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我有一个 600 Mb 的 FASTA 文件，其中包含来自 12 个物种的许多对齐块，我想将它们拆分为较小的 FASTA 文件，每个文件包含一个块及其对应的对齐

我有一个看起来像这样的 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。我不认为这是我正在运行的计算机的问题。

有谁知道如何使它更快？

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-CTCTGATTGTGAATCattattattattattatacaatta(-):dp4.chr25593491-5593642|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 GGCCGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattatttatttatttattttatacaatta.R5883047-5883198|sequence_index=0|block_index=4|species=droYak2|droYak2_4_0 GGCCGAGATCAAGAATCGCGTCGGGCCGCCATCCAGCGCCACCGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattttattatacaatta 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-CTCTGATTGTGAATCattattattattattatacaatta4366350-4366501|sequence_index=0|block_index=4|species=droSim1|droSim1_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattattattatatacaatta4366350-4366501|sequence_index=0|block_index=4|species=droSim1|droSim1_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattattattatatacaattasuper_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 -CTCTGATTGTGAATCattattttattatacaattasuper_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 -CTCTGATTGTGAATCattattttattatacaatta4366350-4366501|sequence_index=0|block_index=4|species=droSim1|droSim1_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattattattatatacaatta4366350-4366501|sequence_index=0|block_index=4|species=droSim1|droSim1_4_0 GGCGGAGATCAAGAATCGCGTCGGGCCGCCGTCCAGCGCCACTGACAACGCTAGCAAAGTGAAAATCGATCAAGGACGTCCAGTGGAAAACACCAAATCCGGTTGCTGCTGAATAA-CTCTGATTGTGAATCattattattattatatacaatta

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 GAGTACGCAAATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCGAAGAGTGCCACCAATGTGGAACAGGCATTCATGACGATGGC1248033-1248119|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 GAGTACGCAAATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCGAAGAGTGCCACCAATGTGGAACAGGCATTCATGACGATGGC1248033-1248119|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 GAGTACGCAAATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCGAAGAGTGCCACCAATGTGGAACAGGCATTCATGACGATGGC33866225-33866311|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 GAGTACGCAAATCAGTTAGGCATTCCATTCCTTGAAACTTCGGCGAAGAGTGCCACCAATGTGGAACAGGCATTCATGACGATGGC33866225-33866311|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

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1 回答 1

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这是一个 awk oneliner 可以帮助您入门 - 它使用与 sed 相同的正则表达式范围 - 匹配的 block_index 在 m[1] 中 - 600MB 只需几分钟

awk 'match($0, /block_index=([0-9]+)\|/, m),/^$/ {print >"bloque"m[1]".fasta"}'
于 2016-08-26T06:41:57.337 回答