Python Tabix Api - Getnames ?

Question

[Zev.Kronenberg]

I am very new to python.

I was wondering if the python Tabix API provides a way to get the names of all seqids?

If not is there a way to query without providing a regions and return the whole file?

These calls are used in perl API. I would be shocked if they didn't exist in the python API.

Answer 1

[Aaronquinlan]

If you can use pysam, you should be in business.

http://www.cgat.org/~andreas/documentation/pysam/api.html#pysam.Tabixfile

>>> import pysam
>>> tabixfile = pysam.Tabixfile( "/usr/local/share/gemini/data/hg19.CpG.bed.gz" )
>>> print tabixfile.contigs
['chr1', 'chr10', 'chr11', 'chr11_gl000202_random', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr17_ctg5_hap1', 'chr17_gl000204_random', 'chr17_gl000205_random', 'chr18', 'chr19', 'chr1_gl000191_random', 'chr1_gl000192_random', 'chr2', 'chr20', 'chr21', 'chr22', 'chr3', 'chr4', 'chr4_ctg9_hap1', 'chr4_gl000193_random', 'chr4_gl000194_random', 'chr5', 'chr6', 'chr6_apd_hap1', 'chr6_cox_hap2', 'chr6_dbb_hap3', 'chr6_mann_hap4', 'chr6_mcf_hap5', 'chr6_qbl_hap6', 'chr6_ssto_hap7', 'chr7', 'chr8', 'chr8_gl000197_random', 'chr9', 'chr9_gl000199_random', 'chr9_gl000200_random', 'chr9_gl000201_random', 'chrUn_gl000211', 'chrUn_gl000212', 'chrUn_gl000213', 'chrUn_gl000214', 'chrUn_gl000215', 'chrUn_gl000216', 'chrUn_gl000217', 'chrUn_gl000218', 'chrUn_gl000219', 'chrUn_gl000220', 'chrUn_gl000221', 'chrUn_gl000222', 'chrUn_gl000223', 'chrUn_gl000224', 'chrUn_gl000225', 'chrUn_gl000228', 'chrUn_gl000229', 'chrUn_gl000231', 'chrUn_gl000235', 'chrUn_gl000236', 'chrUn_gl000237', 'chrUn_gl000240', 'chrUn_gl000241', 'chrUn_gl000242', 'chrUn_gl000243', 'chrX', 'chrY']

Answer 2

[Matt Shirley]

If this is a question about a tabix indexed GTF, see:

import gzip
gtf = gzip.GzipFile('gtf.gz')
seqids = [line.decode('ascii').split('\t')[0] for line in gtf]
gtf.close()

I know this isn't really tabix-specific, but I think this is what you want.

[lh3]

Tabix keeps all the reference sequence names in the tabix index. In principle, you can get those by reading index alone.

[Zev.Kronenberg]

Can you read the index (tbi) in the python API? I know in perl it is as simple as $tabix_obj->getnames(). We know you are not busy (jk) so maybe you could write that up real quick ;-)?

[lh3]

Theoretically speaking, possible, but I do not know Python well enough to do that... Just use Pysam.

[Zev.Kronenberg]

doesn't for line require that the whole file is read?

[Matt Shirley]

Yes, and I can see why you would rather read these values from a smaller index file. Just thought it might help!

[Zev.Kronenberg]

It is helpful and it is one valid solution.