ali_dirstringThe attribute can contain 2 string values "left" or "right".
ali_dir (string)
left or right.The alignment generated by obipairing is a 3’-end gap free algorithm. Two cases can occur when aligning the forward and reverse reads. If the barcode is long enough, both the reads overlap only on their 3’ ends. In such case, the alignment direction ali_dir is set to left. If the barcode is shorter than the read length, the paired reads overlap by their 5’ ends, and the complete barcode is sequenced by both the reads. In that later case, ali_dir is set to right.
ali_lengthali_length (int)
Length of the aligned parts when merging forward and reverse reads
-count : the number of sequence occurrencesThe count attribute indicates how-many strictly identical sequences have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.
Count()count (int)
Count()SetCount(int)The count attribute indicates how-many strictly identical reads have been merged in a single record. It contains an integer value. If it is absent this means that the sequence record represents a single occurrence of the sequence.
The Count() method allows to access to the count attribute as an integer value. If the count attribute is not defined for the given sequence, the value 1 is returned
merged_*map[string]intmerged_* (map[string]int)
The -m option of the obiuniq tools allows for keeping track of the distribution of the values stored in given attribute of interest. Often this option is used to summarise distribution of a sequence variant accross samples when obiuniq is run after running obimultiplex. The actual name of the attribute depends on the name of the monitored attribute. If -m option is used with the attribute sample, then this attribute names merged_sample.
modeobitag_ref_index
mode (string)
join or alignment.obitag_ref_index (map[string]string)
It resumes to which taxonomic annotation a match to that sequence must lead according to the number of differences existing between the query sequence and the reference sequence having that tag.
-Count()pairing_mismatchesscorescore_norm {"0":"9606@Homo sapiens@species",
+ "2":"207598@Homininae@subfamily",
+ "3":"9604@Hominidae@family",
+ "8":"314295@Hominoidea@superfamily",
+ "10":"9526@Catarrhini@parvorder",
+ "12":"1437010@Boreoeutheria@clade",
+ "16":"9347@Eutheria@clade",
+ "17":"40674@Mammalia@class",
+ "22":"117571@Euteleostomi@clade",
+ "25":"7776@Gnathostomata@clade",
+ "29":"33213@Bilateria@clade",
+ "30":"6072@Eumetazoa@clade"}pairing_mismatches (map[string]string)
seq_a_single (int)
seq_ab_match (int)
seq_b_single (int)
score (int)
score_norm (float)
Score of the alignment between forward and reverse reads expressed as a fraction of identity.
-Sequences can be selected on several of their caracteristics, their length, their id, their sequence. Options allow for specifying the condition if selection.
+Selection based on the sequence
+Sequence records can be selected according if they match or not with a pattern. The simplest pattern is as short sequence (e.g AACCTT). But the usage of regular patterns allows for looking for more complex pattern. As example, A[TG]C+G matches a A, followed by a T or a G, then one or several C and endly a G.
Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive. A complete description of the regular pattern grammar is available here.
+Selects only the sequence records that contain an EcoRI restriction site.
+obigrep -s 'GAATTC' seq1.fasta > seq2.fasta: Selects only the sequence records that contain a stretch of at least 10 A.
obigrep -s 'A{10,}' seq1.fasta > seq2.fasta: Selects only the sequence records that do not contain ambiguous nucleotides.
+obigrep -s '^[ACGT]+$' seq1.fasta > seq2.fastaonly sequences reprensenting no more than COUNT reads will be selected. That option rely on the count attribute. If the count attribute is not defined for a sequence record, it is assumed equal to \(1\).
Selecting sequence records representing at least five reads in the dataset.
obigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fastaobigrep -c 5 data_SPER01.fasta > data_norare_SPER01.fastalen(x)is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.len(x)It is a generic function allowing to retreive the size of a object. It returns the length of a sequences, the number of element in a map like annotations, the number of elements in an array. The reurned value is an int.
int(x) converts if possible the x value to an integer value. The function returns an int.numeric(x) converts if possible the x value to a float value. The function returns a float.bool(x) converts if possible the x value to a boolean value. The function returns a bool.int(x)Converts if possible the x value to an integer value. The function returns an int.
numeric(x)Converts if possible the x value to a float value. The function returns a float.
bool(x)Converts if possible the x value to a boolean value. The function returns a bool.
ifelse(condition,val1,val2)The condition value has to be a bool value. If it is true the function returns val1, otherwise, it is returning val2.
Id()Definition()sequence.Id()