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linux - 如何在拆分 fastq 文件时附加变量名？

问题描述

我在下面有一个 fastq 文件，我想将文件拆分为lane=$2. 我的代码完成了拆分它的工作，但我还希望输出文件附加 $SM 变量。有人可以让我知道我的命令中缺少什么吗？

SM="sample1"
awk 'BEGIN {FS = ":"} {lane=$2 ; print > "${SM}."lane".fastq" ; for (i = 1; i <= 3; i++) {getline ; print > "${SM}."lane".fastq"}}' < File.fastq

文件.fastq

@HS2000-1015_160:7:1108:13370:100570/2
CTTGACTGCCAGAGACGCTCCTTTGCAATGCCTTCCGGTAACCAAATTTTTGGGCACAACACACAGCTGGCCTTCATTTCTTCAGGGGCTGGTAAACAGA
+
@@@ADFFFHHHFD=EF@:GHIIFHH<ECHGF@DDBB:6@D60?F=888)8='--(=5@EAE5?'(..((.;?@>>A>3;@####################
@HS2000-1015_160:5:2306:10070:71746/2
GAACCTCAAGGACTATTGGGAGAGCGGCGAGTGGGCCATCATCAAAGCCCCAGGCTACAAACACGACATCAAGTACAACTGCTGCGAGGAGATCTACCCC
+
@CCFFFFDHGHFHIJJJJJJGGGIIJJIGHI@FHGIIGHHEFGHHFFFFFBCDDDDDCDDDDDDDD;@BDCCDACDD@>ACCDDDDBDB<BA?C@CC@BD
@HS2000-1015_160:6:2116:4077:79041/2
GGTCCCCGCCTACGCCCACTGGGTTGGTGCACCTGGTGGTGGTGGCCGCCAAGAAGCTGGTGAACCGCCTCCAAGTGGCTCCCAAGACGCAGCTGGATGA
+
CCCFFFFFHHFHHJHJJJJJJJJGGHJHIGAGIIJIFHJ;@F;CHHFHFDDDDDCDDCDD9CCCDDBDDBBDDCDACDD8@BD3>?BCDBDDDACCDC@>
@HS2000-1015_160:5:2113:11446:94436/2
CGTCAGGGCCAACCCCGCCCCACCCTGACCCTACCTGGCACCCCTCACCTGTGGCCTGCCAGCACAGCCTCGCCCCTGCTGGCCAATGTGTCCCCCGTCA
+
?@@DA@DDFHH?DHI)<@@FHDBGGCHCBDH;DFA<)6.=7D;@CBCHD)).7@=>;?==AABC95<(5(5309@D########################
@HS2000-1015_160:6:2209:18284:44195/2
TAAAATGTCACAAAGCTGGAAACTCTTCCCTATCACAAACCAAAACTTAAAAGGACGTTACCTGGCTGGGTCTAAACTCCACATAACTCGCTTGCAGTTG
+
CCCFFFFEHHHGHJIIIJJIJJHIIJEHJJHIJJJIIJJIJIJJIJIIHJJIJGGHGHGIIHHIIIIHFH@DFFFDEEEECDDDCDDDDBDDBBDCDACC
@HS2000-1015_160:7:1215:18781:100685/2
ATAAAACAGTAAACAAAATAAAGTCAGTTTTTTTTTTTTTTTTTAAAGAACAAAATGAAACTTGAGGGAAAACTTCATGGAGTTACAGTTTATCCTGATA
+
CCCFFFFFHFHHFJJJJIIGIGI<CFHHIIJJJJJIJJHFDDD=ACC(38+9CB?:(>C(+:@>(4?05<?C?###########################
@HS2000-1015_160:6:1215:6292:43622/2
GGGTCCTGAGACCTGAGGGACCATTGGCCCTCTTCTGGCTTGCTTATCCTTTGTACCTGATGGCCAATGAATGTCAGAGATGGTCCTGTCTCCATCCAGT
+
BCCDFFFFHGHHHJJJIIJJJJJIJJJGIJIJJIHIIJJIEFHEIJJJJIGIGIIIIIJHFHIJJJJIHGHEC?BCEFFFEECCCEACCCCDDDDDDCCC
@HS2000-1015_160:7:2311:1291:4696/2
GATCTGGTGCTCGTATTCCATCCACCTCCCAAGCTATACATAATAACGGCCAAAGGACCTGGATGAAAGTGTCTGAAGCAGTTGTGTGTGTCTCACCTTC
+
?=?ABDDBCFDFHGGHBFCHHGD@GFDGCBDFGFFECCHHD@DDFHJEIIHGG3CE9C(7@E(.7=?;;@C?@ECA>@C3A(;A-5595<9:AC3@AC:A
@HS2000-1015_160:7:1205:18979:53766/2
TCTTGTTTTGACCAATAGTAAAGCACATTTCTCTAATTTGGATTTCTACAATATCCATATCTTGGTTTATGAAAGGTAGGGAAGAGACTTCAGGTACTGC
+
CCCFFDFFHHHHHIJIJJJIHIJHJJIJJJJIJIGIIIJJJJJHJIJJIJDHIJIIIIIJJJJIJGIJJJIIIGEEGCD@AHHFFEDFFCDDDDCCDD@C
@HS2000-1015_160:7:1205:5641:24287/2
ATAAGAAGGGAAGAATGATTAGGTGTCAAATGTTCTTTTTATTTTCTTTCAGTTCAATGCAAAAACTTTCCAGTGATTATGTAAATGCAGAATCATGTGG
+
CCCFFFFFHHHGHJIJJFJJGIGEHEHIJJJJGJGJJIJJJJJJJJJJJIJIIIJJJIJJIEHGIHGJJJJIGGGHIIIIEEEHCHHC>DFBEEA@CCCC
@HS2000-1015_160:7:1310:19879:73973/2
TTCTTGAGTTCTGATACCTGTTTCCACAATCGTTTCTGTTTCTGTTGTCTCCAGCCCATCCATGCTGTCCTCATCTTCCACTGCAGTTTTCACCCTACTT
+
@<@FFFDFHHH>FGGIJAEFHABHHIAGHAE=F@EF?FB@F:F<GGBGEHGGG9F=BGAGIIIHH;=.=CHG@CEHE3)7?=>)7@C>)(6(.6;A?ACC
@HS2000-1015_160:7:1215:4243:29984/2
ATCTACACCCAAAACAGAACTTTCACAAAAAAACTGTTGATACGAAGCTCATGAAAATCATGATGAATACTCCAACAATTAATGAATAAAACTATACAAT
+
;@@A;D;ADDFHFIIF3EG@A>ACEHE>EH=:DH@<9DB@F?B7C87'@)=)7@>@7==)7...).;?@C)6;((;(5;(>A:(:3;@3>:@>:@(4@::
@HS2000-1015_160:7:1314:6987:62989/2
ATAGCTGTCTGTTCAGAGTCTGATGTTTTCAGTAACACTCTTGATACATTAAGTGAGATAGAATGGAATCCAGCAACAAAGCTACTAAATCAGGTAACTT
+
C@CFFFFDHHHHHJIJJJBHHIIIIHJIJHGJIJJIEHGHJJIJJJJJJJJIGBGHHIJGHGIIHJJIJIIJIGIGHIGGGCHHHHBEFCCEFE>CCEEE
@HS2000-1015_160:6:1208:20370:97766/2
TTTACTTTTTCCCAAACAATAATGATGATAATGTGGCCATACTGGTGCATGAGGGCTCTTATTAAGGATAGGGGCCATGTCAGGCTCTATTGACTCCTAT
+
CCCFFFFFDHDFHJJJIJJJIIJGHJJJIIIIGHIJJIJJJIJIHIJJIIHGHIFHIFHJGIJJIJJJJJJJJHHHFFFFFEEEEEDDCDEDDDDDDCDD
@HS2000-1015_160:6:1108:20693:2521/2
CCCATTTTCTGATGAGGAAACAGGATCAGGGACATTGAGACCTACCAAAGTTACATAATACCAGTAGTAGAAATGGGACTTCAACACAGGCCTCTTGACT
+
7@@DDDDDHHHBDIGIB@F?A+AF@3+2AFE@1:BFE??HH6?BG9BD99??F49BC=88=:;F8=77/@EH=EHF9)=A>C>7?;(6@???C?>@####
@HS2000-1015_160:6:1206:11472:64908/2
AGTTTGTTGGACATTTGAGACCCCAGGAAATCCCCTTTCTCGTAACGTTCTCCGCTTGGATCTGATCTCAACAGGGTGTCGTAGTCATTCTTCAGCACAA
+
B@BDFFFFHHHHHIJGIIJIJJIJJJJGEGHHIJJJJJJIJIFFHIIHCHHIJJJGIIJH:CHHFFFFFFFEEEDD=@BDDDAB@DCDDDDDDD>CCB<?
@HS2000-1015_160:7:1114:4995:49287/2
CCTCCGCTCAGCACTGGCATTGGCATCGGTTTCTATGGCAACAGTGAGACCAGTGATGGGGTGTCCCAGCTCAGCTCTGCGCTGCTGCACGCCAACCACA
+
BCCFDFFFHHHHHJJJJJGHEIIJHIGIIFGHGIIIGHEHIIJJDHIJJJJJJEGIGGIDE:?BCEEAE@CCDCDDCDDDDDDDBCCDDD85?9BB@BDD
@HS2000-1015_160:7:1206:16723:26612/2
TTAGATATGCTGTATGTGAAGAAGAGGAGGTTAAAGAACACTGTTTTATGTAAATGTCTCATTCCTTATCCTACAGAAATTGCATTTTTAATTAAATCTT
+
BC@FFFFFHHHHHICIGGHEIGJJIJIEGHGHIJJGGIIIIJIFGIJJIIJIIIJJIIJJJJJIHHGJJGIIIIGIIIHIIFHGHFADFFFDFDE(;@CE
@HS2000-1015_160:5:2101:1745:52266/2
CCCCAGAATTCTCTTGTTTTTTCCTTGGTGATCCAGGAAAACGAAGCCCCCTCCTGTATTGACAGCTGGGAATTGTGGAGTCCACCGTCCTCCACCTGAG
+
C@CFFFFFHHHHHJIJJIJJJJJIIICHCEGIIIEHGIIHIJIGGGIJCHGIHHHGEFHHHGHEEFFDEDAC?CDDCDCD>95>:,,99@DCC?<AB9AC

我得到的结果文件名：

${SM}.5.fastq
${SM}.6.fastq
${SM}.7.fastq

我想要的结果文件名：

sample1.5.fastq 
sample1.6.fastq
sample1.7.fastq

标签： linuxshellawkfastq

解决方案

编辑：根据 OP 的评论添加解决方案（改进的一个），包括更改输出文件名。

SM="sample1"
awk -v sm="$SM" '
BEGIN{FS = ":"} 
/^@HS/{
  split($1,arr,"_")
  sub(/^@[a-zA-Z]+/,"",arr[1])
  lane=$2
  close(outputFile)  
  outputFile=sm"."arr[1]"."lane".fastq"
}
{
  print >> (outputFile)
}' File.fastq

修复 OP 的尝试：您能否尝试以下操作，您实际上也可以使用-v awk_var_name="$shell_var"我在评论部分共享的链接，我也在您的代码中修复了一些东西。

SM="sample1"
awk -v sm="$SM" '
BEGIN{FS = ":"} 
{
  close(outputFile)
  lane=$2
  outputFile=sm count "."lane".fastq"
  print > (outputFile)
  for (i = 1; i <= 3; i++){getline ; print  > (outputFile)}
}' File.fastq

OP 尝试中的修复：

  • 为清楚起见，创建了具有输出文件名的 outputFile 变量。
  • 使用close命令关闭输出文件，这样我们就不会得到too many file opened error
  • 根据专家getline的建议，建议不要太多，因此更改了检查行号检查的方法FNR%4==0

理想的方式可能是：

SM="sample1"
awk -v sm="$SM" '
BEGIN{FS = ":"} 
/^@HS/{
  lane=$2
  close(outputFile)  
  outputFile=sm count "."lane".fastq"
}
{
  print >> (outputFile)
}' File.fastq

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