Use API to get fusion transcript sequence for probe design with 512 fusion entries from COSMIC database (https://cancer.sanger.ac.uk/cosmic)
1.parse fusion gene entries from COSMIC to get fusion gene breakpoint location using regular expression
2.use python request and API by Ensemble and NCBI to get sequence by breakpoint location
3.parse .xml results received API by xml.etree
TMPRSS2 from exon 1 (UTR) to ERG exon 2 (inclusive).
TMPRSS2{NM_005656.2}:r.1_71_ERG{NM_004449.3}:r.38_3097
TMPRSS2 from intron after exon 1 to intron before ERG exon 2, intronic breakpoints known (374bp downstream of TMPRSS2 exon 1 and 54bp upstream of ERG exon 2).
TMPRSS2{NM_005656.2}:r.1_71+374_ERG{NM_004449.3}:r.38-54_3097
TRMPSS2 from intron after exon 1 to intron before ERG exon 2, intronic breakpoints NOT known (but remarked on in the paper).
TMPRSS2{NM_005656.2}:r.1_71+?_ERG{NM_004449.3}:r.38-?_3097
Mutation Id - links to the fusion summary page for more details of the inferred breakpoint.
Gene Name - 5' partner gene involved in the fusion.
Last Observed Exon - The last exon observed before the fusion breakpoint. In the 5' gene it can be ‘UTR’ or have ‘?’ if the breakpoint is unknown.
Inferred breakpoint - mRNA breakpoint position in the 5'gene. A '+' followed by a number denotes a breakpoint downstream of the mRNA position given (in an intron or UTR). If the number is in parentheses the position is approximate.
Gene Name - The 3' partner gene involved in the fusion.
First Observed Exon - The first exon observed after the fusion breakpoint in the 3' gene. It can be ‘UTR’ or have ‘?’ if the breakpoint is unknown.
Inferred breakpoint - mRNA breakpoint position in the 3'gene. A '?' indicates that the precise breakpoint is unknown. A '-' followed by a number denotes a breakpoint upstream of the mRNA position given (in an intron or UTR). If the number is in parentheses the position is approximate.
Mutations - Number of unique samples found with this mutation.
Mutation Frequency - Frequency (as a percentage) of mutated samples / total number of samples with this mutation.