Parsing columns with awk

Question

[pablo]

Hi,

I have this test.txt file :

gene 1:362273700-362275735
exon 1:362275166-362275246
exon 1:362274811-362275058
exon 1:362274230-362274685
gene 1:362279796-362287281
exon 1:362279796-362280179
exon 1:362280576-362280662
exon 1:362280858-362280958
exon 1:362281056-362281106

I need to get this output :

gene-1 1:362275166-362275246
gene-1 1:362274811-362275058
gene-1 1:362274230-362274685
gene-2 1:362279796-362280179
gene-2 1:362280576-362280662
gene-2 1:362280858-362280958
gene-2 1:362281056-362281106

-> Actually, I need to remove the "gene" lines, and replace each "exon" lines with "gene-X" (where X starts by 1).

I struggle with that.

 awk '$1~/exon/ {print $0 (/^exon/ ? "-" (++c) : "")}' test.txt

exon 1:362275166-362275246-1
exon 1:362274811-362275058-2
exon 1:362274230-362274685-3
exon 1:362279796-362280179-4
exon 1:362280576-362280662-5
exon 1:362280858-362280958-6
exon 1:362281056-362281106-7

awk '$1~/exon/ {$1=$1 "-" (++count[$1])}1' test.txt

gene 1:362273700-362275735
exon-1 1:362275166-362275246
exon-2 1:362274811-362275058
exon-3 1:362274230-362274685
gene 1:362279796-362287281
exon-4 1:362279796-362280179
exon-5 1:362280576-362280662
exon-6 1:362280858-362280958
exon-7 1:362281056-362281106

[genetixs]

Can you try it?

# Read the input file
with open("test.txt", "r") as input_file:
    lines = input_file.readlines()

gene_count = 0
output_lines = []

for line in lines:
    if line.startswith("gene"):
        gene_count += 1
    elif line.startswith("exon"):
        output_lines.append(f"gene-{gene_count} {line}")

# Write the modified lines to a new file
with open("output.txt", "w") as output_file:
    output_file.writelines(output_lines)

[Pierre Lindenbaum]

Review all your previous questions. validate or comment the answers please.

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• k-mer distribution to estimate the heterozygosity of my assembly
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• Salmon Algorithm Binary Search
• Bayesian algorithm / HISAT & STAR
• Difference between HTSeq-count & Salmon quant results
• Salmon / IGV

[Darked89]

Any chance you can use easier to write and comprehend language like Python?