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108 lines
3.1 KiB
Plaintext
108 lines
3.1 KiB
Plaintext
# Annexes
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## Sequence attributes
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**ali_dir (`string`)**
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- Set by the *obipairing* tool
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- The attribute can contain 2 string values `left` or `right`.
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The alignment generated by *obipairing* is a 3'-end gap free algorithm.
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Two cases can occur when aligning the forward and reverse reads. If the
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barcode is long enough, both the reads overlap only on their 3' ends. In
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such case, the alignment direction `ali_dir` is set to *left*. If the
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barcode is shorter than the read length, the paired reads overlap by
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their 5' ends, and the complete barcode is sequenced by both the reads.
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In that later case, `ali_dir` is set to *right*.
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**ali_length (`int`)**
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- Set by the *obipairing* tool
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Length of the aligned parts when merging forward and reverse reads
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**count (`int`)**
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- Set by the *obiuniq* tool
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- Getter : method `Count()`
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- Setter : method `SetCount(int)`
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The `count` attribute indicates how-many strictly identical reads
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have been merged in a single record. It contains an integer value. If it
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is absent this means that the sequence record represents a single
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occurrence of the sequence.
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The `Count()` method allows to access to the count attribute as an
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integer value. If the `count` attribute is not defined for the given
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sequence, the value *1* is returned
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**merged_* (`map[string]int`)**
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- Set by the *obiuniq* tool
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The `-m` option of the *obiuniq* tools allows for keeping track of the
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distribution of the values stored in given attribute of interest. Often
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this option is used to summarise distribution of a sequence variant
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accross samples when *obiuniq* is run after running *obimultiplex*. The
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actual name of the attribute depends on the name of the monitored
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attribute. If `-m` option is used with the attribute *sample*, then this
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attribute names *merged_sample*.
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**mode (`string`)**
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- Set by the *obipairing* tool
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- The attribute can contain 2 string values `join` or `alignment`.
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**obitag_ref_index (`map[string]string`)**
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- Set by the *obirefidx* tool.
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It resumes to which taxonomic annotation a match to that sequence must
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lead according to the number of differences existing between the query
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sequence and the reference sequence having that tag.
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```json
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{"0":"9606@Homo sapiens@species",
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"2":"207598@Homininae@subfamily",
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"3":"9604@Hominidae@family",
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"8":"314295@Hominoidea@superfamily",
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"10":"9526@Catarrhini@parvorder",
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"12":"1437010@Boreoeutheria@clade",
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"16":"9347@Eutheria@clade",
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"17":"40674@Mammalia@class",
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"22":"117571@Euteleostomi@clade",
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"25":"7776@Gnathostomata@clade",
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"29":"33213@Bilateria@clade",
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"30":"6072@Eumetazoa@clade"}
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```
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**pairing_mismatches (`map[string]string`)**
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- Set by the *obipairing* tool
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**seq_a_single (`int`)**
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- Set by the *obipairing* tool
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**seq_ab_match (`int`)**
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- Set by the *obipairing* tool
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**seq_b_single (`int`)**
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- Set by the *obipairing* tool
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**score (`int`)**
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- Set by the *obipairing* tool
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**score_norm (`float`)**
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- Set by the *obipairing* tool
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- The value ranges between 0 and 1.
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Score of the alignment between forward and reverse reads expressed as a fraction of identity.
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