segatalab / export2graphlan Goto Github PK

Hello,

I'm experiencing compatibility issues when using MetaPhlan3 (3.0.9) input in export2graphlan (0.22). I'm not getting any error but the resulting Graphlan (1.1.3) graph is incorrect. See image below.

ZR_BioPool_DNA_I_15308_metaphlan_profile.txt

I've tried the --legacy-output option in MetaPhlan but the results remain the same.

ZR_BioPool_DNA_I_15308_metaphlan_profile.txt

When running export2graphlan and graphlan with the same versions and code for MetaPhlan2 output, the graph is displayed correctly. Are there any parameters that need to be set differently in conjunction with metaphlan3?

metaphlan ZR_BioPool_DNA_I_15308.fastq --bowtie2out ZR_BioPool_DNA_I_15308_bowtie.bz2 --nproc 8 --input_type fastq --bowtie2db /nfs/databases/metaphlan3/20210602/ -x mpa_v30_CHOCOPhlAn_201901 --biom ZR_BioPool_DNA_I_15308_biom.txt > ZR_BioPool_DNA_I_15308_metaphlan_profile.txt

export2graphlan.py -i ZR_BioPool_DNA_I_15308_metaphlan_profile.txt --tree ZR_BioPool_DNA_I_15308.tree.txt --annotation ZR_BioPool_DNA_I_15308.annot.txt --most_abundant 100 --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 --external_annotations 7 --min_clade_size 1 --annotation_legend_font_size 8 --fname_row 3 --skip_rows 0,1,2,3

graphlan_annotate.py --annot ZR_BioPool_DNA_I_15308.annot.txt ZR_BioPool_DNA_I_15308.tree.txt ZR_BioPool_DNA_I_15308.xml
graphlan.py --dpi 300 ZR_BioPool_DNA_I_15308.xml ZR_BioPool_DNA_I_15308.png

Is this a known issue?

Hi,

I'm trying to use export2graphlan on my humann3 abundance table output. but when I RUN:
"Traceback (most recent call last):
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 768, in
main()
File "/home/meta/miniconda2/envs/meta/bin/export2graphlan.py", line 511, in main
lefse_input = DataMatrix(args.lefse_input, args)
File "/home/meta/miniconda2/envs/meta/bin/hclust2.py", line 149, in init
index_col = self.args.sname_row if self.args.sname_row > -1 else None
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 678, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 446, in _read
data = parser.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1036, in read
ret = self._engine.read(nrows)
File "/home/meta/miniconda2/envs/meta/lib/python2.7/site-packages/pandas/io/parsers.py", line 1886, in read
values = data.pop(self.index_col[i])
IndexError: list index out of range".
物种.xlsx

Any ideas what's going wrong?
Thanks in advance!

Hi,

I'm trying to use export2graphlan on my MetaPhlAn3 abundance table output. I installed this and graphlan in another Conda env as they require python 2.7.

When I run:
export2graphlan.py --skip_rows 1 -i statemerged_abundance_table_g.txt--tree merged_abundance.tree.txt --annotation merged_abundance.annot.txt --most_abundant 100 --abundance_threshold 1 --least_biomarkers 10 --annotations 5,6 --external_annotations 7 --min_clade_size 1

I get the error:
Traceback (most recent call last): File "/pub38/cchong/miniconda2/envs/graphlan/bin/export2graphlan.py", line 770, in <module> main() File "/pub38/cchong/miniconda2/envs/graphlan/bin/export2graphlan.py", line 599, in main biomarkers = get_biomarkes(abundant, args.least_biomarkers) File "/pub38/cchong/miniconda2/envs/graphlan/bin/export2graphlan.py", line 381, in get_biomarkes while lvl < len(max(cc)): ValueError: max() arg is an empty sequence

statemerged_abundance_table_g.txt
Any ideas what's going wrong?

Thanks in advance!

Hi,

From your requirements list it is not immediately obvious why export2graphlan should be Python 2.7 only. Could you comment on that? I'd be happy to submit a patch that makes it 2&3 compatible.