We have contigstat.pl, but it provides only total contigs count and total N50 values for all contigs etc. But I want to know the full statistics regarding my contig file.
In short, I want information for each contig in my contig file. Can anyone help?
You can use this following command to get your required stats out of your fasta. I assumed that you will be using a Linux machine because this command is AWK command. If you want to run this in Windows, you might have to install some packages in Windows.
awk 'BEGIN{flag=0;print "Contig ID\tContig Length\tA\tT\tG\tC\tN\tOtherCharacters"}{if($0~/^>/){if(flag==1){tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}id=$0;flag=1;aCount=gCount=cCount=tCount=nCount=xCount=0;}else{aCount+=gsub(/[aA]/,"A",$0);tCount+=gsub(/[tT]/,"T",$0);gCount+=gsub(/[gG]/,"G",$0);cCount+=gsub(/[cC]/,"C",$0);nCount+=gsub(/[nN]/,"N",$0);xCount+=gsub(/[^ATGCNatgcn]/,"X",$0);}}END{tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}' INPUT_FILE >OUTPUT_FILE
PS: INPUT FILE= your fasta file OUTPUT_FILE=file to redirect the output (don't forget to use the '>' before output file....
The whole should go in one line...
Could you give more details about what kind of information you need for each contig?
Hey Saleem, thanks for replying. I want to know length, base distribution at this point of time. it would help me in analyzing my some huge data more precisely.
You can use this following command to get your required stats out of your fasta. I assumed that you will be using a Linux machine because this command is AWK command. If you want to run this in Windows, you might have to install some packages in Windows.
awk 'BEGIN{flag=0;print "Contig ID\tContig Length\tA\tT\tG\tC\tN\tOtherCharacters"}{if($0~/^>/){if(flag==1){tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}id=$0;flag=1;aCount=gCount=cCount=tCount=nCount=xCount=0;}else{aCount+=gsub(/[aA]/,"A",$0);tCount+=gsub(/[tT]/,"T",$0);gCount+=gsub(/[gG]/,"G",$0);cCount+=gsub(/[cC]/,"C",$0);nCount+=gsub(/[nN]/,"N",$0);xCount+=gsub(/[^ATGCNatgcn]/,"X",$0);}}END{tot=aCount+tCount+gCount+cCount+nCount+xCount;print id"\t"tot"\t"aCount"\t"tCount"\t"gCount"\t"cCount"\t"nCount"\t"xCount;}' INPUT_FILE >OUTPUT_FILE
PS: INPUT FILE= your fasta file OUTPUT_FILE=file to redirect the output (don't forget to use the '>' before output file....
The whole should go in one line...
Thanks saleem, I am really very thankful to you. Hope to be in touch with you!!
Gaurav
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