Tabixpy
Tabix reader written 100% in Python
Install / Use
/learn @bejobioinformatics/TabixpyREADME
tabixpy
Tabix parser writtern in Python3.
Website
https://pypi.org/project/tabixpy/
Install
pip install tabixpy
Usage
import tabixpy
ingz = "example.vcf.gz"
data = tabixpy.readTabix(ingz)
tabixpy.save(data, ingz, compress=True)
JSON Schema
https://www.liquid-technologies.com/online-json-schema-validator
https://www.jsonschemavalidator.net/
Example output
{
"n_ref": 1,
"format": 2,
"col_seq": 1,
"col_beg": 2,
"col_end": 0,
"meta": "#",
"skip": 0,
"l_nm": 11,
"names": [
"SL2.50ch00"
],
"refs": [{
"ref_n": 0,
"ref_name": "SL2.50ch00",
"n_bin": 86,
"bins": [{
"bin_n": 0,
"bin": 4681,
"n_chunk": 1,
"chunks": {
"chunk_begin": [{
"bin_n": 0,
"chunk_n": 0,
"real": 0,
"bytes": 29542,
"block_len": 8031,
"bin_pos": 280,
"first_pos": 280,
"last_pos": 1506
}],
"chunk_end": [{
"bin_n": 0,
"chunk_n": 0,
"real": 124525,
"bytes": 19630,
"block_len": 9015,
"bin_pos": 16388,
"first_pos": 16141,
"last_pos": 17830
}]
},
"chunks_begin": {
"bin_n": 0,
"chunk_n": 0,
"real": 0,
"bytes": 29542,
"block_len": 8031,
"bin_pos": 280,
"first_pos": 280,
"last_pos": 1506
},
"chunks_end": {
"bin_n": 0,
"chunk_n": 0,
"real": 124525,
"bytes": 19630,
"block_len": 9015,
"bin_pos": 16388,
"first_pos": 16141,
"last_pos": 17830
}
},
{
"bin_n": 85,
"bin": 4766,
"n_chunk": 1,
"chunks": {
"chunk_begin": [{
"bin_n": 84,
"chunk_n": 0,
"real": 7021611,
"bytes": 4631,
"block_len": 6621,
"bin_pos": 1392700,
"first_pos": 1392519,
"last_pos": 1393974
}],
"chunk_end": [{
"bin_n": 85,
"chunk_n": 0,
"real": 7039684,
"bytes": 0,
"block_len": -1,
"bin_pos": -1,
"first_pos": -1,
"last_pos": -1
}]
},
"chunks_begin": {
"bin_n": 84,
"chunk_n": 0,
"real": 7021611,
"bytes": 4631,
"block_len": 6621,
"bin_pos": 1392700,
"first_pos": 1392519,
"last_pos": 1393974
},
"chunks_end": {
"bin_n": 85,
"chunk_n": 0,
"real": 7039684,
"bytes": 0,
"block_len": -1,
"bin_pos": -1,
"first_pos": -1,
"last_pos": -1
}
}
],
"bins_begin": {
"bin_n": 0,
"chunk_n": 0,
"real": 0,
"bytes": 29542,
"block_len": 8031,
"bin_pos": 280,
"first_pos": 280,
"last_pos": 1506
},
"bins_end": {
"bin_n": 84,
"chunk_n": 0,
"real": 7021611,
"bytes": 4631,
"block_len": 6621,
"bin_pos": 1392700,
"first_pos": 1392519,
"last_pos": 1393974
},
"first_block": {
"bin_n": 0,
"chunk_n": 0,
"real": 0,
"bytes": 29542,
"block_len": 8031,
"bin_pos": 280,
"first_pos": 280,
"last_pos": 1506
},
"last_block": {
"bin_n": -1,
"chunk_n": -1,
"real": 7035849,
"bytes": 0,
"block_len": 3835,
"bin_pos": -1,
"first_pos": 1395124,
"last_pos": 1395638
},
"n_intv": 86,
"intvs": [{
"bin_n": 0,
"chunk_n": 0,
"real": 0,
"bytes": 29542,
"block_len": 8031,
"bin_pos": 280,
"first_pos": 280,
"last_pos": 1506
},
{
"bin_n": 84,
"chunk_n": 0,
"real": 7021611,
"bytes": 4631,
"block_len": 6621,
"bin_pos": 1392700,
"first_pos": 1392519,
"last_pos": 1393974
}
]
}],
"n_no_coor": null,
"__format_name__": "TBJ",
"__format_ver__": 5
}
Timming
2020-06-12 11:30:34,716 - tabixpy - INFO - reading annotated_tomato_150.100000.vcf.gz
2020-06-12 11:30:34,738 - tabixpy - INFO - saving annotated_tomato_150.100000.vcf.gz.tbj
,024
2020-06-12 11:31:16,506 - tabixpy - INFO - reading annotated_tomato_150.vcf.bgz
2020-06-12 11:31:24,152 - tabixpy - INFO - saving annotated_tomato_150.vcf.bgz.tbj
8,646
File Sizes
TBI Tabix Index
TBK Binary TabixPy 'all chunks' index
TBJ Compressed JSON Tabix index
TBJ.json Uncompressed JSON Tabix Index
6.8M annotated_tomato_150.100000.vcf.gz
1.1K annotated_tomato_150.100000.vcf.gz.tbi
5.9K annotated_tomato_150.100000.vcf.gz.tbk 6.5X
8.9K annotated_tomato_150.100000.vcf.gz.tbj 8.1X
104K annotated_tomato_150.100000.vcf.gz.tbj.json 94.5X
44M annotated_tomato_150.SL2.50ch00-01-02.vcf.gz
4.3K annotated_tomato_150.SL2.50ch00-01-02.vcf.gz.tbi
40K annotated_tomato_150.SL2.50ch00-01-02.vcf.gz.tbk 9.3X
39K annotated_tomato_150.SL2.50ch00-01-02.vcf.gz.tbj 9.1X
468K annotated_tomato_150.SL2.50ch00-01-02.vcf.gz.tbj.json 108.3X
5.6G annotated_tomato_150.vcf.bgz
727K annotated_tomato_150.vcf.bgz.tbi
Tabix
https://samtools.github.io/hts-specs/tabix.pdf
Field Description Type Value
---------------------------------------------------------------------------------------
magic Magic string char[4] TBI 1
n_ref # sequences int32_t
format Format (0: generic; 1: SAM; 2: VCF) int32_t
col_seq Column for the sequence name int32_t
col_beg Column for the start of a region int32_t
col_end Column for the end of a region int32_t
meta Leading character for comment lines int32_t
skip # lines to skip at the beginning int32_t
l_nm Length of concatenated sequence names int32_t
names Concatenated names, each zero terminated char[l_nm]
======================= List of indices (n=n_ref ) =======================
n_bin # distinct bins (for the binning index) int32_t
======================= List of distinct bins (n=n_bin) =======================
bin Distinct bin number uint32_t
n_chunk # chunks int32_t
======================= List of chunks (n=n_chunk) =======================
cnk_beg Virtual file offset of the start of the chunk uint64_t
cnk_end Virtual file offset of the end of the chunk uint64_t
n_intv # 16kb intervals (for the linear index) int32_t
======================= List of distinct intervals (n=n_intv) =======================
ioff File offset of the first record in the interval uint64_t
n_no_coor (optional) # unmapped reads without coordinates set uint64_t
Notes
-
The index file is BGZF compressed.
-
All integers are little-endian.
-
When (format&0x10000) is true, the coordinate follows the BED rule (i.e. half-closed-half-open and zero based); otherwise, the coordinate follows the GFF rule (closed and one based).
-
For the SAM format, the end of a region equals POS plus the reference length in the alignment, inferred from CIGAR. For the VCF format, the end of a region equals POS plus the size of the deletion.
-
Field col beg may equal col end, and in this case, the end of a region is end=beg+1.
-
Example:
- For GFF, format=0 , col seq=1, col beg=4, col end=5, meta=‘#’ and skip=0.
- For BED, format=0x10000, col seq=1, col beg=2, col end=3, meta=‘#’ and skip=0.
-
Given a zero-based, half-closed and half-open region [beg, end), the bin number is calculated with the following C function:
int reg2b
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