partition generate empty fiel

I run this command as follow and the partition.pl generate empty file with just chr01 directory.

draft_asm=litchi.contigs.fasta
partition.pl -g Allele.gene.table -r $draft_asm -b sample.clean.bam -d wrk_dir 1>HG_parttion.log 2>&1

I found the Allele.gene.table and Allele.ctg.table are different to your post in https://github.com/tangerzhang/ALLHiC/wiki/ALLHiC:-identify-allelic-contigs while I used the same pipline in that page.

And my Allele.gene.table like:

Acyan01G0001000	chr01	121248	LITCHI034715,	NA
Acyan01G0002000	chr01	455756	LITCHI015286,	LITCHI034706,
Acyan01G0002100	chr01	460633	LITCHI015287,	LITCHI034705,
Acyan01G0002200	chr01	470217	LITCHI015288,	LITCHI034704,
Acyan01G0002300	chr01	473171	LITCHI015289,	LITCHI034703,
Acyan01G0002400	chr01	481720	LITCHI034702,	LITCHI015290,
Acyan01G0002500	chr01	518690	LITCHI015669,	LITCHI034701,
Acyan01G0002600	chr01	531431	LITCHI034700,	LITCHI015670,
Acyan01G0002800	chr01	563876	LITCHI015675,	LITCHI034697,
Acyan01G0002900	chr01	570771	LITCHI015676,	LITCHI034696,

And Allele.ctg.table like:

chr01	121248
chr02	305700
chr03	14690
chr04	44447
chr05	638524
chr06	24554
chr07	73333
chr08	8314
chr09	61186
chr10	26867

If what I thought is true, may this foreach my $i(3..$#data) should change to foreach my $i(4..$#data) in partition.pl scripts? I tried, but it can't work.

### Assign ctgs to pre-defined clusters

my %ctgdb;
open(IN, $table) or die"";
while(<IN>){
    chomp;
    my @data = split(/\s+/,$_);
    my $chrn = $data[1];
    foreach my $i(3..$#data){
        my $ctg = (split/,/,$data[$i])[1];
        $ctgdb{$ctg}->{$chrn}++;
        }
    }
close IN;

Could you tell me how to make parition.pl works? to change Allel.gene.table?

Very thanks. jun3234

tangerzhang / ALLHiC

partition generate empty fiel #58