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SunPengChuanSunPengChuan
fusion positions database
Dec 13, 2024
4cb5d25 · Dec 13, 2024

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01.getgff.py
01.getgff.py
 
 
02.gff_lens.py
02.gff_lens.py
 
 
03.seq_newname.py
03.seq_newname.py
 
 
GCF_007210705.1_Tcal_SD_v2.1_cds_from_genomic.fna.gz
GCF_007210705.1_Tcal_SD_v2.1_cds_from_genomic.fna.gz
 
 
GCF_007210705.1_Tcal_SD_v2.1_genomic.gff.gz
GCF_007210705.1_Tcal_SD_v2.1_genomic.gff.gz
 
 
GCF_007210705.1_Tcal_SD_v2.1_protein.faa.gz
GCF_007210705.1_Tcal_SD_v2.1_protein.faa.gz
 
 
deal_gff.py
deal_gff.py
 
 
deal_gff_ncbi.py
deal_gff_ncbi.py
 
 
fox1s.cds.fa
fox1s.cds.fa
 
 
fox1s.gff
fox1s.gff
 
 
fox1s.lens
fox1s.lens
 
 
fox1s.pep.fa
fox1s.pep.fa
 
 
fusarium_oxysporum_Fol007.cds-transcripts.fa
fusarium_oxysporum_Fol007.cds-transcripts.fa
 
 
fusarium_oxysporum_Fol007.gff3
fusarium_oxysporum_Fol007.gff3
 
 
fusarium_oxysporum_Fol007.proteins.fa
fusarium_oxysporum_Fol007.proteins.fa
 
 
readme.md
readme.md
 
 
tig2s.cds.fa
tig2s.cds.fa
 
 
tig2s.gff
tig2s.gff
 
 
tig2s.lens
tig2s.lens
 
 
tig2s.pep.fa
tig2s.pep.fa
 
 

readme.md

Due to the mismatch of downloaded data (cds, pep, gff), I now provide two scripts that can quickly process them into the format required by WGDI. Please select the appropriate program according to the example format.

python deal_gff.py fusarium_oxysporum_Fol007.gff3 fusarium_oxysporum_Fol007.cds-transcripts.fa fusarium_oxysporum_Fol007.proteins.fa fox1s
python deal_gff_ncbi.py GCF_007210705.1_Tcal_SD_v2.1_genomic.gff GCF_007210705.1_Tcal_SD_v2.1_cds_from_genomic.fna GCF_007210705.1_Tcal_SD_v2.1_protein.faa tig2s