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openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
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Cannot Access the coding sequence in specific transcript #267

Open HealHer opened 1 year ago

HealHer commented 1 year ago

Hi,

Thank you very much for this package. I am using it daily for getting sequence and relevant information about transcripts.

I am getting a bit confused with one particular example regarding the transcript named ENST00000429617. I am following this method to get it: 

pyensembl install --release 55 --species homo_sapiens
python3
>>> ensembl = pyensembl.EnsemblRelease(release=75)
>>> tx = ensembl.transcript_by_id("ENST00000429617")

I am trying to recover the coding sequence so I tried: tx.coding_sequence with the error which stitulate that there are no start codon involved.

When I looked inside the GTF there is a coding sequence associated for this specific transcript (starting from exon 2) grep "ENST00000429617" Homo_sapiens.GRCh37.75.gtf

10      protein_coding  transcript      115438942       115486178       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115438942       115439108       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "1"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00001604369"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115457253       115457362       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "2"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00003512533"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  CDS     115457253       115457362       .       +       0       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "2"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; protein_id "ENSP00000400094"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115480791       115480927       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "3"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00003505017"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  CDS     115480791       115480927       .       +       1       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "3"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; protein_id "ENSP00000400094"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115481410       115481538       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "4"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00003555462"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  CDS     115481410       115481538       .       +       2       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "4"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; protein_id "ENSP00000400094"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115485121       115485296       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "5"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00003542525"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  CDS     115485121       115485296       .       +       2       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "5"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; protein_id "ENSP00000400094"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  exon    115486064       115486178       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "6"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; exon_id "ENSE00001632192"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  CDS     115486064       115486178       .       +       0       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; exon_number "6"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; protein_id "ENSP00000400094"; tag "cds_end_NF"; tag "mRNA_end_NF";
10      protein_coding  UTR     115438942       115439108       .       +       .       gene_id "ENSG00000165806"; transcript_id "ENST00000429617"; gene_name "CASP7"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "CASP7-004"; transcript_source "havana"; tag "cds_end_NF"; tag "mRNA_end_NF";

And this is also confirmed by the UCSC genome browser (link to specific region)

Can you please point me to where I can access this coding sequence?