tomiilab/homologysearch

Establish datasets

Convert blastp, psi-blast, last, ssearch and cs-blast results to tsv files.

python filter_aln.py ./repo/raw/YOURDIR

Parse block infomation into tsv files

python parse_blocksize.py ./repo/raw/scop20_training/psiblast_block_BL62_scop20_training_8/0.002/uniref50/
python parse_blocksize.py ./repo/raw/scop20_validation/psiblast_block_BL62_scop20_validation_8/0.002/uniref50/
python parse_blocksize.py ./repo/raw/cath20-scop/psiblast_block_BL62_cath20-scop_8/0.002/uniref50/

Decompress ./repo/raw.tar.bz2 to use previously established tsv files.

tar jxf repo/raw.tar.bz2

Generate figs and datasets

Oda et al. Fig 2

draw block size density until the 5th itration

python draw_blocksize_density.py 5

draw block size density until the 8th itration

python draw_blocksize_density.py 8

Oda et al. Fig 3A

python calc_roc.py draw_roc ./args/scop20_training.iter5.blocksizes.json -standards JG -ylim 1100

Oda et al. Fig 3B

python calc_roc.py draw_roc ./args/scop20_validation.iter2_3_5.json -standards JG -ylim 1100

Oda et al. Fig 3C

python calc_roc.py draw_roc ./args/cath20-scop.iter5.json -standards superfamily -ylim 600

Oda et al. Fig 5

python calc_roc.py draw_roc ./args/scop20_validation.msa.iter3_5.json -standards JG -ylim 1100

Oda et al. Fig 4A raw data

python calc_roc.py roc5_stats ./args/scop20_training.iter2.json -standards JG -rocn_max_evalue 1.0

Oda et al. Fig 4B raw data

python calc_roc.py roc5_stats ./args/scop20_validation.iter2.json -standards JG -rocn_max_evalue 1.0

Oda et al. Fig 4C raw data

python calc_roc.py roc5_stats ./args/cath20-scop.iter2.json -standards superfamily -rocn_max_evalue 1.0