sequence Package¶
fasta
Module¶
fastq
Module¶
-
class
galaxy_utils.sequence.fastq.
fastqAggregator
[source]¶ Bases:
object
-
VALID_FORMATS
= ['solexa', 'sanger', 'cssanger', 'illumina']¶
-
-
class
galaxy_utils.sequence.fastq.
fastqCSSangerRead
[source]¶ Bases:
galaxy_utils.sequence.fastq.fastqSequencingRead
-
ascii_max
= 126¶
-
ascii_min
= 33¶
-
format
= 'cssanger'¶
-
quality_max
= 93¶
-
quality_min
= 0¶
-
score_system
= 'phred'¶
-
sequence_space
= 'color'¶
-
valid_sequence_list
= ['0', '1', '2', '3', '4', '5', '6', '.']¶
-
-
class
galaxy_utils.sequence.fastq.
fastqFakeFastaScoreReader
(format='sanger', quality_encoding=None)[source]¶ Bases:
object
-
class
galaxy_utils.sequence.fastq.
fastqIlluminaRead
[source]¶ Bases:
galaxy_utils.sequence.fastq.fastqSequencingRead
-
ascii_max
= 126¶
-
ascii_min
= 64¶
-
format
= 'illumina'¶
-
quality_max
= 62¶
-
quality_min
= 0¶
-
score_system
= 'phred'¶
-
sequence_space
= 'base'¶
-
-
class
galaxy_utils.sequence.fastq.
fastqJoiner
(format, force_quality_encoding=None)[source]¶ Bases:
object
-
class
galaxy_utils.sequence.fastq.
fastqNamedReader
(fh, format='sanger', apply_galaxy_conventions=False)[source]¶ Bases:
object
-
class
galaxy_utils.sequence.fastq.
fastqReader
(fh, format='sanger', apply_galaxy_conventions=False)[source]¶ Bases:
object
-
class
galaxy_utils.sequence.fastq.
fastqSangerRead
[source]¶ Bases:
galaxy_utils.sequence.fastq.fastqSequencingRead
-
ascii_max
= 126¶
-
ascii_min
= 33¶
-
format
= 'sanger'¶
-
quality_max
= 93¶
-
quality_min
= 0¶
-
score_system
= 'phred'¶
-
sequence_space
= 'base'¶
-
-
class
galaxy_utils.sequence.fastq.
fastqSequencingRead
[source]¶ Bases:
galaxy_utils.sequence.sequence.SequencingRead
-
ascii_max
= 126¶
-
ascii_min
= 33¶
-
format
= 'sanger'¶
-
get_ascii_quality_scores_len
()[source]¶ Compute ascii quality score length, without generating relatively expensive qualty score array.
-
quality_max
= 93¶
-
quality_min
= 0¶
-
score_system
= 'phred'¶
-
sequence_space
= 'base'¶
-
-
class
galaxy_utils.sequence.fastq.
fastqSolexaRead
[source]¶ Bases:
galaxy_utils.sequence.fastq.fastqSequencingRead
-
ascii_max
= 126¶
-
ascii_min
= 59¶
-
format
= 'solexa'¶
-
quality_max
= 62¶
-
quality_min
= -5¶
-
score_system
= 'solexa'¶
-
sequence_space
= 'base'¶
-
-
class
galaxy_utils.sequence.fastq.
fastqVerboseErrorReader
(fh, **kwds)[source]¶ Bases:
galaxy_utils.sequence.fastq.fastqReader
-
MAX_PRINT_ERROR_BYTES
= 1024¶
-
-
class
galaxy_utils.sequence.fastq.
fastqWriter
(fh, format=None, force_quality_encoding=None)[source]¶ Bases:
object
-
galaxy_utils.sequence.fastq.
format
¶ alias of
fastqCSSangerRead
sequence
Module¶
transform
Module¶
-
class
galaxy_utils.sequence.transform.
ColorSpaceConverter
(fake_adapter_base='G')[source]¶ Bases:
object
-
base
= 'N'¶
-
base_to_color_dict
= {'A': {'A': '0', 'C': '1', 'T': '3', 'G': '2', 'N': '4'}, 'C': {'A': '1', 'C': '0', 'T': '2', 'G': '3', 'N': '4'}, 'T': {'A': '3', 'C': '2', 'T': '0', 'G': '1', 'N': '4'}, 'G': {'A': '2', 'C': '3', 'T': '1', 'G': '0', 'N': '4'}, 'N': {'A': '5', 'C': '5', 'T': '5', 'G': '5', 'N': '6'}}¶
-
color_dict
= {'1': 'N', '0': 'N', '3': 'N', '2': 'N', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}¶
-
color_to_base_dict
= {'A': {'1': 'C', '0': 'A', '3': 'T', '2': 'G', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}, 'C': {'1': 'A', '0': 'C', '3': 'G', '2': 'T', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}, 'T': {'1': 'G', '0': 'T', '3': 'A', '2': 'C', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}, 'G': {'1': 'T', '0': 'G', '3': 'C', '2': 'A', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}, 'N': {'1': 'N', '0': 'N', '3': 'N', '2': 'N', '5': 'N', '4': 'N', '6': 'N', '.': 'N'}}¶
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key
= '.'¶
-
unknown_base
= 'N'¶
-
unknown_color
= '.'¶
-
value
= 'N'¶
-
vcf
Module¶
-
class
galaxy_utils.sequence.vcf.
VariantCall
(vcf_line, metadata, sample_names)[source]¶ Bases:
object
-
header_startswith
= None¶
-
required_header_fields
= None¶
-
required_header_length
= None¶
-
version
= None¶
-
-
class
galaxy_utils.sequence.vcf.
VariantCall33
(vcf_line, metadata, sample_names)[source]¶ Bases:
galaxy_utils.sequence.vcf.VariantCall
-
header_startswith
= '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO'¶
-
required_header_fields
= ['#CHROM', 'POS', 'ID', 'REF', 'ALT', 'QUAL', 'FILTER', 'INFO']¶
-
required_header_length
= 8¶
-
version
= 'VCFv3.3'¶
-
-
class
galaxy_utils.sequence.vcf.
VariantCall40
(vcf_line, metadata, sample_names)[source]¶ Bases:
galaxy_utils.sequence.vcf.VariantCall33
-
version
= 'VCFv4.0'¶
-
-
class
galaxy_utils.sequence.vcf.
VariantCall41
(vcf_line, metadata, sample_names)[source]¶ Bases:
galaxy_utils.sequence.vcf.VariantCall40
-
version
= 'VCFv4.1'¶
-
-
galaxy_utils.sequence.vcf.
format
¶ alias of
VariantCall41