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