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The extended OBITools fasta and fastq format
--------------------------------------------
.. _obitools-fasta:
The *extended OBITools Fasta format* is a strict :doc:`fasta format file <fasta>`.
The file in *extended OBITools Fasta format* can be readed by all programs
reading fasta files.
Difference between standard and extended fasta is just the structure of the title
line. For OBITools title line is divided in three parts :
- Seqid : the sequence identifier
- key=value; : a set of key/value keys
- the sequence definition
::
>my_sequence taxid=3456; direct=True; sample=A354; this is my pretty sequence
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
AACGACGTTGCAGTACGTTGCAGT
Following these rules, the title line can be parsed :
- The sequence identifier of this sequence is : *my_sequence*
- Three keys are assigned to this sequence :
- Key *taxid* with value *3456*
- Key *direct* with value *True*
- Key *sample* with value *A354*
- The definition of this sequence is this is *my pretty sequence*
Values can be any valid python expression. If a key value cannot be evaluated as
a python expression, it is them assumed as a simple string. Following this rule,
taxid value is considered as an integer value, direct value as a boolean and sample
value is not a valid python expression so it is considered as a string value.
Names reserved for attributes
.............................
The following attribute names are created by some obitools programs and used by others.
They have a special meaning. So we recommend not to use them with another semantic.
Contents:
.. toctree::
:maxdepth: 2
attributes/ali_dir
attributes/ali_length
attributes/avg_quality
attributes/best_match
attributes/best_identity
attributes/class
attributes/cluster
attributes/complemented
attributes/count
attributes/cut
attributes/direction
attributes/distance
attributes/error
attributes/experiment
attributes/family
attributes/family_name
attributes/forward_error
attributes/forward_match
attributes/forward_primer
attributes/forward_score
attributes/forward_tag
attributes/forward_tm
attributes/genus
attributes/genus_name
attributes/head_quality
attributes/id_status
attributes/merged_star
attributes/merged
attributes/mid_quality
attributes/mode
attributes/obiclean_cluster
attributes/obiclean_count
attributes/obiclean_head
attributes/obiclean_headcount
attributes/obiclean_internalcount
attributes/obiclean_samplecount
attributes/obiclean_singletoncount
attributes/obiclean_status
attributes/occurrence
attributes/order
attributes/order_name
attributes/pairend_limit
attributes/partial
attributes/rank
attributes/reverse_error
attributes/reverse_match
attributes/reverse_primer
attributes/reverse_score
attributes/reverse_tag
attributes/reverse_tm
attributes/sample
attributes/scientific_name
attributes/score
attributes/score_norm
attributes/select
attributes/seq_ab_match
attributes/seq_a_single
attributes/seq_a_mismatch
attributes/seq_a_deletion
attributes/seq_a_insertion
attributes/seq_b_single
attributes/seq_b_mismatch
attributes/seq_b_deletion
attributes/seq_b_insertion
attributes/seq_length
attributes/seq_length_ori
attributes/seq_rank
attributes/sminL
attributes/sminR
attributes/species
attributes/species_list
attributes/species_name
attributes/status
attributes/strand
attributes/tail_quality
attributes/taxid
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