chep_plot IndexError: string index out of range

[warthmann]

Hello,
I have provided chep_pileup_to_array with a fasta file and a bam file with illumina reads aligned to said genome fasta file. It ran fine as per example in your README and produced chep_3D.txt. Feeding this into chep_plot, however, again as per example, has issues. First it complained that it wanted a -g and -o, providing this then led to the error below. I hope you can point me in the right direction. My genome has 33 chromosomes, labeled chr01..chr33. Thank you very much!
I am using Python 3.12.6, samplot 1.21, snakemake 8.20.5, seaborn 0.13.2, bedtools 2.31.1, pandas 2.2.3

(chep) norman@Workstation:~/chep-analysis-for-heterozygosity$ chep_plot -f chep_3D.txt -x 0 -X 200 -d \
> -g genome_plus_chloroplast.fa \
> -o test

Traceback (most recent call last):
File "chep_plot", line 380, in
sys.exit(main(args))
^^^^^^^^^^
File "chep_plot", line 366, in main
genome_size = get_genome_size(args["genome"])
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "chep_plot", line 361, in get_genome_size
if line[0] != ">":
~~~~^^^
IndexError: string index out of range

[conchoecia]

Hello! I haven't developed this in a long time, but it looks like the error comes from some weakness in the fasta parser. if line[0] != ">": is the line that breaks it, so I am guessing that the fasta file is malformed? Let me know if changing the fasta file does not correct the problem. To future-proof this, a more robust fasta parser should be used.

…

On Thu, Oct 3, 2024 at 11:56 AM Norman Warthmann ***@***.***> wrote: Hello, I have provided chep_pileup_to_array with a fasta file and a bam file with illumina reads aligned to said genome fasta file. It ran fine as per example in your README and produced chep_3D.txt. Feeding this into chep_plot, however, again as per example, has issues. First it complained that it wanted a -g and -o, providing this then led to the error below. I hope you can point me in the right direction. My genome has 33 chromosomes, labeled chr01..chr33. Thank you very much! I am using Python 3.12.6, samplot 1.21, snakemake 8.20.5, seaborn 0.13.2, bedtools 2.31.1, pandas 2.2.3 (chep) ***@***.***:~/chep-analysis-for-heterozygosity$ chep_plot -f chep_3D.txt -x 0 -X 200 -d \> -g genome_plus_chloroplast.fa \> -o test Traceback (most recent call last): File "chep_plot", line 380, in sys.exit(main(args)) ^^^^^^^^^^ File "chep_plot", line 366, in main genome_size = get_genome_size(args["genome"]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "chep_plot", line 361, in get_genome_size if line[0] != ">": ~~~~^^^ IndexError: string index out of range — Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAX2QSMB3FJT3MAYOHYBCJDZZUID3AVCNFSM6AAAAABPJNWVHKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGU3DGNRRGMYTGMA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[warthmann]

Hello Darrin, thanks for getting back.
Funny, I am just 40 km down the road from Vienna, in Seibersdorf. I didn't notice anything funny with the fasta file, which I am using as downloaded. Can you give me a hint what to look out for? Ie, will it fail on empty lines? multi-word sequence names? or maybe the line breaks, or the wrapping? What exact format does your fasta parser expect? Note that the same fasta file worked for 'chep_pileup_to_array'. thanks a lot, best wishes, Norman