zstephens / corgi Goto Github PK

Hi! Did you use python 2 to write this program?

Hello,

Thanks for developing this tool.
I am trying to run CORGi chromosome-wide with multiple samples but failed to do so. Please see the issue below.

Issue description

The command I ran:
python corgi.py -r ref.fa -b sample1.bam -c chr2 -p 0 $chrEnd -o out/chr2/

First error message:

[formatdb] WARNING: Cannot add sequence number 1 because it has zero length.
[formatdb] FATAL ERROR: Fatal error when adding sequence to BLAST database.

After going through the output files, I noticed that the RefChunk.fa file that formatdb uses to create the blast-db was empty. This is what causes formatdb to fail.

I hence debugged the code and found the issue.

Source of the problem

The RefChunk.fa file is created by:

1. reading the reference file,
2. obtaining the fasta entry that corresponds to the selected chromosome,
3. joining all of the fasta lines of the chromosome into a single string,
4. and finally subsetting this string with the start and end coordinates that the user provided.

Step 4, which occurs in line 70 of samFunc.py is the problematic one:

70 refChunk = readRef(refFile,refInds[refIndex])[samPos_s-1:samPos_e-1]

Python is a 0-based language, which the script correctly accounted for by adding a -1 to both coordinates when subsetting the string. However, when using the start coordinate 0, the subset becomes [-1:chrLength], which returns an empty string!

I suspect #2 is related to the same bug.

(temporal) Solution

Simply remove the -1 in line 70. Or, of course, use 1 instead of 0 in the arguments.

A future version of the script should add more information in the documentation or include an exemption to account for chromosome-wide subsets and prevent the start coordinate from being less than 0.

Hi,

I want to run the whole chromosome, say chr20. I set -p start from 0 to the length of chr20, but it fails. While I give another region, it runs but pretty slow.

So, is that possible to run whole chromosome and also in multi-threads?

Thanks