Use awk/bash to add 1 to all columns but first

Question

I have a table in which the header is the sample list and the first column is the gene list, and the rest is expression values for each gene in each sample. I want to add a pseudocount of 1 to all values, and I currently do it as such:

cat <(head -n 1 TPM/QuickTest_Dataset.table) \
<(tail -n +2 TPM/QuickTest_Dataset.table | awk '{print $1, $2+1, $3+1, $4+1, $5+1, $6+1, $7+1, $8+1, $9+1, $10+1, $11+1, $12+1, $13+1, $14+1, $15+1, $16+1, $17+1, $18+1, $19+1, $20+1, $21+1}' | sed 's, ,\t,g') > StringTie-TPM_Homo_sapiens_GRCh38.Exp9-PMacrophageM1.protein_coding.table

However, the amount of samples isn't always 20 (amount of columns isn't always 21), sometimes more sometimes less and I have to manually adjust it each time.

Is there a simpler way?

Please add sample input (no descriptions, no images, no links) and your desired output for that sample input to your question (no comment). — Cyrus, Mar 29 '20 at 14:59

score 3 · Answer 1 · answered Mar 29 '20 at 15:09

3

awk is great language. Just iterate over fields and increment them.

awk '{ for (i = 2; i <= NR; ++i) $i += 1; } 1'

answered Mar 29 '20 at 15:09

KamilCuk

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score 1 · Accepted Answer · answered Mar 29 '20 at 15:09

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You can do this with one awk call:

awk 'BEGIN{OFS="\t"} FNR==1{print; next} {for (i=2;i<=NF;i++)$i=$i+1}1' infile > outfile

answered Mar 29 '20 at 15:09

Freddy

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could be done in single block too: `FNR>1{for(i=2; i<=NF; i++) $i++} 1'` – Sundeep Mar 29 '20 at 15:19
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`$i=$i+1` = `$i+=1` or just `$i++`. – Ed Morton Mar 29 '20 at 15:28

score 0 · Answer 3 · answered Mar 29 '20 at 15:09

The Google-search "awk Number of fields" let me to this post, mentioning the variable NF you might use.

The search for "awk for-loop" redirects to this URL, where the following simple awk for-loop is demonstrated (this also uses the NF variable):

awk '{ for (i = 1; i <= NF; i++) total = total+$i }; END { print total }'

This might give you a good start to solve this issue.

Use awk/bash to add 1 to all columns but first

3 Answers3