KOnezumiAID 0.1.1

Project description

Hello KOnezumi-AID

Input data set

genomic sequence

mm39.fa.gz from UCSC

Locus information

refFlat.text from UCSC

Download scripts (bash)

mkdir -p data
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz |
    gzip -dc > data/mm39.fa
wget -O - https://hgdownload.soe.ucsc.edu/goldenPath/mm39/database/refFlat.txt.gz |
    gzip -dc > data/refFlat.txt

Use as pandas.DataFrame in this code

DataFrame refFlat has 11 columns.

• string geneName; "Name of gene as it appears in Genome Browser."
• string name; "Name of gene"
• string chrom; "Chromosome name"
• char[1] strand; "+ or - for strand"
• uint txStart; "Transcription start position"
• uint txEnd; "Transcription end position"
• uint cdsStart; "Coding region start"
• uint cdsEnd; "Coding region end"
• uint exonCount; "Number of exons"
• uint[exonCount] exonStarts; "Exon start positions"
• uint[exonCount] exonEnds; "Exon end positions"