【发布时间】：2016-08-26 14:41:57
【问题描述】：
我有一个 600 Mb 的 FASTA 文件，其中包含来自 12 个物种的许多比对块，我想将它们拆分成更小的 FASTA 文件，每个文件包含一个块及其对应的比对
我有一个如下所示的 sed 脚本：
#!/bin/bash
echo
for i in {0..Nblocks}; do
sed -n "/block_index=$i|/,/^$/p" genome12species.fasta > bloque$i.fasta
done
这适用于小规模，但对于 600Mb 的大文件，它需要很长时间，大约 2 天。我认为这与我正在运行的计算机无关。
有谁知道如何加快速度？
输入的 Fasta 文件如下所示：
dm3.chr3R(-):17092630-17092781|sequence_index=0|block_index=4|species=dm3|dm3_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta droGri2.scaffold_15074(-):2610183-2610334|sequence_index=0|block_index=4|species=droGri2|droGri2_4_0 GGCGGAGATCAAGAATCGTGTTGGGCCGCCGTCGAGCGCCACCGATAACGCTAGCAAAGTGAAAATCGATCAGGGACGCCCAGTGGAAAACAATAGATCTGGTTGCTGCTAAATAA-CTCTGATTGTGAATCATTATTTTATTATACAATTa droMoj3.scaffold_6540(+):33866311-33866462|sequence_index=0|block_index=4|species=droMoj3|droMoj3_4_0 TGCCGAGATTAAGAATCGTGTCGGTCCGCCGTCCAGCGCAACCGACAATGCAAGCAAAGTGAAAATCGATCAGGGACGTCCAGTGGAGAACACCAGATCTGGTTGCTGCTGAATAA-CTCTGATTGTGAATCATTATTTTATTatacaatta droVir3.scaffold_12822(+):1248119-1248270|sequence_index=0|block_index=4|species=droVir3|droVir3_4_0 GGCCGAGATTAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACCGATAATGCTAGCAAAGTGAAAATCGATCAGGGTCGTCCAGTGGAGAACACCAAATCTGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta droWil1.scaffold_181130(-):16071336-16071488|sequence_index=0|block_index=4|species=droWil1|droWil1_4_0 GGCCGAGATTAAGAATCGTGTTGGGCCGCCGTCCAGCGCCACTGATAATGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAATACCAAATCCGGTTGCTGCTGAATAAACTCTGATTGTGAATCATTATTTTATTATACAATTA droPer1.super_19(-):1310088-1310239|sequence_index=0|block_index=4|species=droPer1|droPer1_4_0 GGCTGAGATCAAGAATCGCGTCGGACCGCCGTCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAAACCCAATTCTGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta dp4.chr2(-):5593491-5593642|sequence_index=0|block_index=4|species=dp4|dp4_4_0 GGCTGAGATCAAGAATCGCGTCGGACCGCCGTCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAAGCCCAATTCTGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta droAna3.scaffold_13340(-):3754154-3754305|sequence_index=0|block_index=4|species=droAna3|droAna3_4_0 GGCCGAGATCAAGAATCGCGTCGGGCCACCGTCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAGATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattataaaatta droEre2.scaffold_4770(+):4567591-4567742|sequence_index=0|block_index=4|species=droEre2|droEre2_4_0 GGCCGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta droYak2.chr3R(-):5883047-5883198|sequence_index=0|block_index=4|species=droYak2|droYak2_4_0 GGCCGAGATCAAGAATCGCGTCGGGCCGCCATCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattattattattatacaatta droSec1.super_38(+):36432-36583|sequence_index=0|block_index=4|species=droSec1|droSec1_4_0 GGCGGAGATCAAGAATCGCGTCGGTCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta droSim1.chr3R(+):4366350-4366501|sequence_index=0|block_index=4|species=droSim1|droSim1_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta
dm3.chr3R(-):17092781-17092867|sequence_index=0|block_index=5|species=dm3|dm3_5_0 GAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTTGAGCAGGCCTTCATGACGATGGC droSim1.chr3R(+):4366264-4366350|sequence_index=0|block_index=5|species=droSim1|droSim1_5_0 GAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTTGAGCAGGCCTTTATGACGATGGC droSec1.super_38(+):36346-36432|sequence_index=0|block_index=5|species=droSec1|droSec1_5_0 GAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTTGAGCAGGCCTTCATGACGATGGC droYak2.chr3R(-):5883198-5883284|sequence_index=0|block_index=5|species=droYak2|droYak2_5_0 GAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACATCGGCCAAGAGCGCCACCAACGTGGAGCAGGCCTTCATGACGATGGC droEre2.scaffold_4770(+):4567505-4567591|sequence_index=0|block_index=5|species=droEre2|droEre2_5_0 GAGTACGCCGCCCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTGGAGCAGGCCTTCATGACGATGGC droAna3.scaffold_13340(+):20375068-20375148|sequence_index=0|block_index=5|species=droAna3|droAna3_5_0 ------GCCGAAAACTTCGACATGCCCTTCTTCGAGGTCTCTTGCAAGTCAAACATCAATATTGAAGATGCGTTTCTTTCCCTGGC dp4.chr2(-):5593642-5593728|sequence_index=0|block_index=5|species=dp4|dp4_5_0 GAGTATGCAGCTCAGTTAGGCATTCCATTTCTTGAAACTTCGGCCAAGAGCGCCACGAACGTGGAGCAGGCCTTCATGACGATGGC droPer1.super_19(-):1310239-1310325|sequence_index=0|block_index=5|species=droPer1|droPer1_5_0 GAGTATGCAGCTCAGTTAGGCATTCCATTTCTTGAAACTTCGGCCAAGAGCGCCACGAACGTGGAGCAGGCCTTCATGACGATGGC droWil1.scaffold_181130(-):16071488-16071574|sequence_index=0|block_index=5|species=droWil1|droWil1_5_0 GAATATGCGGCTCAGTTAGGCATTCCATTCCTTGAAACTTCGGCAAAGAGTGCCACCAATGTGGAGCAGGCCTTTATGACGATGGC droVir3.scaffold_12822(+):1248033-1248119|sequence_index=0|block_index=5|species=droVir3|droVir3_5_0 GAGTACGCACATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAACGTGGAGCAGGCATTTATGACGATGGC droMoj3.scaffold_6540(+):33866225-33866311|sequence_index=0|block_index=5|species=droMoj3|droMoj3_5_0 GAGTATGCACATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCCAAGAGCGCCACCAATGTAGAGCAGGCATTCATGACGATGGC droGri2.scaffold_15074(-):2610334-2610420|sequence_index=0|block_index=5|species=droGri2|droGri2_5_0 GAGTACGCAAATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCGAAGAGTGCCACCAATGTGGAACAGGCATTCATGACGATGGC
【问题讨论】：
-
肯定
awk将能够为您解决此问题，只需通过文件 1 次，并且只需几分钟。如果您与 sed “结婚”，那么更改为.../^$/{p,q}'可能有助于加快速度，但仍远不及 awk。添加一小组假/样本数据来说明您的文件格式（最多 5-10 行，最多 30-60 个字符宽），人们会对此进行深入研究。 （我要出去了 ;-/ ） 。祝你好运。 -
{0..Nblocks}真的有效吗？ （我认为不会。） -
@shellter。感谢您的洞察力。我没有嫁给 sed，我只是一个信息学的菜鸟，sed 是我唯一的想法。直到今天我才知道 awk 存在。
-
@BenjaminW。它没有，我必须手动输入块数。
标签： sed fasta sequence-alignment