Compare splicing site between genomes (CSS)

required environment

• Python ≥ 3.6
• pandas
• numpy
• pysam
• pyliftover

importance!, you must to change the lastz.py in this package to specify absolute paths to software like lastz and UCSC et al.

#* lastz.py
lastZ = 'software/lastz-1.04.03/lastz-distrib/bin/lastz'
axtChain = 'software/ucsc_kentUtils/v389/bin/axtChain'
chainSwap = 'software/opt/bio/software/ucsc_kentUtils/v389/bin/chainSwap'
chainSort = 'software/opt/bio/software/ucsc_kentUtils/v389/bin/chainSort'

paraments:

• -g1 GTF/GFF3 for genome A
• -g2 GTF/GFF3 for genome B
• b1 gene bed file for genome A
• b2 gene bed file for genome B
• -fa1 genome sequence file for genome A, the sequence must be index with samtools
• -fa2 genome sequence file for genome B, the sequence must be index with samtools
• -orth homoeologous pairs file
• -w flank sequence between splicing site, default 100bp
• -o output file

python main.py  -h 
usage: main.py [-h] [-g1 G1] [-g2 G2] [-b1 B1] [-b2 B2] [-fa1 FA1] [-fa2 FA2] [-orth ORTH] [-w W] [-o O]

optional arguments:
  -h, --help  show this help message and exit
  -g1 G1      GTF/GFF3 for genome A
  -g2 G2      GTF/GFF3 for genome B
  -b1 B1      gene bed file for genome A
  -b2 B2      gene bed file for genome A
  -fa1 FA1    genome sequence file for genome A
  -fa2 FA2    genome sequence file for genome B
  -orth ORTH  homoeologous gene pair file
  -w W        window size, default 100bp flank from splicing site
  -o O        output file

header of output

1. geneId1 geneID from genome A
2. geneId2 geneID from genome B
3. isoformId1 isoform ID from genome A
4. isoformId2 isoform ID from genome B
5. IntronCount1 intron count for isoformId1
6. IntronCount2 intron count for isoformId2
7. ConservedSiteCount count of conserved splicing site between genomes
8. ConservedSites conserved splicing sites between genomes