Issue with `awk` syntax in `fetch_sequence.py`

[mimonti]

Hi all! Thank you for the tool- I have been trying to run the example set before proceeding with my snoRNA of interest but I am getting this error:

awk: syntax error at source line 1 context is $3 - $2 >= 13 {print $1 " " $2 - 1 " " $3 - 1 " "$4" "$5" "$6 > >>> "/path/to/git_repo/snoGloBe/example/temp_84637/example_output.tsv.targetwindows.bed.chromo"$ <<< 1} awk: illegal statement at source line 1

Before trying to edit the fetch_sequence.py file I thought I would see if you have come across this before!

P.S. of course the path is not '/path/to/git_repo/' I have just simplified it for this example !

[Gabrielle-DF]

I recall facing this issue once, but I was not able to reproduce it with my current environments.

Could you share a sample of your file "/path/to/git_repo/snoGloBe/example/temp_84637/example_output.tsv.targetwindows.bed"? Also, could you tell me which version of bedtools and awk you are using?

[mimonti]

Hi Gabrielle! Thanks so much for the help with this- re your questions

• bedtools v2.31.0
• awk version 20200816

This is the head of the file:

4 1793307 1793320 4_+1793307 0 + 4 1793308 1793321 4+1793308 0 + 4 1793309 1793322 4+1793309 0 + 4 1793310 1793323 4+1793310 0 + 4 1793311 1793324 4+1793311 0 + 4 1793312 1793325 4+1793312 0 + 4 1793313 1793326 4+1793313 0 + 4 1793314 1793327 4+1793314 0 + 4 1793315 1793328 4+1793315 0 + 4 1793316 1793329 4+_1793316 0 +

Let me know if you need any other info, and thanks again!