[2] | 1 | """ |
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| 2 | Qualityscore class |
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| 3 | """ |
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| 4 | |
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| 5 | import data |
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| 6 | import logging |
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| 7 | from galaxy.datatypes.sniff import * |
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| 8 | from galaxy import util |
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| 9 | |
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| 10 | log = logging.getLogger(__name__) |
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| 11 | |
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| 12 | class QualityScore ( data.Text ): |
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| 13 | """ |
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| 14 | until we know more about quality score formats |
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| 15 | """ |
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| 16 | file_ext = "qual" |
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| 17 | |
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| 18 | class QualityScoreSOLiD ( QualityScore ): |
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| 19 | """ |
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| 20 | until we know more about quality score formats |
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| 21 | """ |
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| 22 | file_ext = "qualsolid" |
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| 23 | |
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| 24 | def sniff( self, filename ): |
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| 25 | """ |
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| 26 | >>> fname = get_test_fname( 'sequence.fasta' ) |
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| 27 | >>> QualityScoreSOLiD().sniff( fname ) |
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| 28 | False |
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| 29 | >>> fname = get_test_fname( 'sequence.qualsolid' ) |
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| 30 | >>> QualityScoreSOLiD().sniff( fname ) |
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| 31 | True |
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| 32 | """ |
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| 33 | try: |
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| 34 | fh = open( filename ) |
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| 35 | readlen = None |
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| 36 | goodblock = 0 |
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| 37 | while True: |
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| 38 | line = fh.readline() |
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| 39 | if not line: |
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| 40 | if goodblock > 0: |
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| 41 | return True |
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| 42 | else: |
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| 43 | break #EOF |
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| 44 | line = line.strip() |
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| 45 | if line and not line.startswith( '#' ): #first non-empty non-comment line |
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| 46 | if line.startswith( '>' ): |
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| 47 | line = fh.readline().strip() |
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| 48 | if line == '' or line.startswith( '>' ): |
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| 49 | break |
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| 50 | try: |
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| 51 | [ int( x ) for x in line.split() ] |
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| 52 | if not(readlen): |
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| 53 | readlen = len(line.split()) |
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| 54 | assert len(line.split()) == readlen #SOLiD reads should be of the same length |
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| 55 | except: |
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| 56 | break |
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| 57 | goodblock += 1 |
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| 58 | if goodblock > 10: |
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| 59 | return True |
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| 60 | else: |
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| 61 | break #we found a non-empty line, but it's not a header |
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| 62 | fh.close() |
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| 63 | except: |
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| 64 | pass |
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| 65 | return False |
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| 66 | |
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| 67 | def set_meta( self, dataset, **kwd ): |
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| 68 | if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize: |
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| 69 | dataset.metadata.data_lines = None |
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| 70 | return |
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| 71 | return QualityScore.set_meta( self, dataset, **kwd ) |
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| 72 | |
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| 73 | |
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| 74 | |
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| 75 | class QualityScore454 ( QualityScore ): |
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| 76 | """ |
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| 77 | until we know more about quality score formats |
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| 78 | """ |
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| 79 | file_ext = "qual454" |
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| 80 | |
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| 81 | def sniff( self, filename ): |
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| 82 | """ |
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| 83 | >>> fname = get_test_fname( 'sequence.fasta' ) |
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| 84 | >>> QualityScore454().sniff( fname ) |
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| 85 | False |
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| 86 | >>> fname = get_test_fname( 'sequence.qual454' ) |
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| 87 | >>> QualityScore454().sniff( fname ) |
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| 88 | True |
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| 89 | """ |
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| 90 | try: |
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| 91 | fh = open( filename ) |
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| 92 | while True: |
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| 93 | line = fh.readline() |
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| 94 | if not line: |
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| 95 | break #EOF |
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| 96 | line = line.strip() |
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| 97 | if line and not line.startswith( '#' ): #first non-empty non-comment line |
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| 98 | if line.startswith( '>' ): |
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| 99 | line = fh.readline().strip() |
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| 100 | if line == '' or line.startswith( '>' ): |
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| 101 | break |
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| 102 | try: |
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| 103 | [ int( x ) for x in line.split() ] |
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| 104 | except: |
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| 105 | break |
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| 106 | return True |
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| 107 | else: |
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| 108 | break #we found a non-empty line, but it's not a header |
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| 109 | fh.close() |
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| 110 | except: |
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| 111 | pass |
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| 112 | return False |
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| 113 | |
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| 114 | class QualityScoreSolexa ( QualityScore ): |
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| 115 | """ |
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| 116 | until we know more about quality score formats |
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| 117 | """ |
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| 118 | file_ext = "qualsolexa" |
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| 119 | |
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| 120 | class QualityScoreIllumina ( QualityScore ): |
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| 121 | """ |
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| 122 | until we know more about quality score formats |
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| 123 | """ |
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| 124 | file_ext = "qualillumina" |
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