bash – 如何在列表中的单行上并行运行grep

在Intel Xeon E5上花费大约1分钟,检查10,000种物品的6GB伪造数据文件 – 但是即使在10,000个块中,物种列表也增加到100,0000是有问题的,因为我遇到了创建的许多文件的磁盘问题附加到一个目录中 – 问题在物种列表超过50,000时开始 – 这个数字在其他系统上会有所不同 – 我修改了脚本以创建100个子目录并将每个目录限制为1000个文件 – 这很有效并且生成了所有100,000个文件无需将物种列表或6GB数据文件分块

另外,为了让您了解grep的速度有多快 – 在6GB文件中花费6秒钟来匹配100,000种物种

specieslist=$1
nspecies=$(wc -l $specieslist|cut -f1 -d' ')
echo -e "grep $nspecies species from $specieslistn"
grep -A1 -F -f $specieslist|
awk '
# skip context marker
/^--$/{next}
# process pair of lines
# first line is matching species header line
# species is semicolon-delimited field 7 of first line
# second line is sequence - both lines are written to a file with sanitized species name
{
  split($0,flds,";")
  species=flds[7]
  filekey=gensub(/W/,".","g",species)
  file="fastaout." filekey
  if(!(filekey in outfiles))  {
    outfiles[filekey]=file
    printf("species "%s" outfile "%s" first match line %d: "%s"n",species,file,NR,$0)
    print >file
  }
  getline; print >>file
# close may be needed on systems where awk cannot juggle too many open files
close(outfile)
}
'
outfiles=(fastaout.*)
noutfiles=${#outfiles[*]}
echo -e "ncreated $noutfiles fastaout.* files"
head -5 fastaout*

输出和略微修改的测试输入如下 – 物种列表有一些实际的匹配 – fasta文件序列行以小写物种为前缀以验证正确性并避免再次匹配物种

产量

$head out.*
==> out.Brachyspira_innocens <==
brachyspira_innocens.1:-UC-U-G--G-U---------------------------
brachyspira_innocens.2:-UC-U-G--G-U---------------------------

==> out.Methanohalophilus_portucalensis_FDF-1 <==
methanohalophilus_portucalensis_fdf-1:-UC-U-G--G-U---------------------------

==> out.Pucciniomycotina <==
pucciniomycotina:-UC-U-G--G-U---------------------------

物种清单

Allobacillus_halotolerans
Allochromatium_truperi
Allochromatium_vinosum
Methanohalophilus_portucalensis_FDF-1
Brachyspira_innocens
Pucciniomycotina

fasta文件

HP451749.6.1794_Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Basidiomycota;Pucciniomycotina;Pucciniomycetes;Pucciniales;Pucciniaceae;Puccinia;Puccinia_triticina;.............................................................................
pucciniomycotina:-UC-U-G--G-U---------------------------
>EF164983.1.1433_Bacteria;Spirochaetae;Spirochaetes;Spirochaetales;Brachyspiraceae;Brachyspira;Brachyspira_innocens
brachyspira_innocens.1:-UC-U-G--G-U---------------------------
>X96499.1.1810_Eukaryota;Archaeplastida;Chloroplastida;Charophyta;Phragmoplastophyta;Streptophyta;Embryophyta;Marchantiophyta;Jungermanniales;Calypogeia;Plagiochila_adiantoides
plagiochila_adiantoides:-UC-U-G--G-U---------------------------
>AB034906.1.1763_Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Ascomycota;Saccharomycotina;Saccharomycetes;Saccharomycetales;Saccharomycetaceae;Citeromyces;Citeromyces_siamensis
citeromyces_siamensis:-UC-U-G--G-U---------------------------
>AY290717.1.1208_Archaea;Euryarchaeota;Methanomicrobia;Methanosarcinales;Methanosarcinaceae;Methanohalophilus;Methanohalophilus_portucalensis_FDF-1
methanohalophilus_portucalensis_fdf-1:-UC-U-G--G-U---------------------------
>EF164984.1.1433_Bacteria;Spirochaetae;Spirochaetes;Spirochaetales;Brachyspiraceae;Brachyspira;Brachyspira_pulli
brachyspira_pulli:-UC-U-G--G-U---------------------------
>AY291120.1.1477_Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Lampropedia;Lampropedia_hyalina
lampropedia_hyalina:-UC-U-G--G-U---------------------------
>EF164987.1.1433_Bacteria;Spirochaetae;Spirochaetes;Spirochaetales;Brachyspiraceae;Brachyspira;Brachyspira_alvinipulli
brachyspira_alvinipulli:-UC-U-G--G-U---------------------------
>JQ838073.1.1461_Bacteria;Actinobacteria;Actinobacteria;Streptomycetales;Streptomycetaceae;Streptomyces;Streptomyces_sp._QLS01
streptomyces_sp._qls01:-UC-U-G--G-U---------------------------
>EF164989.1.1433_Bacteria;Spirochaetae;Spirochaetes;Spirochaetales;Brachyspiraceae;Brachyspira;Brachyspira_alvinipulli
brachyspira_alvinipulli:-UC-U-G--G-U---------------------------
>JQ838076.1.1460_Bacteria;Actinobacteria;Actinobacteria;Streptomycetales;Streptomycetaceae;Streptomyces;Streptomyces_sp._QLS04
streptomyces_sp._qls04:-UC-U-G--G-U---------------------------
>AB035584.1.1789_Eukaryota;Opisthokonta;Nucletmycea;Fungi;Dikarya;Basidiomycota;Agaricomycotina;Tremellomycetes;Tremellales;Trichosporonaceae;Trichosporon;Trichosporon_debeurmannianum
trichosporon_debeurmannianum:-UC-U-G--G-U---------------------------
>JQ838080.1.1457_Bacteria;Actinobacteria;Actinobacteria;Streptomycetales;Streptomycetaceae;Streptomyces;Streptomyces_sp._QLS11
streptomyces_sp._qls11:-UC-U-G--G-U---------------------------
>EF165015.1.1527_Bacteria;Firmicutes;Clostridia;Clostridiales;Family_XI;Tepidimicrobium;Clostridium_sp._PML3-1
clostridium_sp._pml3-1:-UC-U-G--G-U---------------------------
>U85867.1.1424_Bacteria;Proteobacteria;Gammaproteobacteria;Alteromonadales;Alteromonadaceae;Marinobacter;Marinobacter_sp.
Marinobacter_sp.:-UC-U-G--G-U---------------------------
>EF165044.1.1398_Bacteria;Proteobacteria;Alphaproteobacteria;Rhizobiales;Methylobacteriaceae;Methylobacterium;Methylobacterium_sp._CBMB38
methylobacterium_sp._cbmb38:-UC-U-G--G-U---------------------------
>U85870.1.1458_Bacteria;Proteobacteria;Gammaproteobacteria;Pseudomonadales;Pseudomonadaceae;Pseudomonas;Pseudomonas_sp.
pseudomonas_sp.:-UC-U-G--G-U---------------------------
>EF165046.1.1380_Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Pantoea;Pantoea_sp._CBMB55
pantoea_sp._cbmb55:-UC-U-G--G-U---------------------------
>EF164983.1.1433_Bacteria;Spirochaetae;Spirochaetes;Spirochaetales;Brachyspiraceae;Brachyspira;Brachyspira_innocens
brachyspira_innocens.2:-UC-U-G--G-U---------------------------