Python
- Under centos: yum install python
Please unpack the tar file.
CISA - 2014.03.04
CISA - 2013.08.22
CISA - 2012.09.04
[Aug 22, 2013] CISA1.3: Unlimited number for representative contigs.
Available commands:
>tar xvf CISA.tar
Execute access:
>chmod 755 -R CISA1.0
Mergy.py can convert data format to fit CISA. This is an essentail pre-work.
Available commands:
>python Merge.py Merge.config
The content of configuration file:
count=3 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
Please note that dos2unix may be necessary if your data are in DOS/MAC format.
>dos2unix assembly1.fasta assembly2.fasta assembly3.fasta
Available commands:
>python CISA.py CISA.config
The content of configuration file:
genome=genome size infile=file outfile=file nucmer=your installed path/nucmer R2_Gap=0.95 (default:0.95) CISA=your installed path/CISA1.0 makeblastdb=your installed path/makeblastdb blastn=your installed path/blastn
Error message:
f=open('CISA1/result'+str(count)+'.coords') IOError: [Errno 2] No such file or directory: 'CISA1/result0.coords' |
Please check the path for nucmer.
Error message:
f=open(path+'/result_blast.txt') IOError: [Errno 2] No such file or directory: |
Please check the path for blast.
In the case of Ecoli, we used five softwares including Abyss, CLC, Edena, SOAPdenovo and Velvet to generate five assemblies.
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
Input files: Abyss_contigs.fa, Edena_contigs.fa, SOAPdenovo_contigs.fa, CLC_contigs.fa, Velvet_contigs.fa
Statistics of the input assemblies:
Abyss_contigs.fa
Number of contigs: 133
Length of the longest contig: 222425
whole:4626205
N50: 96511
Edena_contigs.fa
Number of contigs: 211
Length of the longest contig: 186686
whole:4569446
N50: 57790
SOAPdenovo_contigs.fa
Number of contigs: 553
Length of the longest contig: 103369
whole:4547211
N50: 17944
CLC_contigs.fa
Number of contigs: 378
Length of the longest contig: 107342
whole:4546827
N50: 29905
Velvet_contigs.fa
Number of contigs: 283
Length of the longest contig: 166094
whole:4550675
N50: 54359
Output file: Contigs.fa
The content of the configuration file (CISA.config):
genome=4626205 infile=Contigs.fa outfile=CISA.fa nucmer=path/nucmer R2_Gap=0.95 CISA=path/CISA1.0 makeblastdb=path/makeblastdb blastn=path/blastn |
The genome is set to 4626205 based on the genome size of Abyss.
>python CISA.py CISA.config
Input file: Contigs.fa
Output file: CISA.fa