Mercurial > repos > galaxyp > map_peptides_to_bed

comparison map_peptides_to_bed.py @ 0:c770d523bd28 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deseq2 commit 34a8020a7810edc543c6adf6ec58f5437302b703
author galaxyp
date Tue, 12 Jan 2016 20:25:34 -0500
parents
children 88d2c4c2cb0a
comparison
equal deleted inserted replaced
-1:000000000000 0:c770d523bd28
1 #!/usr/bin/env python
2 """
3 #
4 #------------------------------------------------------------------------------
5 # University of Minnesota
6 # Copyright 2014, Regents of the University of Minnesota
7 #------------------------------------------------------------------------------
8 # Author:
9 #
10 # James E Johnson
11 #
12 #------------------------------------------------------------------------------
13 """
14
15 """
16 Input: list of protein_accessions, peptide_sequence
17 GFF3 with fasta
18 Output: GFF3 of peptides
19
20 Filter: Must cross splice boundary
21
22 """
23
24 import sys,re,os.path
25 import tempfile
26 import optparse
27 from optparse import OptionParser
28 from Bio.Seq import reverse_complement, transcribe, back_transcribe, translate
29
30 class BedEntry( object ):
31 def __init__(self, line):
32 self.line = line
33 try:
34 fields = line.rstrip('\r\n').split('\t')
35 (chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,itemRgb,blockCount,blockSizes,blockStarts) = fields[0:12]
36 seq = fields[12] if len(fields) > 12 else None
37 self.chrom = chrom
38 self.chromStart = int(chromStart)
39 self.chromEnd = int(chromEnd)
40 self.name = name
41 self.score = int(score)
42 self.strand = strand
43 self.thickStart = int(thickStart)
44 self.thickEnd = int(thickEnd)
45 self.itemRgb = itemRgb
46 self.blockCount = int(blockCount)
47 self.blockSizes = [int(x) for x in blockSizes.split(',')]
48 self.blockStarts = [int(x) for x in blockStarts.split(',')]
49 self.seq = seq
50 except Exception, e:
51 print >> sys.stderr, "Unable to read Bed entry" % e
52 exit(1)
53 def __str__(self):
54 return '%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s%s' % (
55 self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount,
56 ','.join([str(x) for x in self.blockSizes]),
57 ','.join([str(x) for x in self.blockStarts]),
58 '\t%s' % self.seq if self.seq else '')
59 def get_splice_junctions(self):
60 splice_juncs = []
61 for i in range(self.blockCount - 1):
62 splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
63 splice_juncs.append(splice_junc)
64 return splice_juncs
65 def get_exon_seqs(self):
66 exons = []
67 for i in range(self.blockCount):
68 # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
69 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
70 if self.strand == '-': #reverse complement
71 exons.reverse()
72 for i,s in enumerate(exons):
73 exons[i] = reverse_complement(s)
74 return exons
75 def get_spliced_seq(self):
76 seq = ''.join(self.get_exon_seqs())
77 return seq
78 def get_translation(self,sequence=None):
79 translation = None
80 seq = sequence if sequence else self.get_spliced_seq()
81 if seq:
82 seqlen = len(seq) / 3 * 3;
83 if seqlen >= 3:
84 translation = translate(seq[:seqlen])
85 return translation
86 def get_translations(self):
87 translations = []
88 seq = self.get_spliced_seq()
89 if seq:
90 for i in range(3):
91 translation = self.get_translation(sequence=seq[i:])
92 if translation:
93 translations.append(translation)
94 return translations
95 ## (start,end)
96 def get_subrange(self,tstart,tstop):
97 chromStart = self.chromStart
98 chromEnd = self.chromEnd
99 r = range(self.blockCount)
100 if self.strand == '-':
101 r.reverse()
102 bStart = 0
103 for x in r:
104 bEnd = bStart + self.blockSizes[x]
105 ## print >> sys.stderr, "%d chromStart: %d chromEnd: %s bStart: %s bEnd: %d" % (x,chromStart,chromEnd,bStart,bEnd)
106 if bStart <= tstart < bEnd:
107 if self.strand == '+':
108 chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
109 else:
110 chromEnd = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstart - bStart)
111 if bStart <= tstop < bEnd:
112 if self.strand == '+':
113 chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
114 else:
115 chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
116 bStart += self.blockSizes[x]
117 return(chromStart,chromEnd)
118 #get the blocks for sub range
119 def get_blocks(self,chromStart,chromEnd):
120 tblockCount = 0
121 tblockSizes = []
122 tblockStarts = []
123 for x in range(self.blockCount):
124 bStart = self.chromStart + self.blockStarts[x]
125 bEnd = bStart + self.blockSizes[x]
126 if bStart > chromEnd:
127 break
128 if bEnd < chromStart:
129 continue
130 cStart = max(chromStart,bStart)
131 tblockStarts.append(cStart - chromStart)
132 tblockSizes.append(min(chromEnd,bEnd) - cStart)
133 tblockCount += 1
134 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
135 return (tblockCount,tblockSizes,tblockStarts)
136
137 ## [[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts],[start,end,seq,blockCount,blockSizes,blockStarts]]
138 ## filter: ignore translation if stop codon in first exon after ignore_left_bp
139 def get_filterd_translations(self,untrimmed=False,filtering=True,ignore_left_bp=0,ignore_right_bp=0):
140 translations = [None,None,None,None,None,None]
141 seq = self.get_spliced_seq()
142 ignore = (ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3
143 block_sum = sum(self.blockSizes)
144 exon_sizes = self.blockSizes
145 if self.strand == '-':
146 exon_sizes.reverse()
147 splice_sites = [sum(exon_sizes[:x]) / 3 for x in range(1,len(exon_sizes))]
148 print >> sys.stderr, "splice_sites: %s" % splice_sites
149 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
150 if seq:
151 for i in range(3):
152 translation = self.get_translation(sequence=seq[i:])
153 if translation:
154 tstart = 0
155 tstop = len(translation)
156 if not untrimmed:
157 tstart = translation.rfind('*',0,junc) + 1
158 stop = translation.find('*',junc)
159 tstop = stop if stop >= 0 else len(translation)
160 if filtering and tstart > ignore:
161 continue
162 trimmed = translation[tstart:tstop]
163 #get genomic locations for start and end
164 offset = (block_sum - i) % 3
165 print >> sys.stderr, "tstart: %d tstop: %d offset: %d" % (tstart,tstop,offset)
166 if self.strand == '+':
167 chromStart = self.chromStart + i + (tstart * 3)
168 chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
169 else:
170 chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
171 chromEnd = self.chromEnd - i - (tstart * 3)
172 #get the blocks for this translation
173 tblockCount = 0
174 tblockSizes = []
175 tblockStarts = []
176 for x in range(self.blockCount):
177 bStart = self.chromStart + self.blockStarts[x]
178 bEnd = bStart + self.blockSizes[x]
179 if bStart > chromEnd:
180 break
181 if bEnd < chromStart:
182 continue
183 cStart = max(chromStart,bStart)
184 tblockStarts.append(cStart - chromStart)
185 tblockSizes.append(min(chromEnd,bEnd) - cStart)
186 tblockCount += 1
187 print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount,tblockStarts,tblockSizes)
188 translations[i] = [chromStart,chromEnd,trimmed,tblockCount,tblockSizes,tblockStarts]
189 return translations
190 def get_seq_id(self,seqtype='unk:unk',reference='',frame=None):
191 ## Ensembl fasta ID format
192 # >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
193 # >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
194 frame_name = ''
195 chromStart = self.chromStart
196 chromEnd = self.chromEnd
197 strand = 1 if self.strand == '+' else -1
198 if frame != None:
199 block_sum = sum(self.blockSizes)
200 offset = (block_sum - frame) % 3
201 frame_name = '_' + str(frame + 1)
202 if self.strand == '+':
203 chromStart += frame
204 chromEnd -= offset
205 else:
206 chromStart += offset
207 chromEnd -= frame
208 location = "chromosome:%s:%s:%s:%s:%s" % (reference,self.chrom,chromStart,chromEnd,strand)
209 seq_id = "%s%s %s %s" % (self.name,frame_name,seqtype,location)
210 return seq_id
211 def get_line(self, start_offset = 0, end_offset = 0):
212 if start_offset or end_offset:
213 s_offset = start_offset if start_offset else 0
214 e_offset = end_offset if end_offset else 0
215 if s_offset > self.chromStart:
216 s_offset = self.chromStart
217 chrStart = self.chromStart - s_offset
218 chrEnd = self.chromEnd + e_offset
219 blkSizes = self.blockSizes
220 blkSizes[0] += s_offset
221 blkSizes[-1] += e_offset
222 blkStarts = self.blockStarts
223 for i in range(1,self.blockCount):
224 blkStarts[i] += s_offset
225 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])]]
226 return '\t'.join(items) + '\n'
227 return self.line
228
229 def __main__():
230 #Parse Command Line
231 parser = optparse.OptionParser()
232 parser.add_option( '-t', '--translated_bed', dest='translated_bed', default=None, help='A bed file with added 13th column having a translation' )
233 parser.add_option( '-i', '--input', dest='input', default=None, help='Tabular file with peptide_sequence column' )
234 parser.add_option( '-p', '--peptide_column', type='int', dest='peptide_column', default=1, help='column ordinal with peptide sequence' )
235 parser.add_option( '-n', '--name_column', type='int', dest='name_column', default=None, help='column ordinal with protein name' )
236 parser.add_option( '-s', '--start_column', type='int', dest='start_column', default=None, help='column with peptide start position in protein' )
237 parser.add_option( '-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation' )
238 ## parser.add_option( '-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file' )
239 ## parser.add_option( '-f', '--fasta', dest='fasta', default=None, help='Protein fasta' )
240 parser.add_option( '-T', '--gffTags', dest='gffTags', action='store_true', default=False, help='Add #gffTags to bed output for IGV' )
241 parser.add_option( '-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stderr' )
242 (options, args) = parser.parse_args()
243 # Input files
244 if options.input != None:
245 try:
246 inputPath = os.path.abspath(options.input)
247 inputFile = open(inputPath, 'r')
248 except Exception, e:
249 print >> sys.stderr, "failed: %s" % e
250 exit(2)
251 else:
252 inputFile = sys.stdin
253 inputBed = None
254 if options.translated_bed != None:
255 inputBed = open(os.path.abspath(options.translated_bed),'r')
256 peptide_column = options.peptide_column - 1
257 name_column = options.name_column - 1 if options.name_column else None
258 start_column = options.start_column - 1 if options.start_column else None
259 # Read in peptides
260 # peps[prot_name] = [seq]
261 prot_peps = dict()
262 unassigned_peps = set()
263 try:
264 for i, line in enumerate( inputFile ):
265 ## print >> sys.stderr, "%3d\t%s" % (i,line)
266 if line.startswith('#'):
267 continue
268 fields = line.rstrip('\r\n').split('\t')
269 ## print >> sys.stderr, "%3d\t%s" % (i,fields)
270 if peptide_column < len(fields):
271 peptide = fields[peptide_column]
272 prot_name = fields[name_column] if name_column is not None and name_column < len(fields) else None
273 if prot_name:
274 offset = fields[start_column] if start_column is not None and start_column < len(fields) else -1
275 if prot_name not in prot_peps:
276 prot_peps[prot_name] = dict()
277 prot_peps[prot_name][peptide] = offset
278 else:
279 unassigned_peps.add(peptide)
280 if options.debug:
281 print >> sys.stderr, "prot_peps: %s" % prot_peps
282 print >> sys.stderr, "unassigned_peps: %s" % unassigned_peps
283 except Exception, e:
284 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
285 exit(1)
286 # Output files
287 bed_fh = None
288 ## gff_fh = None
289 ## gff_fa_file = None
290 gff_fa = None
291 outFile = None
292 if options.bed:
293 bed_fh = open(options.bed,'w')
294 bed_fh.write('track name="%s" type=bedDetail description="%s" \n' % ('novel_junction_peptides','test'))
295 if options.gffTags:
296 bed_fh.write('#gffTags\n')
297 ## if options.gff:
298 ## gff_fh = open(options.gff,'w')
299 ## gff_fh.write("##gff-version 3.2.1\n")
300 ## if options.reference:
301 ## gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
302 try:
303 for i, line in enumerate( inputBed ):
304 ## print >> sys.stderr, "%3d:\t%s" % (i,line)
305 if line.startswith('track'):
306 continue
307 entry = BedEntry(line)
308 if entry.name in prot_peps:
309 for (peptide,offset) in prot_peps[entry.name].iteritems():
310 if offset < 0:
311 offset = entry.seq.find(peptide)
312 if options.debug:
313 print >> sys.stderr, "%s\t%s\t%d\t%s\n" % (entry.name, peptide,offset,entry.seq)
314 if offset >= 0:
315 tstart = offset * 3
316 tstop = tstart + len(peptide) * 3
317 if options.debug:
318 print >> sys.stderr, "%d\t%d\t%d" % (offset,tstart,tstop)
319 (pepStart,pepEnd) = entry.get_subrange(tstart,tstop)
320 if options.debug:
321 print >> sys.stderr, "%d\t%d\t%d" % (offset,pepStart,pepEnd)
322 if bed_fh:
323 entry.thickStart = pepStart
324 entry.thickEnd = pepEnd
325 bedfields = str(entry).split('\t')
326 if options.gffTags:
327 bedfields[3] = "ID=%s;Name=%s" % (entry.name,peptide)
328 bed_fh.write("%s\t%s\t%s\n" % ('\t'.join(bedfields[:12]),peptide,entry.seq))
329 except Exception, e:
330 print >> sys.stderr, "failed: Error reading %s - %s" % (options.input if options.input else 'stdin',e)
331
332 if __name__ == "__main__" : __main__()
333