CODEWITHSUNDEEP
bashfor-loop
upendra
upendra

Reputation: 2189

How to convert the new line character to tab and then insert new line character in a loop in bash

I have some bam files in my input directory and for each bam file i want to calculate the number of mapped reads (using Samtools view command) and print that number along with the name of the bam file into a output file. Though it is working, i am not getting the output that i desired.

Here is how my code looks like

for file in input/*;
        do
        echo $file >> test.out;
        samtools view -F 4 $file | wc -l >> output;
        done

This works fine but the problem is it ouputs the name of the file and number of reads in different lines. Here is an example

sample_data/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam
1784867
sample_data/wgEncodeUwRepliSeqBg02esG2AlnRep1.bam
2280544

I tried to convert the new line characters to tab by doing this

for file in input/*;
            do
            echo $file >> output;
            samtools view -F 4 $file | wc -l >> output;
            tr '\n' '\t' < output > output2
            done

Here is the output for the same

sample_data/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam      1784867 sample_data/wgEncodeUwRepliSeqBg02esG2AlnRep1.bam       2280544

How can now i insert the new line character after each line? For example

sample_data/wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam      1784867     
sample_data/wgEncodeUwRepliSeqBg02esG2AlnRep1.bam       2280544

Thanks

Upvotes: 1

Views: 84

Answers (3)

chepner
chepner

Reputation: 531798

Just use a command substitution:

for file in input/*
do
    printf '%s\t%d\n' "$file" "$(samtools view -F 4 $file | wc -l)"
done >> output

Upvotes: 1

gilez
gilez

Reputation: 679

You could get the desired output by writing everything in one line. Something like:

echo -e "$file\t$(samtools view -F 4 $file | wc -l)" >> output;

If you want to do it in two pieces, note that echo has a -n option to suppress trailing newlines, and -e to interpret escapes like \t, so you could do:

echo -ne "$file\t" >> $output
samtools view -F 4 $file | wc -l >> output

Writing what you want the first time is cleaner than trying to post-process your output.

Upvotes: 1

purplezzh
purplezzh

Reputation: 97

If the output of every file definitely consists of a filename and a number, I think you can easily change

tr '\n' '\t' < output > output2

to

tr '\n' '\t' < output | sed -r 's/([0-9]+\t)/\1\n/' > output2

It will match the number followed by a tab and add a new line character afterwards.

Upvotes: 1

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