returns: sed: 1: "1~4s/\/1$//": invalid command code ~
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michaela_boell
Parse file to remove two characters from the ends of a lot of lines
Dear all,
I have a txt file with data of this form:
@HWI-ST999:188:C49E6ACXX:8:1101:11404:1998/1
NCGAGGGATGGGAGACCTGGTTGGAAATCCGTGGCTGTTTGGTTGGGGGAT
+
#4=DDFFDHDHHGJIIJIJIFHIIIJJIJJJDHIGIEDGHGI=CGHJJH9>
@HWI-ST999:188:C49E6ACXX:8:1101:1754:2212/1
TCGAATGCATGATAACAATAACCCTGGAACAGGCAACCGTTGTCCCTGACC
+
CCCFFFFFHHHGHJJJJJJJJJJJJJJJJJJJJIJJJJJIIJJJJJJJJJJ
I would like to remove the /1 of the end of every 5th line.
Is this possible with a one liner in bash, maybe with sed (OSX)?
Context: I extracted reads from a bam file with Bam2Fastq into the format fastq. But the subsequent processing does not cope with the /1 or /2 in my two files of paired-end reads.
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1 answer
$ brew list
boost hdf5 libxml2 sratoolkit tophat
bowtie2 htslib openssl szip wget
gnu-sed libmagic samtools tbb
I installed gnu-sed with homebrew. Now it returns: sed: 1: "s_188_1_seq.txt": bad flag in substitute command: 's'
EDIT: homebrew put it in a weird location, so I used it like this now:
/usr/local/Cellar/gnu-sed/4.2.2/bin/gsed -i '1~4s/\/1$//' s_188_1_seq.txt
And it worked! Thank you. <3
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Would be more accurate to call this a fastq file, it's not just a txt file...
But someone who does not know what a fastq format is would be put off by it. And basically it can be called a txt file.
That doesn't make sense. You don't want answers from people who don't know what a fastq file is. This is biostars. We read fastq files at breakfast like normal people read the newspaper.
For this question it is unnecessary to know anything about biology. And I want to keep the question as easy to understand as possible. It would be more accurate to call it a fastq file, I guess, but not helpful here and in some cases maybe distracting. Although I guess 99.9% of people here know that it is a fastq file. And for those, I don't need to make it clear anyways.