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求助：給GFF格式的文件里，序列坐標(biāo)排序 [復(fù)制鏈接]

kateji

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發(fā)表于 2013-08-16 13:51 |只看該作者 |倒序?yàn)g覽

各位大俠，初來(lái)乍到，有事求助~~初學(xué)perl有問(wèn)題需解決，還請(qǐng)各位高手幫忙解答一下，感激不盡~~~

我有GFF格式的文件，內(nèi)容如下:
問(wèn)題1：想對(duì)第四列進(jìn)行排序，從小到大就可以，然后輸出排序文件。
問(wèn)題2：按scaffold的名稱(chēng)排序（如scaffold1，scaffold2，scaffold3.。。），同時(shí)將同一個(gè)scaffold的中的第四列按從小到大的序列排列，輸出排序文件。

本來(lái)想用哈希的，可是如果將第四列作為key值，因?yàn)閿?shù)字可能有重復(fù)，導(dǎo)致key不唯一，請(qǐng)各位指點(diǎn)迷津呀~~~~謝謝

scaffold1    Cuff mRNA 248934  263293  1000 -    .    ID=PAU000001.1;source_id=CUFF1.1.2;
scaffold1    Cuff UTR_5 263107  263293  1000 -    .    Parent=PAU000001.1;support_id=CUFF1.1.2;
scaffold1    Cuff CDS    263029  263106  1000 -    0    Parent=PAU000001.1;
scaffold2    Cuff CDS    262889  262942  1000 -    0    Parent=PAU000001.1;
scaffold2    Cuff CDS    262188  262355  1000 -    0    Parent=PAU000001.1;
scaffold1    Cuff CDS    260817  260915  1000 -    0    Parent=PAU000001.1;
scaffold1    Cuff CDS    260452  260538  1000 -    0    Parent=PAU000001.1;
scaffold5    Cuff CDS    257095  257177  1000 -    0    Parent=PAU000001.1;
scaffold5    Cuff CDS    256154  256267  1000 -    1    Parent=PAU000001.1;
scaffold1    Cuff CDS    255009  255063  1000 -    1    Parent=PAU000001.1;
scaffold3    Cuff CDS    254856  254942  1000 -    0    Parent=PAU000001.1;
scaffold3    Cuff CDS    252445  252500  1000 -    0    Parent=PAU000001.1;
scaffold1    Cuff CDS    252289  252348  1000 -    1    Parent=PAU000001.1;
scaffold4    Cuff CDS    252092  252179  1000 -    1    Parent=PAU000001.1;
scaffold4    Cuff CDS    251243  251992  1000 -    0    Parent=PAU000001.1;
scaffold1    Cuff CDS    251068  251128  1000 -    0    Parent=PAU000001.1;
scaffold1    Cuff CDS    250638  250740  1000 -    2    Parent=PAU000001.1;

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afukada

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2樓 [報(bào)告]

發(fā)表于 2013-08-16 16:02 |只看該作者

看不懂再問(wèn)吧

=Q1
while(<DATA>)
{
chomp;
@my_data=split(/\s+/);
push(@all_data,[@my_data]);
}
@all_data=sort{$a->[3]<=>$b->[3]}@all_data;
print join("\t",@$_),"\n" for(@all_data);
=cut
=Q2
while(<DATA>)
{
chomp;
@my_data=split(/\s+/);
$my_data[0]=~s/scaffold//g;
push(@all_data,[@my_data]);
}
@all_data=sort{$a->[0]<=>$b->[0]||$a->[3]<=>$b->[3]}@all_data;
print "scaffold",join("\t",@$_),"\n" for(@all_data);
=cut
__DATA__
scaffold1 Cuff mRNA 248934 263293 1000 - . ID=PAU000001.1;source_id=CUFF1.1.2;
scaffold1 Cuff UTR_5 263107 263293 1000 - . Parent=PAU000001.1;support_id=CUFF1.1.2;
scaffold1 Cuff CDS 263029 263106 1000 - 0 Parent=PAU000001.1;
scaffold2 Cuff CDS 262889 262942 1000 - 0 Parent=PAU000001.1;
scaffold2 Cuff CDS 262188 262355 1000 - 0 Parent=PAU000001.1;
scaffold1 Cuff CDS 260817 260915 1000 - 0 Parent=PAU000001.1;
scaffold1 Cuff CDS 260452 260538 1000 - 0 Parent=PAU000001.1;
scaffold5 Cuff CDS 257095 257177 1000 - 0 Parent=PAU000001.1;
scaffold5 Cuff CDS 256154 256267 1000 - 1 Parent=PAU000001.1;
scaffold1 Cuff CDS 255009 255063 1000 - 1 Parent=PAU000001.1;
scaffold3 Cuff CDS 254856 254942 1000 - 0 Parent=PAU000001.1;
scaffold3 Cuff CDS 252445 252500 1000 - 0 Parent=PAU000001.1;
scaffold1 Cuff CDS 252289 252348 1000 - 1 Parent=PAU000001.1;
scaffold4 Cuff CDS 252092 252179 1000 - 1 Parent=PAU000001.1;
scaffold4 Cuff CDS 251243 251992 1000 - 0 Parent=PAU000001.1;
scaffold1 Cuff CDS 251068 251128 1000 - 0 Parent=PAU000001.1;
scaffold1 Cuff CDS 250638 250740 1000 - 2 Parent=PAU000001.1;