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Hi,

I have been updating hg19 position files and came across a problem I am not sure how to deal with. For example Z14 is represented in ISOGG as follows and Yleaf cannot parse that line.

Z14 R1b1a1b1a1a1b1 17364720..17364737 15252840..15252857 CAGATAGATAGATAGATA->CAGATAGATAGATA

Thanks!

Hi, my fastq files are generated by paired-end sequencing, so that I have two fq files for each sample (e.g. sample.1.fq.gz and sample.2.fq.gz). Does Yleaf support two fq files input like -fastq sample.1.fastq -fastq sample.2.fastq?

Best wishes
Xb

Hello!

Would it be possible to add T2T to Yleaf positions and support for T2T-CHM13v2.0 reference?

Thanks!

Hello!

Thank you for the tool! Do you plan to release the 2.3 version?

Hi genid, I found there are three versions of 'Position File' (MCS_Ampliseq/Visage_Ampliseq/WGS). What are the differences between them? How to choose one? I use the GRCh37 (100 genomes) as the reference and I don't know which one I can use. Thanks!

Are there plans to add Yleaf to PyPI and/or bioconda? (I did not find it on either. Sorry if it is already there.)

The existing conda environment file is already great for standalone running, but including Yleaf into PyPI (and from there bioconda) would get you a docker/singularity container for each release without any extra effort, via biocontainers. That in turn would make it possible to include Yleaf in reproducible workflows and pipelines.

Hi. Thanks for the nice software. I have 2 queries.

1. Is there a way to ignore C->T and G->A SNPs in the tool's prediction? That will be invaluable for ancient DNA.
2. Is there a way to run this on multiple bam files in one command?

Thank you.

Dear developer:

The species we are engaged in is pig, a very good medical model animal.

But we have noticed that this software is designed for humans, I would like to ask whether this software can be used in pigs at this stage?

Best

Dong

After a conda install of Yleaf on Centos 7, I receive the following error message. This does not prevent the run but it indicates a problem:
Error processing line 1 of /home/grange/miniconda2/envs/yleaf/lib/python3.7/site-packages/distutils-precedence.pth:

Traceback (most recent call last):
File "/home/grange/miniconda2/envs/yleaf/lib/python3.7/site.py", line 168, in addpackage
exec(line)
File "", line 1, in
ModuleNotFoundError: No module named '_distutils_hack'

Any suggestions of script modification or of why this module is not installed?

Thanks

Thierry

Hello, after migration from Yleaf v3.0.1 to latest version (not using v3.1 due to #15 and #16 in v3.1 release) we've got some differences:

You can see two major differences - Hg (and Hg_marker) and Total_reads (and Valid_markers btw).

• First difference come from sorting order changed in bc03016:

Is this intended, that instead of N1a1a1a1a2a1a1~ we're getting N1~?

• Second difference come from code refactoring:

Total_reads and Valid_markers come from 2nd and last positions of log:
https://github.com/genid/Yleaf/blob/master/yleaf/old_predict_haplogroup.py#L255-L287

def process_log(log_file):
    log_file += "info"
    total_reads = "NA"
    valid_markers = "NA"

    try:
        df_log = pd.read_csv(log_file, sep=":", header=None)
        log_array = df_log[1].values
        total_reads = log_array[1]
        valid_markers = log_array[-1]
    except FileNotFoundError:
        print("Warning: log file not found!")
    return total_reads, valid_markers


def main():
    print("\tY-Haplogroup Prediction")

    args = get_arguments()

    path_samples = args.Input  # .out files are collected
    samples = check_if_folder(path_samples, '.out')
    out_file = args.Outputfile
    hg_intermediate = str(yleaf_constants.DATA_FOLDER / yleaf_constants.HG_PREDICTION_FOLDER)
    intermediate_tree_table = hg_intermediate + "/Intermediates.txt"
    h_flag = True
    log_output = []
    for sample_name in samples:
        putative_hg = "NA"
        out_name = str(sample_name.split("/")[-1])
        out_name = out_name.split(".")[0]

        total_reads, valid_markers = process_log(sample_name[:-3])

In v3.0.1 it was correct:

• https://github.com/genid/Yleaf/blob/3.0.1/Yleaf.py#L509 - first line (Command)
• https://github.com/genid/Yleaf/blob/3.0.1/Yleaf.py#L304-L320 - second to last line (Total_reads, Unmapped_reads, Valid_markers)
• https://github.com/genid/Yleaf/blob/3.0.1/Yleaf.py#L562 - log printing - lines from predict_haplogroup doesn't appear in log due to previous printing

But now it is not correct:

• https://github.com/genid/Yleaf/blob/master/yleaf/Yleaf.py#L387 - first two lines (Total_reads, Unmapped_reads)
• https://github.com/genid/Yleaf/blob/master/yleaf/Yleaf.py#L518 - third line (Valid_markers)
• https://github.com/genid/Yleaf/blob/master/yleaf/Yleaf.py#L580-L587 - fourth to last line
• https://github.com/genid/Yleaf/blob/master/yleaf/Yleaf.py#L288 - log printing

Log for our data:

Total of mapped reads: 5549131
Total of unmapped reads: 4124
Valid markers: 64797
Markers with zero reads: 0
Markers below the read threshold {1}: 0
Markers below the base majority threshold {90}: 28
Markers with discordant genotype: 1
Markers without haplogroup information: 29
Markers with haplogroup information: 64768

Now we need first and third line, not second and last.

Hello!

The link in the readme points to: https://academic.oup.com/mbe/article/35/7/1820/4993044, which is:

This is a correction to:
Molecular Biology and Evolution, Volume 35, Issue 5, May 2018, Pages 1291–1294, https://doi.org/10.1093/molbev/msy032
This article published with a comment intended only to the editors of the journal. The comment has been removed. The author regrets the error.

So the correct link is the original one?
https://academic.oup.com/mbe/article/35/5/1291/4922696

Hello!

Thank you for this great tool! I think it would be great to mention in the readme, that the index file for input BAM-file should be named as alignment.bam.bai, not alignment.bai. This restriction is due to this line: https://github.com/genid/Yleaf/blob/master/Yleaf.py#L434

And this is not obvious, because different tools process differently named indesxes.

Hi,
is hg19 the one from UCSC or the equivalent of GRCh37, b37, h37 etc?
I have my samples mapped against hs37d5 (1000 Genomes project phase II). Is it proper for use with Yleaf?

Also when I am running yleaf 3.1 (conda installation as proposed in the manual) I get the following when the program starts

_Error processing line 1 of /home/psonisns/miniconda3/envs/yleaf/lib/python3.7/site-packages/distutils-precedence.pth:

Traceback (most recent call last):
File "/home/psonisns/miniconda3/envs/yleaf/lib/python3.7/site.py", line 168, in addpackage
exec(line)
File "", line 1, in
ModuleNotFoundError: No module named '_distutils_hack'

Remainder of file ignored_

But then it continues with the analysis without any issues (I think) ...

I created #15 as the first of a few changes that are needed to fix the old prediction option.

The next part should be to fix the intermediates.txt file look up since currently it's missing a /, so you'd see an error that the file wasn't found at .../data/hg_prediction_tablesIntermediates.txt

One option I found was to change Intermediates.txt to /Intermediates.txt at

This however hasn't yet fixed all the issues that I'm having with old predictions.

Hi, do you know what might be the problem?

##################
mikael@mikael-HP-Z600-Workstation[Yleaf] python Yleaf.py -bam /media/hd01/data/genome_mikael/cleanreads/md.chrY.bam -ref hg38 -pos /usr/local/bioinf/Yleaf/hg38.txt -out /media/hd01/data/genome_mikael/cleanreads/ydna_out -r 1 -q 20 -b 90 -t 1
Erasmus MC Department of Genetic Identification

Yleaf: software tool for human Y-chromosomal 
phylogenetic analysis and haplogroup inference v2.1



       |
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     /\|/\    
    \\\|///   
     \\|//  
      |||   
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usage: Yleaf.py [-h] [-fastq PATH] [-bam PATH] [-f PATH] -pos PATH -out STRING
[-r READS_THRESH] -q QUALITY_THRESH -b BASE_MAJORITY
[-t THREADS]
Yleaf.py: error: argument -r/--Reads_thresh: invalid int value: 'ef'

usage: Yleaf.py [-h] [-fastq PATH] [-bam PATH] [-f PATH] -pos PATH -out STRING
[-r READS_THRESH] -q QUALITY_THRESH -b BASE_MAJORITY
[-t THREADS]
Yleaf.py: error: argument -r/--Reads_thresh: invalid int value: 'ef'
##############

hi, I want to infer Y-haplogroups of 100 samples using their bam files merged as one, so when I run this tool, (using the command: Yleaf -bam input.bam -o output -rg hg19), in the output folder, the .out file contains haplogroup per position which is confusing, I don't know where to get haplogroups per sample, can you please help me? thanks

Hi I had installed and using a previous version.

I updated to 3.0 and now I get the following error:
[mpileup] 1 samples in 1 input files
--- 0.20 seconds in run PileUp ---
Extracting haplogroups...
Traceback (most recent call last):
File "/home/psonis/software/Yleaf/Yleaf.py", line 587, in
main()
File "/home/psonis/software/Yleaf/Yleaf.py", line 561, in main
output_file = samtools(args.threads, folder, folder_name, bam_file, args.Quality_thresh,
File "/home/psonis/software/Yleaf/Yleaf.py", line 454, in samtools
extract_haplogroups(markerfile, args.Reads_thresh, args.Base_majority,
File "/home/psonis/software/Yleaf/Yleaf.py", line 413, in extract_haplogroups
tree = Tree("Hg_Prediction_tables/tree.json")
File "/home/psonis/software/Yleaf/tree.py", line 33, in init
self._construct_tree(file)
File "/home/psonis/software/Yleaf/tree.py", line 41, in _construct_tree
with open(file) as f:
FileNotFoundError: [Errno 2] No such file or directory: 'Hg_Prediction_tables/tree.json'

Where is this file?

Also, I updated to 3.01 and everything is different. Not sure which is the executable, which are the proper files to use...
when testing python yleaf/Yleaf.py I get
Traceback (most recent call last):
File "/home/psonis/software/Yleaf/yleaf/Yleaf.py", line 30, in
from yleaf import version
ModuleNotFoundError: No module named 'yleaf'

I'm using Yleaf with the option -r 2 and -r 1 in order to make some comparisons between the two outputs but I get stucked because of a strange result has occured: the haplogorup prediction for the -r 1 doesn't show any result, even if the -r 2 one has shown the haplogorup R1b1a1b1a as well.
I didnt't expect a result like this because the -r1 option is less stringent and so it may creates a finer result then the -r2 option.
Why's this happening? What's gone wrong?
I copy the lines I used for both the -r2 analysis' steps below:

Yleafv2.2/Yleaf.py -bam C-58_picard.bam -pos /Yleafv2.2/WGS_hg19_noChr.txt -out mysample_Y_r2_DNA_Yleaf -r 2 -q 20 -b 90 -t 6

/Yleafv2.2/predict_haplogroup.py -input mysample_Y_r2_DNA_Yleaf -out 58_r2_y.hg 2> hg.err

the log file contains this information: Set max per-file depth to 8000