submit assembly to NCBI
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二、submit assembly to NCBI
1、prepare data
首先要具有fasta格式数据(NO .gz)，这是处理的基础，具体格式如下：
>Scaffold633TCATTTCTCCACTCTCGATGAACAAATCTGGAGGGATTTTTTTTCATTCCACTCAATAGGTTGTCTATAAAGGTGTGATTCGTGGAACTTCTTCACACAGCAGCTAGTCTATATAATACAGAAGATCG>Scaffold553AAAAAATTTTTTTTTTAAACTATCATCTCATGGATCAGCAGCAATTCTGAGTGTAACGTCTTCATTAAATGCGTATATAAATTTGCATAAAGATATGCGACCAATATTGAGCCTGGAAATATATGCGCAGAGTGCAAAATTGTGTTTTTTGATCGGTTAATTAAAGG>Scaffold641GTTTCCCAGTAGGTCTCTCCCGCTACGGCGTCCGCACGAACGCGATCTGCCCTCGTGCCCGCACCGCCATGACGGCAGAAGCCTTCGGCGAGAACAACACCGGCGTCGTCGGCCTCGATCCGCTTGCACCCGAGCGCGTCGCGACCCTGGTCAGCTACCTCGCATCCCCCGATTCCGACGAGATCAACGGACAGGTCTTCGTCGTCTACGGCAAGATGGTGGCGTTGATGGAAGCACCCAAGGTCGAGAACCGTTTCGACGCAGCCGGATCCGCGTTCACCGTCGAAGAACTCGGTGGCCAGCTCTCGTCTTACTTCTCCGGCCGTGGGCCGTACGAGACCTACTGGGAAAC
2、处理数据
分为几步：
(1)生成.greater, short.list和ZERO_BASE_COUNT文件
perl ../ scaf_filter_2k.pl Ascaris_suum.scaf.fa
scaf_filter_2k.pl代码
#!/usr/bin/perluse strict;use warnings; my $file=shift;#my $cutoff=shift;my $outfile="short.list";my $outfile2="$file.greater";my $outfile3="ZERO_BASE_COUNT"; open IN,"< $file" or die $!;open OUT,"> $outfile" or die $!;open OUT1,"> $outfile2" or die $!;open OUT2, "> $outfile3" or die $!;$/='>';<IN>;$/="\n";while(<IN>){ chomp; my $id=$1 if(/^(\S+)/); $/='>'; my $seq=<IN>; chomp($seq); $/="\n"; $seq=~s/\s//g; my $len=length($seq); if ($len < 200){ print OUT "$id\t$len\n"; next; } else{ my $a=$seq=~tr/aA/aA/; my $t=$seq=~tr/tT/tT/; my $c=$seq=~tr/cC/cC/; my $g=$seq=~tr/gG/gG/; if($a==0 || $c==0 || $g==0 || $t==0){ print OUT2 "$id\t$len\n"; next; } print OUT1 ">$id\n$seq\n"; }}close IN;close OUT;close OUT1;close OUT2;(2)生成.Nchange文件。
perl ../ info_N_plus.pl Ascaris_suum.scaf.fa.greater > Ascaris_suum.scaf.fa.greater.Nchange
info_N_plus.pl代码：
#!/usr/bin/perl -wuse strict;#use Getopt::Long;sub usage{ print STDERR <<USAGE; ############################################ Version 1.1 by Wing-L 2011.07.15 usage: $0 <sequence.fa> <len> >STDOUT ############################################USAGEexit;}&usage if(@ARGV <1);my ($fa,$len)=@ARGV;$len||=10;open IN,"<$fa" or die("$!\n");$/='>';<IN>;$/="\n";while(my $line=<IN>){ my @block; $line=~/^\S+/; my $tag={1}; $/='>'; my $seq=<IN>; chomp $seq; $/="\n"; $seq=~s/\s//g; my $chr_length=length $seq; while($seq=~/[^N]N{1,9}[^N]/g){ substr ($seq,$-[0]+1,$len)=~s/\S/N/g; } while($seq=~/N([^N]{1,49})N/g){ my $tlen=length $1; substr ($seq,$-[0]+1,$tlen)=~s/\S/N/g; } if($seq=~/^N?[^N]{0,49}N+/){ print STDERR "$tag\t1\t{1}[0]\n"; substr($seq,0,{1}[0]-$-[0])=''; } if($seq=~/N+[^N]{0,49}N{0,}$/){ print STDERR "$tag\t$-[0]\t$chr_length\n"; substr($seq,$-[0],$chr_length-$-[0])=''; } print ">$tag\n$seq\n";}close IN;#open IN,"<" or die("$!\n");#while(my $line=<IN>){}#foreach my $e (){}#(split /\s+/,$line)[0]#open OUT,">" or die("$!\n");############### sub ###############(3)生成分割文件
perl ../get_scaftig.pl Ascaris_suum.scaf.fa.greater.Nchange > Ascaris_suum.scaf.fa.greater.Nchange.split
get_scaftig.pl代码：
#!/usr/bin/perl -w##Author: Ruan Jue <ruanjue@genomics.org.cn>#use warnings;use strict; my $min_length = 0;my $name = '';my $seq = ''; while(<>){ if(/^>(\S+)/){ &print_scafftig($name, $seq) if($seq); $name = $1; $seq = ''; } else { chomp; $seq .= {1}
; }}&print_scafftig($name, $seq) if($seq); 1; sub print_scafftig { my $name = shift; my $seq = shift; my $temp = $seq; my $id = 1; my $flag = 0; my $pos = 1; while($seq=~/([ATGCatgc]+)/g){ my $s = $1; if($flag==1){ if($temp=~/([ATGCatgc]+[Nn]+)/g){ my $g = $1; $pos+=length($g); } } else{$flag=1;} next if(length($s) < $min_length); my $length=length($s); my $end=$pos+$length-1;# print ">$name\_$id start=$pos length=".length($s)."\n"; print ">$name\_$id\t$pos\t$end\t$length\n"; while($s=~/(.{1,60})/g){ print "$1\n"; } $id++;}}(4)生成.agp文件
perl ../AGP.pl Ascaris_suum.scaf.fa.greater.Nchange.split > Ascaris_suum.scaf.fa.agp
AGP.pl 代码：
#!/usr/bin/perluse strict; my $fasta=shift; my %Scaf;open IN,$fasta or die "$!";while(<IN>){ if (/^>(\S+)(_\d+)\s+(\d+)\s+(\d+)\s+(\d+)/){ my $scaf=$1; my $contig=$1.$2; my $start=$3; my $end=$4; my $len=$5; push @{$Scaf{$scaf}},[$contig,$start,$end,$len]; }}close IN; foreach my $id ( sort keys %Scaf ){ @{$Scaf{$id}} = sort {$a->[1]<=>$b->[1]} @{$Scaf{$id}};} foreach my $id ( sort { $Scaf{$b}[-1][2] <=> $Scaf{$a}[-1][2] } keys %Scaf ){ my $p=$Scaf{$id}; my $idx=1; for(my $i=0;$i<@$p;$i++){ if ($i>0){ print join("\t",$id,$p->[$i-1][2]+1,$p->[$i][1]-1,$idx,'N',($p->[$i][1]-1)-($p->[$i-1][2]+1)+1,'fragment','yes',"\t")."\n"; $idx++; } print join("\t",$id,$p->[$i][1],$p->[$i][2],$idx,'W',$p->[$i][0],1,$p->[$i][3],'+')."\n"; $idx++; }}至此为止，第一步准备数据的过程已经完成。下一步就是向3811提交任务。
这个过程需要的东西：
l Ascaris_suum.scaf.fa.greater.Nchange.gz
l Ascaris_suum.agp.gz
和NCBI沟通的文件，主要是确定的Project ID的准确性。
未完待续.........
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