Reorder The Contig=<Id Of The Header Of Vcf File, How?

Question

[Tonyzeng]

HI, I have VCF file with header that I need to change the order of contig ID from

##contig=<ID=1,length=195471971>
##contig=<ID=10,length=130694993>
##contig=<ID=11,length=122082543>
##contig=<ID=12,length=120129022>
##contig=<ID=13,length=120421639>
##contig=<ID=14,length=124902244>
##contig=<ID=15,length=104043685>
##contig=<ID=16,length=98207768>
##contig=<ID=17,length=94987271>
##contig=<ID=18,length=90702639>
##contig=<ID=19,length=61431566>
##contig=<ID=2,length=182113224>
##contig=<ID=3,length=160039680>
##contig=<ID=4,length=156508116>
##contig=<ID=5,length=151834684>
##contig=<ID=6,length=149736546>
##contig=<ID=7,length=145441459>
##contig=<ID=8,length=129401213>
##contig=<ID=9,length=124595110>
##contig=<ID=X,length=171031299>

How can I change it to

##contig=<ID=10,length=130694993>
##contig=<ID=11,length=122082543>
##contig=<ID=12,length=120129022>
##contig=<ID=13,length=120421639>
##contig=<ID=14,length=124902244>
##contig=<ID=15,length=104043685>
##contig=<ID=16,length=98207768>
##contig=<ID=17,length=94987271>
##contig=<ID=18,length=90702639>
##contig=<ID=19,length=61431566>
##contig=<ID=1,length=195471971>
##contig=<ID=2,length=182113224>
##contig=<ID=3,length=160039680>
##contig=<ID=4,length=156508116>
##contig=<ID=5,length=151834684>
##contig=<ID=6,length=149736546>
##contig=<ID=7,length=145441459>
##contig=<ID=8,length=129401213>
##contig=<ID=9,length=124595110>
##contig=<ID=X,length=171031299>

[Devon Ryan]

That's not a BAM header. Do you mean VCF?

[Tonyzeng]

Thank you for the reminding, Dpryan, I corrected it.

[Chris Miller]

Do you need to reorder the whole file, or just the header lines? It's unclear from your question.

[Tonyzeng]

I need just reorder the header lines because the order of read lines have been modified perfectly, Thank you!

[Ashutosh Pandey]

Huh!! I just wrote a code for you to order the read lines. Anyways, its a hightime for you to learn vi commands (http://www.cs.colostate.edu/helpdocs/vi.html). Use unix to edit the file if it is too big for any windows application like Notepad++,

[Tonyzeng]

Thanks, Ashutoshmits, I am sorry not to make it clear that I do generate a VCF file with the correct chromosome order to the READ LINES but not the header line. As for the header line of VCF file, I still need to reorder ##contig=<id=number. i="" assumed="" that="" the="" following="" code="" you="" posted="" works="" for="" order="" the="" read="" lines="" but="" not="" for="" the="" header="" line.="" <="" p="">

[Tonyzeng]

Ashutoshmits, I have done running Basecalibration of GATK without any modification of the order ##contig=, it has done with out any probelm. So I do not need to sort the header anymore.

[Ashutosh Pandey]

Cool. It means GATK doesnt care for the contig order in the header of a VCF file.

[Tonyzeng]

Oh yeah! Thank you so much for your help anyway, Ashutoshmits

Answer 1

[Ashutosh Pandey]

Here is the code that should work. You will have to manually change the order in header but it will take care of the remaining. Make sure your computer has enough RAM if you have a big VCF file.

import os, sys
Argument = []
Argument = sys.argv[1:]

if (len(Argument)) < 1:
        print "Usage:Input_vcf Outputfile"
        sys.exit()

output = open(Argument[1],"w")
input = open(Argument[0])

def numeric_compare(x, y):
        x1 = int(x)
        y1 = int(y)
        return x1 - y1
Chromosome = ["10","11","12","13","14","15","16","17","18","19","X","1","2","3","4","5","6","7","8","9"]
VCF = {}
for line in input:
        if line.startswith("#"):
                output.write(str(line))
                continue
        v = []
        v = line.strip("\n").split("\t")

        if v[0] not in VCF:
                VCF[v[0]] = {}
                VCF[v[0]][v[1]] = line
        else:
                VCF[v[0]][v[1]] = line
for chr in Chromosome:
        for pos in sorted(VCF[chr].keys(),cmp=numeric_compare):
                output.write(str(VCF[chr][pos]))
                output.flush()
output.close()