Python
- Under centos: yum install python
Just to unpack the tar file.
Available commands:
tar xvf CISA.tar
chmod 755 -R CICA1.0
Mergy.pu can convert data format to fit CISA. This is a essentail pre-work.
Available commands:
./Merge.py myconfig
The content of configuration file:
count=3 the number of dataset you would like to merge data=assembly1.fasta,title=Contig_m1 data=assembly2.fasta,title=Contig_m2 data=assembly3.fasta,title=Contig_m3 Master_file=Contigs_m.fa min_length=100 (default:100) Gap=11 此行沒放在config example
The min_length means that contig which is longer than 100 will be conserved. The Gap is a optional variable.
if Gap attends, it will be used to split scoffolding by continuous 11 N.
if Gap is absent, the program will only merge data.
將Mergy.py print 出的資訊(genome size) 同時輸出在螢幕上以及存成檔案(genome_size.txt),以便使用者日後查看
Available commands:
./CISA.py myconfig
The content of myconfig file
genome=genome size The genome size of each genome contain in genome_size.txt file. The largest genome size will be recommended to put here. infile=Contigs.fa nucmer=path/nucmer Please modify the "path" into the 安裝路徑. R2_Gap=0.9 default:0.9 myconfig file中也改成0.9 CISA=path/CISA1.0 Please modify the "path" into the 安裝路徑. makeblastdb=path/makeblastdb Please modify the "path" into the 安裝路徑. blastn=path/blastn Please modify the "path" into the 安裝路徑.
The content of the configuration file:
count=5 data=Abyss_contigs.fa,title=Abyss 設定hyperlink到example file,方便直接下載 data=Edena_contigs.fa,title=Edena data=SOAPdenovo_contigs.fa,title=SOAP data=CLC_contigs.fa,title=CLC data=Velvet_contigs.fa,title=Velvet Master_file=Contigs.fa
./Merge.py myconfig
The content of the configuration file:
genome=4626205 infile=Contigs.fa nucmer=path/nucmer R2_Gap=0.9 CISA=path/CISA1.0 makeblastdb=path/makeblastdb blastn=path/blastn
python CISA.py CISA.config
Ecoli
The content of the configuration file (Merge.config):
count=5 data=Abyss_contigs.fa,title=Abyss data=Edena_contigs.fa,title=Edena data=SOAPdenovo_contigs.fa,title=SOAP data=CLC_contigs.fa,title=CLC data=Velvet_contigs.fa,title=Velvet Master_file=Contigs.fa |
>python Merge.py Merge.config
The content of the configuration file (CISA.config):
genome=4626205 infile=Contigs.fa nucmer=path/nucmer R2_Gap=0.95 CISA=path/CISA1.0 makeblastdb=path/makeblastdb blastn=path/blastn |
4626205 which is the longest whole genome between different result from 5 assemblers is set into genome variable.
>python CISA.py CISA.config