\t0\tCICP27-201\tnone\tnone\t-1\tprocessed_pseudogene\tENSG00000233750\tCICP27\tprocessed_pseudogene\tCCCCTTCTCTGGGCCCAAGCCACCTTGGCTGAGGAGGGGGCGAGGAGGTGTGAGCCCCTGCCAGGAACCCCCTGCCCGGACCAAGTGCTCGGCCCCCAGGCCTGCGTTCAGTGAGGCCTCCCGTGGCGTCAGCATGTTCGTGTGGAGGAATGTGGAAGGTCACTCTGCGGCCGTGTTCTCCTGGTACTCCATCCCCTTCCTGACCCCTCCCTGCAGCCACACGAGGCCCAGCAACCTGCCAGTCACTCAGTGGCCTCCAACCAGAGAAAACAACCTGCCAAGTTGGCAGCTGTTGCTCATGAGCGTCCACCAGGTGGGACAGGGAGTGTTGACCCTGGGCGGCCCCCTGGAGCCACCTGCCCTGAAAGCCCAGGGCCCGCAACCCCACACACTTTGGGGTTGGTGGAACCTGGTAAAAGCTCACCTCCCACCATGGAGGAGGAGCCCTGGGCCCCTCAGGGGAGTCCCTGCTGGACAGTGAGACAGAGAATGACCATGATGATGCTTTCCTCTCCATCATGTCTCCTGACACCCAGTTGCCTCTACCACTCAGATGATGTCAGGCCCAGTCCCTCAGTGCCCTGCGCAAGGAACAGGACTCATCTTCTGAGAAGGATGGACGCAGCCCCAACAAATCAGACAAGGACCACATCCGGTGGCCCATGAGTGGCGCTCATGATCTTCAGCAGGCGGCACCAGGCCCTGGCGGGGCGCACCAGGGTCACCCCAACCAGGATAACCGGACCGTCAGCCAGATGCTGAGCGAGCGGTGGTACACCCTGGGGCCCAATGAGATGCAGAAATACAACCTGGCCTTCCAGGTGAAGGTGGCCCACTTGCAACAAGGACCGAAAGAAGTCCAGCTCAGAGGCCAAGCCCACAAGCCAGGGGCTAGCAGGAGTGTAACAAGGGCTCGTGGGAGCGGAGCATATCAGAGACGGGCACTGCCACTGCCCCTGGGGTGTCCTCTGAACTCCTGTCAGTTGCAGCCCAAACACTCCAGAGCTCGGATACCAAGGAGCAGCTTCTGTGGGGCAGAACGGCTGCACACAGTCAGGGAACCTGGCTCAGCCTGGCCCAAGCCTTCTCCCACAGCGGGGTACACAGCCTGGACGGCAGGGAAATAGACCGTCAGGCACTACGGGAACTGACACAGGTGGTGTCTGGCACTGCATCATACTCTGGCCCAAAGCCTTCTACTCAGCATGGAGCTCCAGGCCACTTTGCAGCCCCTGGTGAGGGAGGTGACCCGTGGGCAGCCCTGCTGCCGCCCACGTGAGCTGCTCATTCCCAGCACATGGCCAGCGAGGTCATAGCGAGTGACGAAGAGCACACGGTCATCCATGAGGAGGAGGGGGTGATGATGTCATTGCTGATGATGGCTTTAGCACCACCGACACCGATCTCAAGTTCAAGGAGTGGGTGACCGACTGAGAGTGGGGACAACTCTGGGGAGGAGCCAGAGGGCAACAAGGGCTTTGGTGGGAAGGTATTTGCACCTGTCATTCCTTCCTCCTTTACTCCTGCCGCCCCTTGCTGGATCCTGAGCCCCCAGGGTCCCCCGATCCACCTGCAGCTTTTGGCAGTCTATGGTCACACCCTGTCCTCCTCCTACACATACTCGGATGCTTCCTCCTCAACCTTGGCACCCACCTCCTTCTTACTGGGCCCAGGAGCCTTCAAAGCCCAGGAGTCTGGTCAACGCAGCAGAGCGGGCCCCCTACGGCCCCAACCCCTGGGGATGGGGGCCCAGGGACGCCTTCCAAGGTGGCCTGTTTCCTCCCAATGGATCCTGCCACCTTCTGGTGCAAGAGACCTGAAAGTGTGGGCGACCTGGAGCTACCAGGCTCCTCAGTCATCAGGGTCCCTCCCAACACTAAGGCTTTCCTAGGCAGGAGCTGGGCTGAGCCACCCGGGGGGCAGAGCCTGAAGAGAAACTGACTGGGCTTTCGGGGTCGGGGCAGAGGGAACCCCACGGACATGGACCCCACACTGGAGGACCCCACCGCGCCCAAATGCAAGATGAGAAGATGCTCCAGCTGCAGTCCAAAGCCCAACACCCCCAAGTGTGCCATGTGTGATGGGGACAGCTTCCCCTTTGCCTGTACAGGTGGAGAAGCCGAGGACAGGCTCAGGGAACCGGAGACCAAGAAGGCGCTGTCCTCTTCACTGCATGTACCCTGGACCAGTGCCGGCCCTGATCATGCAGCTCTTCCAGGCCCACTGCTTCTTCCTGTCCACTAGGCCACAGCCGCCCTCCAGGCCCACTATGCACACATCTTCCCCTCCAAGGTTTGTTCTGCCCCTGCCCTGACTCCCAGCCCTGTGGGGGTCCTGACCGCACCTCACCTGGCTCAGACTCTTGACGCTGCCCTGGCTGCCCCACCAGTGCTTCTGCCCGAGAGTCACGTGAGGCTGAGAGTAGGGGCAGGGGCAGCAGTGGTGCCAGTTGGGGGGCGGTCCAGTGGGAGGAGCCTCAGCCTCGCAGGCTGCTCCGTGGGACTGATGACTGCATGATCTTCTGGGCACCTCACGGATCTTCAACTGCAGGTGAAACGGATGCTGGTGGTGGGTGCAGGGCCGCTGGGAGCTGCTGCATGGTTCCCAGAGGCTGGACTGAGGCAGGTGCCAACTGAAGCTGCTGGGGCAGCATGGGCAGGATGTTCTGCACACAAACCTTGGAGAAGAAGATGTGTGCATAGCAGGTCCACTGCTGCTGCCCCTGCCCTGACTCCCAGCCCTGCCTGACCCCACCTCAACCTGCTCAGGCTCTGGCACAACCCTGGCTGCCCTGCCACTGCCTCTGCCCCAGAGTTGGTGCCTTGACAGCCTGGTTGGAAGGGGACACCCCAGCCCTGCCTCAACACCTGGGGGTCTCCATAACTAGCACAGGCAGGTGGGCAACCCCAAAGATCCCAGGACTCACAGTACCCCCTGAGAACATGGACAGTATGTGGGGGTAGCAATGGAGGGCAGGATGGTTATCTTCTCCCAGGTGAAGCCATTTAATCCTTTCAGTTTGGGACGGAGTAAGGCCTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGAGACCGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGTGGTGCGATCTTGGCTCACTGCAACCTCTTCCCGCTGGGTTCACGCCATTCTCCTGCCTCAGCCTTCCGGGTAGCTAGGATTACAGGTGGACGCTACCACGTCCGGCTAATTTTTGTATTTTTAGTACAGACGGGGCTTCATCATCTTGGCCAGGCTGATTTCGATCTCCTGACATCGTGATCTGCCTGCCTCCCCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCACGCCTGGCCAAGGCCTGCTCCTCTTATCTATACCCCCTACCCCTGCAGCTGTGCCGGGGGAAAGCTGGGCAGTTTCCCTCCTCCGAGCCCCTGTACATACCATGAATTGTGGGACCTTCAGAGCTTTTCACTTTTCGGAAAATAGCTCCTGCTGGGGCTACAAGATGGAGTGTGAAGAGGGCCTTGGGCCACAGGGAGGCGCCTGTGGACTAGGGGGAGTTCATGCACCCCTTCTTTCCCCAGAGGGGCTGGACTCAGGTGAGTATGGGGGTGGGGGCTCCTGCACTTCGACACAGGCAGCAGGAGGGTTTTCTCCCCATTCCCTCTGCACTCCCAACTTGAGCTATACTTTTTAAGAAAGTGATTCACCCTGCCTTTGCCCCCTTCCCCAGAACAGAACACGTTGATCGTGGGCGATATTTTTCATTGTGCCAAAAAGTTGCCATGACCGTCATTAAACCTGTTTAACAC\n' |
| b |
| diff -r 000000000000 -r 038ecf54cbec tool-data/twobit.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/twobit.loc.sample Mon Jan 22 13:59:27 2018 -0500 |
| b |
| @@ -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... |
| b |
| diff -r 000000000000 -r 038ecf54cbec tool_data_table_conf.xml.sample --- /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 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="twobit" comment_char="#"> + <columns>value, path</columns> + <file path="tool-data/twobit.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 038ecf54cbec translate_bed.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/translate_bed.py Mon Jan 22 13:59:27 2018 -0500 |
| [ |
| b'@@ -0,0 +1,303 @@\n+#!/usr/bin/env python\n+"""\n+#\n+#------------------------------------------------------------------------------\n+# University of Minnesota\n+# Copyright 2017, Regents of the University of Minnesota\n+#------------------------------------------------------------------------------\n+# Author:\n+#\n+# James E Johnson\n+#\n+#------------------------------------------------------------------------------\n+"""\n+\n+from __future__ import print_function\n+\n+import argparse\n+import re\n+import sys\n+\n+from Bio.Seq import translate\n+\n+from bedutil import bed_from_line\n+\n+import digest\n+\n+from ensembl_rest import get_cdna\n+\n+from twobitreader import TwoBitFile\n+\n+\n+def __main__():\n+ parser = argparse.ArgumentParser(\n+ description=\'Translate from BED\')\n+ parser.add_argument(\n+ \'input_bed\', default=None,\n+ help="BED to translate, \'-\' for stdin")\n+ pg_seq = parser.add_argument_group(\'Genomic sequence source\')\n+ pg_seq.add_argument(\n+ \'-t\', \'--twobit\', default=None,\n+ help=\'Genome reference sequence in 2bit format\')\n+ pg_seq.add_argument(\n+ \'-c\', \'--column\', type=int, default=None,\n+ help=\'Column offset containing genomic sequence\' +\n+ \'between start and stop (-1) for last column\')\n+ pg_out = parser.add_argument_group(\'Output options\')\n+ pg_out.add_argument(\n+ \'-f\', \'--fasta\', default=None,\n+ help=\'Path to output translations.fasta\')\n+ pg_out.add_argument(\n+ \'-b\', \'--bed\', default=None,\n+ help=\'Path to output translations.bed\')\n+ pg_bed = parser.add_argument_group(\'BED filter options\')\n+ pg_bed.add_argument(\n+ \'-E\', \'--ensembl\', action=\'store_true\', default=False,\n+ help=\'Input BED is in 20 column Ensembl format\')\n+ pg_bed.add_argument(\n+ \'-R\', \'--regions\', action=\'append\', default=[],\n+ help=\'Filter input by regions e.g.:\'\n+ + \' X,2:20000-25000,3:100-500+\')\n+ pg_bed.add_argument(\n+ \'-B\', \'--biotypes\', action=\'append\', default=[],\n+ help=\'For Ensembl BED restrict translations to Ensembl biotypes\')\n+ pg_trans = parser.add_argument_group(\'Translation filter options\')\n+ pg_trans.add_argument(\n+ \'-m\', \'--min_length\', type=int, default=10,\n+ help=\'Minimum length of protein translation to report\')\n+ pg_trans.add_argument(\n+ \'-e\', \'--enzyme\', default=None,\n+ help=\'Digest translation with enzyme\')\n+ pg_trans.add_argument(\n+ \'-M\', \'--start_codon\', action=\'store_true\', default=False,\n+ help=\'Trim translations to methionine start_codon\')\n+ pg_trans.add_argument(\n+ \'-C\', \'--cds\', action=\'store_true\', default=False,\n+ help=\'Only translate CDS\')\n+ pg_trans.add_argument(\n+ \'-A\', \'--all\', action=\'store_true\',\n+ help=\'Include CDS protein translations \')\n+ pg_fmt = parser.add_argument_group(\'ID format options\')\n+ pg_fmt.add_argument(\n+ \'-r\', \'--reference\', default=\'\',\n+ help=\'Genome Reference Name\')\n+ pg_fmt.add_argument(\n+ \'-D\', \'--fa_db\', dest=\'fa_db\', default=None,\n+ help=\'Prefix DB identifier for fasta ID line, e.g. generic\')\n+ pg_fmt.add_argument(\n+ \'-s\', \'--fa_sep\', dest=\'fa_sep\', default=\'|\',\n+ help=\'fasta ID separator defaults to pipe char, \' +\n+ \'e.g. generic|ProtID|description\')\n+ pg_fmt.add_argument(\n+ \'-P\', \'--id_prefix\', default=\'\',\n+ help=\'prefix for the sequence ID\')\n+ parser.add_argument(\'-v\', \'--verbose\', action=\'store_true\', help=\'Verbose\')\n+ parser.add_argument(\'-d\', \'--debug\', action=\'store_true\', help=\'Debug\')\n+ args = parser.parse_args()\n+\n+ input_rdr = open(args.input_bed, \'r\')\\\n+ if args.input_bed != \'-\' else sys.stdin\n+ fa_wtr = open(args.fasta, \'w\')\\\n+ if args.fasta is not None and args.fasta != \'-\' else sys.stdout\n+ bed_wtr = open(args.bed, \'w\') if args.bed is not None else None\n+\n+ enzyme = digest.expasy_rules.get'..b'f args.start_codon:\n+ m = refprot.find(\'M\')\n+ if m < 0:\n+ return 0\n+ elif m > 0:\n+ bed.trim_cds(m*3)\n+ refprot = refprot[m:]\n+ stop = refprot.find(\'*\')\n+ if stop >= 0:\n+ bed.trim_cds((stop - len(refprot)) * 3)\n+ refprot = refprot[:stop]\n+ if len(refprot) >= args.min_length:\n+ write_translation(tbed, bed.name, refprot)\n+ return 1\n+ return 0\n+ if args.debug:\n+ print("%s\\n" % (str(bed)), file=sys.stderr)\n+ print("CDS: %s %d %d" %\n+ (bed.strand, bed.cdna_offset_of_pos(bed.thickStart),\n+ bed.cdna_offset_of_pos(bed.thickEnd)),\n+ file=sys.stderr)\n+ print("refprot: %s" % str(refprot), file=sys.stderr)\n+ for offset in range(3):\n+ seqend = cdna_len - (cdna_len - offset) % 3\n+ aaseq = translate(cdna[offset:seqend])\n+ aa_start = 0\n+ while aa_start < len(aaseq):\n+ aa_end = aaseq.find(\'*\', aa_start)\n+ if aa_end < 0:\n+ aa_end = len(aaseq)\n+ prot = aaseq[aa_start:aa_end]\n+ if args.start_codon:\n+ m = prot.find(\'M\')\n+ aa_start += m if m >= 0 else aa_end\n+ prot = aaseq[aa_start:aa_end]\n+ if enzyme and refprot:\n+ frags = digest._cleave(prot, enzyme)\n+ for frag in reversed(frags):\n+ if frag in refprot:\n+ prot = prot[:prot.rfind(frag)]\n+ else:\n+ break\n+ is_cds = refprot and prot in refprot\n+ if args.debug:\n+ print("is_cds: %s %s" % (str(is_cds), str(prot)),\n+ file=sys.stderr)\n+ if len(prot) < args.min_length:\n+ pass\n+ elif not args.all and is_cds:\n+ pass\n+ else:\n+ tstart = aa_start*3+offset\n+ tend = aa_end*3+offset\n+ prot_acc = "%s_%d_%d" % (transcript_id, tstart, tend)\n+ tbed = bed.trim(tstart, tend)\n+ if args.all or unique_prot(tbed, prot):\n+ translate_count += 1\n+ tbed.name = prot_acc\n+ write_translation(tbed, bed.name, prot)\n+ aa_start = aa_end + 1\n+ return translate_count\n+\n+ if input_rdr:\n+ translation_count = 0\n+ transcript_count = 0\n+ for i, bedline in enumerate(input_rdr):\n+ try:\n+ bed = bed_from_line(bedline, ensembl=args.ensembl,\n+ seq_column=args.column)\n+ if bed is None:\n+ continue\n+ transcript_count += 1\n+ if bed.biotype and biotypea and bed.biotype not in biotypea:\n+ continue\n+ if filter_by_regions(bed):\n+ translation_count += translate_bed(bed)\n+ except Exception as e:\n+ print("BED format Error: line %d: %s\\n%s"\n+ % (i, bedline, e), file=sys.stderr)\n+ break\n+ if args.debug or args.verbose:\n+ print("transcripts: %d\\ttranslations: %d"\n+ % (transcript_count, translation_count), file=sys.stderr)\n+\n+\n+if __name__ == "__main__":\n+ __main__()\n' |
| b |
| diff -r 000000000000 -r 038ecf54cbec translate_bed.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/translate_bed.xml Mon Jan 22 13:59:27 2018 -0500 |
| [ |
| b'@@ -0,0 +1,304 @@\n+<tool id="translate_bed" name="Translate BED transcripts" version="0.1.0">\n+ <description>cDNA in 3frames or CDS</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <expand macro="ensembl_requirements" />\n+ <expand macro="bedutil_requirements" />\n+ <expand macro="twobit_requirements" />\n+ </requirements>\n+ <stdio>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <command detect_errors="aggressive"><![CDATA[\n+ python \'$__tool_directory__/translate_bed.py\' \n+ #if $ref.ref_source == \'cached\':\n+ --twobit=\'$ref.ref_loc.fields.path\'\n+ #elif $ref.ref_source == \'history\':\n+ --twobit=\'$ref.ref_file\'\n+ #elif $ref.ref_source == \'last_column\':\n+ --column \'-1\'\n+ #elif $ref.ref_source == \'select_column\':\n+ --column ${int(str($ref.seq_column)) - 1}\n+ #elif $ref.ref_source == \'ensembl_rest\':\n+ --ensembl\n+ #end if\n+ #if $translations.translate == \'CDS\':\n+ --cds\n+ #elif $translations.translate == \'cDNA\':\n+ --all\n+ #end if \n+ $translations.start_codon\n+ #if $bed_filters.biotypes:\n+ --biotypes \'$bed_filters.biotypes\'\n+ --ensembl\n+ #end if\n+ #if $bed_filters.regions:\n+ --regions \'$bed_filters.regions\'\n+ #end if\n+ --min_length $translations.min_length\n+ #if $translations.enzyme:\n+ --enzyme \'$translations.enzyme\'\n+ #end if\n+ #if $fa_id.fa_db:\n+ --fa_db=\'$fa_id.fa_db\'\n+ #end if\n+ #if $fa_id.fa_sep:\n+ --fa_sep=\'$fa_id.fa_sep\'\n+ #end if\n+ #if $fa_id.reference:\n+ --reference $fa_id.reference\n+ #else:\n+ --reference ${input.metadata.dbkey}\n+ #end if\n+ #if $fa_id.id_prefix:\n+ --id_prefix \'$fa_id.id_prefix\'\n+ #end if\n+ --bed \'$translation_bed\'\n+ --fasta \'$translation_fasta\'\n+ -v\n+ $input\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="bed" label="A BED file with 12 columns" \n+ help="thickStart and thickEnd define protein coding region, blocks define exon regions"/>\n+ <conditional name="ref">\n+ <param name="ref_source" type="select" label="Source for Genomic Sequence Data">\n+ <option value="cached">Locally cached twobit</option>\n+ <option value="history">History dataset twobit</option>\n+ <option value="last_column">Last Column in the BED file</option>\n+ <option value="select_column">Select Column in the BED file</option>\n+ <option value="ensembl_rest">Retrieve sequences from Ensembl (Slow and only for Ensembl Transcripts)</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_loc" type="select" label="Select reference 2bit file">\n+ <options from_data_table="twobit" />\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="twobit" label="reference 2bit file" />\n+ </when>\n+ <when value="last_column"/>\n+ <when value="select_column">\n+ <param name="seq_column" type="data_column" data_ref="input" label="BED column conatining the genomic sequence"\n+ help="unspliced genomic sequence from chromStart to chromEnd (Extract Genomic DNA)"/>\n+ </when>\n+ <when value="ensembl_rest"/>\n+ </conditional>\n+ <section name="bed_filters" expanded="false" title="BED Filtering Options">\n+ <param name="regions" type="text" va'..b' <assert_contents>\n+ <has_text text="generic|test_ENST00000641515" />\n+ <has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="human_transcripts_seq.bed" ftype="bed12"/>\n+ <param name="ref_source" value="last_column"/>\n+ <param name="translate" value="cDNA_minus_CDS"/>\n+ <param name="biotypes" value="protein_coding"/>\n+ <param name="start_codon" value="True"/>\n+ <param name="fa_db" value="generic"/>\n+ <param name="id_prefix" value="test_"/>\n+ <output name="translation_bed">\n+ <assert_contents>\n+ <has_text text="test_ENST00000641515" />\n+ <has_text text="MLSKYSFANS" />\n+ <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />\n+ </assert_contents>\n+ </output>\n+ <output name="translation_fasta">\n+ <assert_contents>\n+ <has_text text="generic|test_ENST00000641515" />\n+ <has_text text="MLSKYSFANS" />\n+ <not_has_text text="ELPHTLPQFIFQQLVCYILEYRYKVIMLSKYSFANS" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input" value="human_transcripts.bed" ftype="bed12"/>\n+ <param name="ref_source" value="history"/>\n+ <param name="ref_file" value="GRCh38.1.2bit" ftype="twobit"/>\n+ <param name="translate" value="cDNA_minus_CDS"/>\n+ <param name="regions" value="1:0-30000"/>\n+ <param name="start_codon" value="True"/>\n+ <param name="fa_db" value="generic"/>\n+ <param name="id_prefix" value="test_"/>\n+ <output name="translation_bed">\n+ <assert_contents>\n+ <has_text text="test_ENST00000488147" />\n+ <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" />\n+ <not_has_text text="ENST00000335137" />\n+ </assert_contents>\n+ </output>\n+ <output name="translation_fasta">\n+ <assert_contents>\n+ <has_text text="generic|test_ENST00000488147" />\n+ <has_text text="MAPSSRAPRTLACRDAPATGSRASTAPWTSGPCRRS" />\n+ <not_has_text text="ENST00000335137" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+Translate transcripts from the input BED file into protein sequences. \n+\n+The genomic sequence:\n+\n+ - may be supplied in an extra column in the BED input file\n+ - retrieved from a twobit genomic reference file \n+ - retrieved from the Ensembl REST API for Ensembl transcripts\n+\n+\n+**INPUTS**\n+\n+ - BED file with at least the standard 12 columns\n+ - Genome reference in twobit format (optional)\n+\n+\n+**OUTPUTS**\n+\n+ - FASTA of transcript translations\n+ - BED with the genomic location of the translated protein. The added 13th column contains the protein sequence.\n+\n+\n+**OPTIONS**\n+\n+ - Feature translation\n+\n+ - cDNA - three frame translations of the cDNA sequences with an output for each sequence between STOP codons\n+ - CDS - three frame translations of CDS (coding sequence defined by thickStart and thickEnd in the BED file) \n+\n+ - Translation filtering\n+\n+ - can be trimmed to a Methionine start codon\n+ - can be split into peptides by an enzyme digestion\n+ - must exceed specified minimum length\n+\n+\n+ - BED Filtering\n+\n+ - genomic regions \n+ - ensembl biotype if the BED contains the 20 columns as retrieved from the Ensembl REST API\n+ \n+\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btu613</citation>\n+ <citation type="doi">10.1093/nar/gku1010</citation>\n+ </citations>\n+</tool>\n' |