Mercurial > repos > galaxyp > translate_bed_sequences

annotate translate_bed_sequences.py @ 2:4221664a2bd0 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
author galaxyp
date Tue, 07 Apr 2020 11:45:53 -0400
parents d723eb657f1d
children
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1 #!/usr/bin/env python
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2 """
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3 #
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4 #------------------------------------------------------------------------------
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5 # University of Minnesota
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6 # Copyright 2014, Regents of the University of Minnesota
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7 #------------------------------------------------------------------------------
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8 # Author:
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9 #
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10 # James E Johnson
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11 #
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12 #------------------------------------------------------------------------------
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13
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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14 Input: BED file (12 column) + 13th sequence column appended by extract_genomic_dna
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15 Output: Fasta of 3-frame translations of the spliced sequence
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16 """
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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17
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18 import optparse
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19 import os.path
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20 import sys
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21 import tempfile
2
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23 from Bio.Seq import (
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24 reverse_complement,
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25 translate
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26 )
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29 class BedEntry(object):
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30 def __init__(self, line):
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31 self.line = line
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32 try:
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33 fields = line.rstrip('\r\n').split('\t')
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34 (chrom, chromStart, chromEnd, name, score, strand, thickStart, thickEnd, itemRgb, blockCount, blockSizes, blockStarts) = fields[0:12]
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35 seq = fields[12] if len(fields) > 12 else None
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36 self.chrom = chrom
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37 self.chromStart = int(chromStart)
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38 self.chromEnd = int(chromEnd)
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39 self.name = name
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40 self.score = int(score)
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41 self.strand = strand
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42 self.thickStart = int(thickStart)
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43 self.thickEnd = int(thickEnd)
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44 self.itemRgb = itemRgb
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45 self.blockCount = int(blockCount)
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46 self.blockSizes = [int(x) for x in blockSizes.split(',')]
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47 self.blockStarts = [int(x) for x in blockStarts.split(',')]
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48 self.seq = seq
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49 except Exception as e:
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50 sys.stderr.write("Unable to read Bed entry %s\n" % e)
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51 exit(1)
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52
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53 def __str__(self):
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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' % (
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55 self.chrom, self.chromStart, self.chromEnd, self.name, self.score, self.strand, self.thickStart, self.thickEnd, self.itemRgb, self.blockCount,
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56 ','.join([str(x) for x in self.blockSizes]),
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57 ','.join([str(x) for x in self.blockStarts]),
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58 '\t%s' % self.seq if self.seq else '')
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59
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60 def get_splice_junctions(self):
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61 splice_juncs = []
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62 for i in range(self.blockCount - 1):
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63 splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i + 1])
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64 splice_juncs.append(splice_junc)
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65 return splice_juncs
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66
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67 def get_exon_seqs(self):
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68 exons = []
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69 for i in range(self.blockCount):
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70 # splice_junc = "%s:%d_%d" % (self.chrom, self.chromStart + self.blockSizes[i], self.chromStart + self.blockStarts[i+1])
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71 exons.append(self.seq[self.blockStarts[i]:self.blockStarts[i] + self.blockSizes[i]])
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72 if self.strand == '-': # reverse complement
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73 exons.reverse()
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74 for i, s in enumerate(exons):
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75 exons[i] = reverse_complement(s)
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76 return exons
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77
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78 def get_spliced_seq(self):
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79 seq = ''.join(self.get_exon_seqs())
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80 return seq
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81
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galaxyp
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82 def get_translation(self, sequence=None):
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galaxyp
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83 translation = None
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galaxyp
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84 seq = sequence if sequence else self.get_spliced_seq()
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galaxyp
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85 if seq:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
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86 seqlen = int(len(seq) / 3) * 3
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galaxyp
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87 if seqlen >= 3:
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galaxyp
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88 translation = translate(seq[:seqlen])
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galaxyp
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89 return translation
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galaxyp
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90
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
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91 def get_translations(self):
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galaxyp
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92 translations = []
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galaxyp
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93 seq = self.get_spliced_seq()
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galaxyp
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94 if seq:
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galaxyp
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95 for i in range(3):
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galaxyp
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96 translation = self.get_translation(sequence=seq[i:])
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galaxyp
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97 if translation:
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98 translations.append(translation)
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galaxyp
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99 return translations
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100
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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101 def get_subrange(self, tstart, tstop):
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102 """
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103 (start, end)
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104 """
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galaxyp
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105 chromStart = self.chromStart
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106 chromEnd = self.chromEnd
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107 r = range(self.blockCount)
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galaxyp
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108 if self.strand == '-':
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109 r = list(r)
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galaxyp
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110 r.reverse()
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111 bStart = 0
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112 for x in r:
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113 bEnd = bStart + self.blockSizes[x]
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114 if bStart <= tstart < bEnd:
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115 if self.strand == '+':
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116 chromStart = self.chromStart + self.blockStarts[x] + (tstart - bStart)
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117 else:
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118 chromEnd = self.chromStart + self.blockStarts[x] + (tstart - bStart)
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119 if bStart <= tstop < bEnd:
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120 if self.strand == '+':
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121 chromEnd = self.chromStart + self.blockStarts[x] + (tstop - bStart)
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122 else:
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123 chromStart = self.chromStart + self.blockStarts[x] + self.blockSizes[x] - (tstop - bStart)
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124 bStart += self.blockSizes[x]
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125 return(chromStart, chromEnd)
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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126
2
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127 def get_blocks(self, chromStart, chromEnd):
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128 """
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129 get the blocks for sub range
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130 """
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131 tblockCount = 0
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132 tblockSizes = []
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133 tblockStarts = []
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134 for x in range(self.blockCount):
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135 bStart = self.chromStart + self.blockStarts[x]
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136 bEnd = bStart + self.blockSizes[x]
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137 if bStart > chromEnd:
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138 break
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139 if bEnd < chromStart:
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diff changeset
140 continue
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141 cStart = max(chromStart, bStart)
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142 tblockStarts.append(cStart - chromStart)
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143 tblockSizes.append(min(chromEnd, bEnd) - cStart)
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144 tblockCount += 1
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145 # print >> sys.stderr, "tblockCount: %d tblockStarts: %s tblockSizes: %s" % (tblockCount, tblockStarts, tblockSizes)
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146 return (tblockCount, tblockSizes, tblockStarts)
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147
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148 def get_filterd_translations(self, untrimmed=False, filtering=True, ignore_left_bp=0, ignore_right_bp=0, debug=False):
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149 """
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galaxyp
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diff changeset
150 [(start, end, seq, blockCount, blockSizes, blockStarts), (start, end, seq, blockCount, blockSizes, blockStarts), (start, end, seq, blockCount, blockSizes, blockStarts)]
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diff changeset
151 filter: ignore translation if stop codon in first exon after ignore_left_bp
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152 """
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153 translations = [None, None, None, None, None, None]
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diff changeset
154 seq = self.get_spliced_seq()
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diff changeset
155 ignore = int((ignore_left_bp if self.strand == '+' else ignore_right_bp) / 3)
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diff changeset
156 block_sum = sum(self.blockSizes)
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diff changeset
157 exon_sizes = [x for x in self.blockSizes]
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158 if self.strand == '-':
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diff changeset
159 exon_sizes.reverse()
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160 splice_sites = [int(sum(exon_sizes[:x]) / 3) for x in range(1, len(exon_sizes))]
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161 if debug:
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diff changeset
162 sys.stderr.write("splice_sites: %s\n" % splice_sites)
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galaxyp
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diff changeset
163 junc = splice_sites[0] if len(splice_sites) > 0 else exon_sizes[0]
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164 if seq:
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165 for i in range(3):
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166 translation = self.get_translation(sequence=seq[i:])
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167 if translation:
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168 tstart = 0
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169 tstop = len(translation)
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170 offset = (block_sum - i) % 3
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171 if debug:
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172 sys.stderr.write("frame: %d\ttstart: %d tstop: %d offset: %d\t%s\n" % (i, tstart, tstop, offset, translation))
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173 if not untrimmed:
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174 tstart = translation.rfind('*', 0, junc) + 1
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175 stop = translation.find('*', junc)
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176 tstop = stop if stop >= 0 else len(translation)
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177 offset = (block_sum - i) % 3
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178 trimmed = translation[tstart:tstop]
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179 if debug:
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180 sys.stderr.write("frame: %d\ttstart: %d tstop: %d offset: %d\t%s\n" % (i, tstart, tstop, offset, trimmed))
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181 if filtering and tstart > ignore:
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182 continue
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183 # get genomic locations for start and end
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184 if self.strand == '+':
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185 chromStart = self.chromStart + i + (tstart * 3)
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186 chromEnd = self.chromEnd - offset - (len(translation) - tstop) * 3
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187 else:
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188 chromStart = self.chromStart + offset + (len(translation) - tstop) * 3
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189 chromEnd = self.chromEnd - i - (tstart * 3)
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190 # get the blocks for this translation
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191 (tblockCount, tblockSizes, tblockStarts) = self.get_blocks(chromStart, chromEnd)
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192 translations[i] = (chromStart, chromEnd, trimmed, tblockCount, tblockSizes, tblockStarts)
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193 if debug:
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194 sys.stderr.write("tblockCount: %d tblockStarts: %s tblockSizes: %s\n" % (tblockCount, tblockStarts, tblockSizes))
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195 # translations[i] = (chromStart, chromEnd, trimmed, tblockCount, tblockSizes, tblockStarts)
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196 return translations
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197
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198 def get_seq_id(self, seqtype='unk:unk', reference='', frame=None):
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199 """
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200 # Ensembl fasta ID format
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201 >ID SEQTYPE:STATUS LOCATION GENE TRANSCRIPT
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202 >ENSP00000328693 pep:splice chromosome:NCBI35:1:904515:910768:1 gene:ENSG00000158815:transcript:ENST00000328693 gene_biotype:protein_coding transcript_biotype:protein_coding
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203 """
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204 frame_name = ''
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205 chromStart = self.chromStart
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206 chromEnd = self.chromEnd
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207 strand = 1 if self.strand == '+' else -1
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208 if frame is not None:
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209 block_sum = sum(self.blockSizes)
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210 offset = (block_sum - frame) % 3
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211 frame_name = '_' + str(frame + 1)
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212 if self.strand == '+':
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213 chromStart += frame
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214 chromEnd -= offset
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215 else:
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216 chromStart += offset
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217 chromEnd -= frame
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218 location = "chromosome:%s:%s:%s:%s:%s" % (reference, self.chrom, chromStart, chromEnd, strand)
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219 seq_id = "%s%s %s %s" % (self.name, frame_name, seqtype, location)
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220 return seq_id
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221
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diff changeset
222 def get_line(self, start_offset=0, end_offset=0):
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223 if start_offset or end_offset:
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224 s_offset = start_offset if start_offset else 0
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225 e_offset = end_offset if end_offset else 0
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226 if s_offset > self.chromStart:
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227 s_offset = self.chromStart
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228 chrStart = self.chromStart - s_offset
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diff changeset
229 chrEnd = self.chromEnd + e_offset
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diff changeset
230 blkSizes = self.blockSizes
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diff changeset
231 blkSizes[0] += s_offset
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diff changeset
232 blkSizes[-1] += e_offset
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diff changeset
233 blkStarts = self.blockStarts
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diff changeset
234 for i in range(1, self.blockCount):
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diff changeset
235 blkStarts[i] += s_offset
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diff changeset
236 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])]]
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
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diff changeset
237 return '\t'.join(items) + '\n'
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diff changeset
238 return self.line
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diff changeset
239
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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diff changeset
240
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
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diff changeset
241 def __main__():
2
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242 # Parse Command Line
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diff changeset
243 parser = optparse.OptionParser()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
244 parser.add_option('-i', '--input', dest='input', help='BED file (tophat junctions.bed) with sequence column added')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
245 parser.add_option('-o', '--output', dest='output', help='Translations of spliced sequence')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
246 parser.add_option('-b', '--bed_format', dest='bed_format', action='store_true', default=False, help='Append translations to bed file instead of fasta')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
247 parser.add_option('-D', '--fa_db', dest='fa_db', default=None, help='Prefix DB identifier for fasta ID line, e.g. generic')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
248 parser.add_option('-s', '--fa_sep', dest='fa_sep', default='|', help='fasta ID separator defaults to pipe char, e.g. generic|ProtID|description')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
249 parser.add_option('-B', '--bed', dest='bed', default=None, help='Output a bed file with added 13th column having translation')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
250 parser.add_option('-G', '--gff3', dest='gff', default=None, help='Output translations to a GFF3 file')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
251 parser.add_option('-S', '--seqtype', dest='seqtype', default='pep:splice', help='SEQTYPE:STATUS for fasta ID line')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
252 parser.add_option('-P', '--id_prefix', dest='id_prefix', default='', help='prefix for the sequence ID')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
253 parser.add_option('-R', '--reference', dest='reference', default=None, help='Genome Reference Name for fasta ID location ')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
254 parser.add_option('-r', '--refsource', dest='refsource', default=None, help='Source for Genome Reference, e.g. Ensembl, UCSC, or NCBI')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
255 parser.add_option('-Q', '--score_name', dest='score_name', default=None, help='include in the fasta ID line score_name:score ')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
256 parser.add_option('-l', '--leading_bp', dest='leading_bp', type='int', default=None, help='leading number of base pairs to ignore when filtering')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
257 parser.add_option('-t', '--trailing_bp', dest='trailing_bp', type='int', default=None, help='trailing number of base pairs to ignore when filtering')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
258 parser.add_option('-U', '--unfiltered', dest='filtering', action='store_false', default=True, help='Do NOT filterout translation with stop codon in the first exon')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
259 parser.add_option('-u', '--untrimmed', dest='untrimmed', action='store_true', default=False, help='Do NOT trim from splice site to stop codon')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
260 parser.add_option('-L', '--min_length', dest='min_length', type='int', default=None, help='Minimun length (to first stop codon)')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
261 parser.add_option('-M', '--max_stop_codons', dest='max_stop_codons', type='int', default=None, help='Filter out translations with more than max_stop_codons')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
262 parser.add_option('-d', '--debug', dest='debug', action='store_true', default=False, help='Turn on wrapper debugging to stdout')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
263 (options, args) = parser.parse_args()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
264 # Input files
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
265 if options.input is not None:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
266 try:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
267 inputPath = os.path.abspath(options.input)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
268 inputFile = open(inputPath, 'r')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
269 except Exception as e:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
270 sys.stderr.write("failed: %s\n" % e)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
271 exit(2)
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
272 else:
2
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
273 inputFile = sys.stdin
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
274 # Output files
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
275 bed_fh = None
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
276 gff_fh = None
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
277 gff_fa_file = None
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
278 gff_fa = None
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
279 outFile = None
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
280 if options.output is None:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
281 # write to stdout
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
282 outFile = sys.stdout
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
283 if options.gff:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
284 gff_fa_file = tempfile.NamedTemporaryFile(prefix='gff_fasta_', suffix=".fa", dir=os.getcwd()).name
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
285 gff_fa = open(gff_fa_file, 'w')
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
286 else:
2
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
287 try:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
288 outPath = os.path.abspath(options.output)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
289 outFile = open(outPath, 'w')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
290 except Exception as e:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
291 sys.stderr.write("failed: %s\n" % e)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
292 exit(3)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
293 if options.gff:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
294 gff_fa_file = outPath
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
295 if options.bed:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
296 bed_fh = open(options.bed, 'w')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
297 bed_fh.write('track name="%s" description="%s" \n' % ('novel_junctioni_translations', 'test'))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
298 if options.gff:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
299 gff_fh = open(options.gff, 'w')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
300 gff_fh.write("##gff-version 3.2.1\n")
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
301 if options.reference:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
302 gff_fh.write("##genome-build %s %s\n" % (options.refsource if options.refsource else 'unknown', options.reference))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
303 leading_bp = 0
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
304 trailing_bp = 0
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
305 if options.leading_bp:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
306 if options.leading_bp >= 0:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
307 leading_bp = options.leading_bp
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
308 else:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
309 sys.stderr.write("failed: leading_bp must be positive\n")
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
310 exit(5)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
311 if options.trailing_bp:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
312 if options.trailing_bp >= 0:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
313 trailing_bp = options.trailing_bp
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
314 else:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
315 sys.stderr.write("failed: trailing_bp must be positive\n")
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
316 exit(5)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
317 # Scan bed file
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
318 try:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
319 for i, line in enumerate(inputFile):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
320 if line.startswith('track'):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
321 if outFile and options.bed_format:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
322 outFile.write(line)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
323 continue
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
324 entry = BedEntry(line)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
325 strand = 1 if entry.strand == '+' else -1
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
326 translations = entry.get_translations()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
327 if options.debug:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
328 exon_seqs = entry.get_exon_seqs()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
329 exon_sizes = [len(seq) for seq in exon_seqs]
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
330 splice_sites = [int(sum(exon_sizes[:x]) / 3) for x in range(1, len(exon_sizes))]
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
331 sys.stderr.write("%s\n" % entry.name)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
332 sys.stderr.write("%s\n" % line.rstrip('\r\n'))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
333 sys.stderr.write("exons: %s\n" % exon_seqs)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
334 sys.stderr.write("%s\n" % splice_sites)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
335 for i, translation in enumerate(translations):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
336 sys.stderr.write("frame %d: %s\n" % (i + 1, translation))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
337 sys.stderr.write("splice: %s\n" % (''.join(['^' if int(((j * 3) + i) / 3) in splice_sites else '-' for j in range(len(translation))])))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
338 sys.stderr.write("\n")
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
339 if options.bed_format:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
340 tx_entry = "%s\t%s\n" % (line.rstrip('\r\n'), '\t'.join(translations))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
341 outFile.write(tx_entry)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
342 else:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
343 translations = entry.get_filterd_translations(untrimmed=options.untrimmed, filtering=options.filtering, ignore_left_bp=leading_bp, ignore_right_bp=trailing_bp, debug=options.debug)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
344 for i, tx in enumerate(translations):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
345 if tx:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
346 (chromStart, chromEnd, translation, blockCount, blockSizes, blockStarts) = tx
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
347 if options.min_length is not None and len(translation) < options.min_length:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
348 continue
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
349 if options.max_stop_codons is not None and translation.count('*') > options.max_stop_codons:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
350 continue
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
351 frame_name = '_%s' % (i + 1)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
352 pep_id = "%s%s%s" % (options.id_prefix, entry.name, frame_name)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
353 if bed_fh:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
354 bed_fh.write('%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%s\t%s\t%s\n' % (str(entry.chrom), chromStart, chromEnd, pep_id, entry.score, entry.strand, chromStart, chromEnd, entry.itemRgb, blockCount, ','.join([str(x) for x in blockSizes]), ','.join([str(x) for x in blockStarts]), translation))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
355 location = "chromosome:%s:%s:%s:%s:%s" % (options.reference, entry.chrom, chromStart, chromEnd, strand)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
356 score = " %s:%s" % (options.score_name, entry.score) if options.score_name else ''
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
357 seq_description = "%s %s%s" % (options.seqtype, location, score)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
358 seq_id = "%s " % pep_id
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
359 if options.fa_db:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
360 seq_id = "%s%s%s%s" % (options.fa_db, options.fa_sep, pep_id, options.fa_sep)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
361 fa_id = "%s%s" % (seq_id, seq_description)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
362 fa_entry = ">%s\n%s\n" % (fa_id, translation)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
363 outFile.write(fa_entry)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
364 if gff_fh:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
365 if gff_fa:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
366 gff_fa.write(fa_entry)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
367 gff_fh.write("##sequence-region %s %d %d\n" % (entry.chrom, chromStart + 1, chromEnd - 1))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
368 gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tID=%s\n" % (entry.chrom, 'splice_junc', 'gene', chromStart + 1, chromEnd - 1, entry.score, entry.strand, 0, pep_id))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
369 for x in range(blockCount):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
370 start = chromStart + blockStarts[x] + 1
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
371 end = start + blockSizes[x] - 1
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
372 phase = (3 - sum(blockSizes[:x]) % 3) % 3
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
373 gff_fh.write("%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d\tParent=%s;ID=%s_%d\n" % (entry.chrom, 'splice_junc', 'CDS', start, end, entry.score, entry.strand, phase, pep_id, pep_id, x))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
374 # ##gff-version 3
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
375 # ##sequence-region 19 1 287484
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
376 # 19 MassSpec peptide 282299 287484 10.0 - 0 ID=TEARLSFYSGHSSFGMYCMVFLALYVQ
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
377 # 19 MassSpec CDS 287474 287484 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
378 # 19 MassSpec CDS 282752 282809 . - 1 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
379 # 19 MassSpec CDS 282299 282310 . - 0 Parent=TEARLSFYSGHSSFGMYCMVFLALYVQ;transcript_id=ENST00000269812
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
380 if bed_fh:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
381 bed_fh.close()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
382 if gff_fh:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
383 if gff_fa:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
384 gff_fa.close()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
385 else:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
386 outFile.close()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
387 gff_fa = open(gff_fa_file, 'r')
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
388 gff_fh.write("##FASTA\n")
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
389 for i, line in enumerate(gff_fa):
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
390 gff_fh.write(line)
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
391 gff_fh.close()
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
392 except Exception as e:
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
393 sys.stderr.write("failed: Error reading %s - %s\n" % (options.input if options.input else 'stdin', e))
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
394 raise
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
395 exit(1)
0
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
396
d723eb657f1d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit e04ed4b4960d6109a85c1cc68a2bf4931c8751ef-dirty
galaxyp
parents:
diff changeset
397
2
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
398 if __name__ == "__main__":
4221664a2bd0 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/translate_bed_sequences commit 2a470e2c775a7427aa530e058510e4dc7b6d8e80"
galaxyp
parents: 0
diff changeset
399 __main__()