- Python โฅ 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'
-g1
GTF/GFF3 for genome A-g2
GTF/GFF3 for genome Bb1
gene bed file for genome Ab2
gene bed file for genome B-fa1
genome sequence file for genome A, the sequence must be index withsamtools
-fa2
genome sequence file for genome B, the sequence must be index withsamtools
-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
geneId1
geneID from genome AgeneId2
geneID from genome BisoformId1
isoform ID from genome AisoformId2
isoform ID from genome BIntronCount1
intron count for isoformId1IntronCount2
intron count for isoformId2ConservedSiteCount
count of conserved splicing site between genomesConservedSites
conserved splicing sites between genomes