How To Get Introns Positions Of A Refseq Protein With Python

Question

[Dror]

I have a list of Refseqs Ids and I want to get the introns position, relative to the protein sequence. Does any one have a python script to grab the introns from the genomic reference of a refseq gene, and get their position in the protein?

[Michael Schubert]

I might have a solution for this. Can you provide some of your RefSeq IDs to test it on?

Answer 1

[Pierre Lindenbaum]

The UCSC has already computed this table: see refGene.txt.gz, refGene.sql, here.

The table contains the postion of the exons separated by a comma, you then "just have to" reconstruct the sequence of protein from the reference sequences (here)

curl -s  "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz" | gunzip -c | head

971 NR_024227   chr19   -   50595745    50595866    50595866    50595866    1   50595745,   50595866,   0   SNAR-A6 unk unk -1,
971 NR_024227   chr19   -   50601082    50601203    50601203    50601203    1   50601082,   50601203,   0   SNAR-A6 unk unk -1,
629 NM_001014809    chr4    -   5822491 5894785 5823486 5894696 14  5822491,5827220,5830215,5837641,5838491,5841248,5843034,5844819,5851118,5853134,5857869,5862752,5868394,5894315,    5823578,5827386,5830395,5837812,5838633,5841405,5843155,5844888,5851199,5853196,5858034,5862937,5868483,5894785,    0   CRMP1   cmpl    cmpl    1,0,0,0,2,1,0,0,0,1,1,2,0,0,
808 NM_001029883    chr2    -   29284557    29297127    29287734    29297127    2   29284557,29293459,  29287933,29297127,  0   C2orf71cmpl cmpl    2,0,
705 NM_024329   chr1    +   15736390    15756839    15736467    15755220    4   15736390,15752366,15753645,15755088,    15736775,15752514,15753780,15756839,    0   EFHD2   cmpl    cmpl    0,2,0,0,
768 NM_024328   chr14   +   24025197    24028786    24025966    24028049    2   24025197,24027903,  24026513,24028786,  0   THTPA   cmpl    cmpl    0,1,
1379    NM_024326   chr10   +   104179570   104182893   104180886   104182750   4   104179570,104181110,104181543,104182560,    104180939,104181264,104182049,104182893,    0   FBXL15  cmpl    cmpl    0,2,0,2,
826 NM_138275   chr6    +   31691160    31692850    31691160    31692850    4   31691160,31691415,31692541,31692746,    31691221,31691763,31692621,31692850,    0   C6orf25 cmpl    incmpl  0,1,1,0,
609 NM_138275   chr6_cox_hap2   +   3200777 3202467 3200777 3202467 4   3200777,3201032,3202158,3202363,    3200838,3201380,3202238,3202467,    0   C6orf25 cmpl    incmpl  0,1,1,0,
607 NM_138275   chr6_dbb_hap3   +   2976730 2978420 2976730 2978420 4   2976730,2976985,2978111,2978316,    2976791,2977333,2978191,2978420,    0   C6orf25 cmpl    incmpl  0,1,1,0,

[Dror]

Yes but this contains only a fraction of the refseq data - I need the ability to do it for any organism in refseq, such as cnidarians and trichoplax