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Keep special character in a .txt file

Hi all,

I have a .txt file including three columns which based on column Annotation, i want to keep only rows including synonymous and missense. I will be grateful if you can help me to solve this problem.

CHROM_POS       ANN     Annotation
CM009840.1_932          A|intergenic_region|MODIFIER|CHR_START-LOC112587351|CHR_START-gene0|||  nongenic
CM009840.1_1096         T|intergenic_region|MODIFIER|CHR_START-LOC112587351|CHR_START-gene0||   nongenic
CM009840.1_4421500      A|missense_variant|MODERATE|LOC102415844|gene14  |1/1|c.298C>T|p.Ar||   missense
CM009840.1_4421553      A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p ||    missense
CM009840.1_4421600      G|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|protei ||   synonymous
CM009840.1_4421630      C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro||   synonymous
awk r
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updated by ahmad mousavi ahmad mousavi • written by mostafarafiepour mostafarafiepour

Hello mostafarafiepour!

We believe that this post does not fit this site. You repeatedly do not show any effort in solving basic unix questions yourselves. For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

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written by WouterDeCoster WouterDeCoster

with awk and sed:

$ sed -nr '/CHROM|mis|\tsyn/p' test.txt 

CHROM_POS   ANN Annotation
CM009840.1_4421500  A|missense_variant|MODERATE|LOC102415844|gene14 |1/1|c.298C>T|p.Ar||    missense
CM009840.1_4421553  A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p  ||  missense
CM009840.1_4421600  G|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|protei    ||  synonymous
CM009840.1_4421630  C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro|| synonymous

.

$ awk 'NR==1 {print}; /\tsynonymous|missense/ {print $0}' test.txt 
CHROM_POS   ANN Annotation
CM009840.1_4421500  A|missense_variant|MODERATE|LOC102415844|gene14 |1/1|c.298C>T|p.Ar||    missense
CM009840.1_4421553  A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p  ||  missense
CM009840.1_4421600  G|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|protei    ||  synonymous
CM009840.1_4421630  C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro|| synonymous

input:

$ cat test.txt 

CHROM_POS   ANN Annotation
CM009840.1_932  A|intergenic_region|MODIFIER|CHR_START-LOC112587351|CHR_START-gene0|||  nongenic
CM009840.1_1096 T|intergenic_region|MODIFIER|CHR_START-LOC112587351|CHR_START-gene0||   nongenic
CM009840.1_4421500  A|missense_variant|MODERATE|LOC102415844|gene14 |1/1|c.298C>T|p.Ar||    missense
CM009840.1_4421553  A|missense_variant|MODERATE|LOC102415844|gene14|transcript|rna37|p  ||  missense
CM009840.1_4421600  G|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|protei    ||  synonymous
CM009840.1_4421630  C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro|| synonymous
CM009840.1_4421630      C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro||     non-synonymous
CM009840.1_4421630      C|synonymous_variant|LOW|LOC102415844|gene14|transcript|rna37|pro||     nonsynonymous
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written by cpad0112 cpad0112

1 answer

Hi

grep 'synonymous' file.txt > new_file.txt
grep "PATTERN1\|PATTERN2" file.txt > new_file.txt
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written by ahmad mousavi ahmad mousavi

Thank you for the good answer.

But for those who close the post to prevent the problem, they should be sorry.

• 0 views • link
written by mostafarafiepour mostafarafiepour

We didn’t close your post to prevent people offering answers, we closed the post because you consistently ask low-effort questions where you do not attempt to learn how to solve the problem yourself.

You will be better off in the long run if you spend extra time trying to learn these very basic command now, even if it takes you a little longer to solve to problem.

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written by Joe Joe

What is the solution if we do not waste the header?

The header is meant : CHROM_POS ANN Annotation

• 0 views • link
written by mostafarafiepour mostafarafiepour

Why dont you read about grep and the other tools you can use for this task, and try to figure this out for yourself. It will not be difficult.

• 0 views • link
written by Joe Joe

I'm agree with @jej.healey , you should try some coding by yourself, millions of people have tried before you, at least 100K. and those question are too simple and have answers for sure.

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written by ahmad mousavi ahmad mousavi

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