usando o awk para o arquivo fastq de subconjunto baseado no comprimento da sequência

Question

Eu tenho um arquivo fastq. Eu vou explicar o que é. É algo parecido com isto

@SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
GATACAGGATGCCTGGGTCTAGGCTGTGTGACCTTGGGCCAGTTCCTCTC
+SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
DDDFFDDBGFEHEHGIGC9F>HG9EH8?DF4?:DF<?3:D?DHIGGDDFH
@SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
CTGCTGCTCATGCTCAT
+SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
BDDDDD<<CC:C+AFFE
@SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
AGCGTGTGCCACCCTACGCCGGC
+SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
DD>DAA@AA@@?2C8AB)?@:DD
@SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100
AGACAGAAGGGGAGTACAGCTCTCTGGAACATGAGAGTGCAAGGGGTTGAGTGTTT
+SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100
DDDFFFCFGEHI@CGFADFGCCFFGHFGCFFFHGGDGHIFHDFGGI<BF=DHIHHH

Agora, 4 linhas correspondem a 1 leitura, então

@SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
GATACAGGATGCCTGGGTCTAGGCTGTGTGACCTTGGGCCAGTTCCTCTC
+SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
DDDFFDDBGFEHEHGIGC9F>HG9EH8?DF4?:DF<?3:D?DHIGGDDFH

corresponde a 1 leitura que é GATACAGGATGCCTGGGTCTAGGCTGTGTGACCTTGGGCCAGTTCCTCTC

Mostrei o arquivo fastq acima. O que eu quero fazer é extrair apenas as leituras em que o comprimento do seq de leitura é < = 25, Então minha saída deve ser

@SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
CTGCTGCTCATGCTCAT
+SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
BDDDDD<<CC:C+AFFE
@SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
AGCGTGTGCCACCCTACGCCGGC
+SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
DD>DAA@AA@@?2C8AB)?@:DD

Eu quero usar o awk para esse propósito.

Eu tentei algo assim

awk 'NR % 2 == 0 {if(length($1) <= 25) print $0}; NR % 2 == 1' test.fastq

MAS isso imprime algo assim

@SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
+SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
@SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
CTGCTGCTCATGCTCAT
+SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
BDDDDD<<CC:C+AFFE
@SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
AGCGTGTGCCACCCTACGCCGGC
+SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
DD>DAA@AA@@?2C8AB)?@:DD
@SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100
+SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100

É evidente que não quero

@SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
+SRR1024120.7 DBRHHJN1:259:D0PM7ACXX:1:1101:1386:1189 length=100
@SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100
+SRR1024120.1 DBRHHJN1:259:D0PM7ACXX:1:1101:1200:1120 length=100

na minha saída.

Qualquer ajuda seria apreciada

Obrigado

    

Answer 1

Você pode usar separadores de registro e campo para impedir que o awk use as novas linhas e espaços. Em vez disso, você pode usar "\ n @" para mostrar a separação de registros e um simples "\ n" para separar os campos.

$ awk 'BEGIN {RS="\n@";FS="\n"} {if (length($2) <= 25) {print "@"$0} }' fastq
@SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
CTGCTGCTCATGCTCAT
+SRR1024120.25 DBRHHJN1:259:D0PM7ACXX:1:1101:1752:1149 length=100
BDDDDD<<CC:C+AFFE
@SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
AGCGTGTGCCACCCTACGCCGGC
+SRR1024120.42 DBRHHJN1:259:D0PM7ACXX:1:1101:2482:1096 length=100
DD>DAA@AA@@?2C8AB)?@:DD

Cada uma das linhas será um campo diferente, para que você possa verificar o comprimento dessa segunda linha com $ 2. Eu tive que adicionar o "@" de volta ao imprimir, uma vez que é comido pelo separador de registro.