KeyError: "None of [Int64Index ... in wgdi -c

[amvarani]

Hi there,
I'm facing the error below when running the "wgdi -c " command
I'm using Ptrichocarpa from Phytozome

blockinfo = Ptrichocarpa_Ptrichocarpa.blockinfo.csv
lens1 = Ptrichocarpa.lens
lens2 = Ptrichocarpa.lens
tandem = false
tandem_length = 200
pvalue = 0.2
block_length = 5
tandem_ratio = 0.5
multiple = 1
homo = -1,1
savefile = Ptrichocarpa_Ptrichocarpa.blockinfo.new.csv
Traceback (most recent call last):
File "/home/amvarani/.local/bin/wgdi", line 8, in
sys.exit(main())
File "/home/amvarani/.local/lib/python3.10/site-packages/wgdi/run.py", line 163, in main
module_to_run(arg, value)
File "/home/amvarani/.local/lib/python3.10/site-packages/wgdi/run.py", line 122, in module_to_run
run_subprogram(program, conf, name)
File "/home/amvarani/.local/lib/python3.10/site-packages/wgdi/run.py", line 87, in run_subprogram
r.run()
File "/home/amvarani/.local/lib/python3.10/site-packages/wgdi/block_correspondence.py", line 47, in run
arr = self.collinearity_region(cor, bkinfo, lens1)
File "/home/amvarani/.local/lib/python3.10/site-packages/wgdi/block_correspondence.py", line 70, in collinearity_region
df1[[int(k) for k in b1]] += 1
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/series.py", line 1007, in getitem
return self._get_with(key)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/series.py", line 1042, in _get_with
return self.loc[key]
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexing.py", line 1073, in getitem
return self._getitem_axis(maybe_callable, axis=axis)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexing.py", line 1301, in _getitem_axis
return self._getitem_iterable(key, axis=axis)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexing.py", line 1239, in _getitem_iterable
keyarr, indexer = self._get_listlike_indexer(key, axis)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexing.py", line 1432, in _get_listlike_indexer
keyarr, indexer = ax._get_indexer_strict(key, axis_name)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 6113, in _get_indexer_strict
self._raise_if_missing(keyarr, indexer, axis_name)
File "/home/amvarani/.local/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 6173, in _raise_if_missing
raise KeyError(f"None of [{key}] are in the [{axis_name}]")
KeyError: "None of [Int64Index([8462, 8465, 8469, 8477, 8481, 8484, 8502, 8503, 8508, 8517, 8520,\n 8534, 8537, 8541, 8545, 8551, 8554, 8558, 8572, 8585, 8591],\n dtype='int64')] are in the [index]"

[SunPengChuan]

The problem with your gff and lens file processing is that the location of a certain gene is likely to exceed the scope of the chromosome.

[SunPengChuan]

You can upload your dataset and I can check it for you.

[amvarani]

Dear @SunPengChuan
Thanks for the quick answer
Here are the files that I've used

Ptrichocarpa_input_file.zip
blastp.zip

And the Phytozome files:

Ptrichocarpa_533_v4.1.cds_primaryTranscriptOnly.fa.gz
Ptrichocarpa_533_v4.1.gene.gff3.gz
Ptrichocarpa_533_v4.1.protein_primaryTranscriptOnly.fa.gz

[SunPengChuan]

In a GFF file, the fourth column, which represents the start of each chromosome, always begins with the number 1.
There are numerous genes with alternative splicing in your GFF file that need to be eliminated.

[amvarani]

Hi @SunPengChuan
Thanks!
I've identified the issue in my GFF file.
For those interested in converting Phytozome GFF3 files, here is a simple AWK script that can accomplish this:

zcat $genome.gff3.gz | awk '{if ($3 == "gene" ) print $1,$4,$5,$7,$9}' | cut -f 1 -d";" | sort -V | sed 's#.#_#g' | sed 's#v4_1##g' | awk '{split($5, a, "[=.]"); if (last != $1) {counter = 1; last = $1} else {counter++} print $1 " " a[2] " " $2 " " $3 " " $4 " " counter " ID" a[2]}'

[kashiff007]

Hi @SunPengChuan

I am getting the similar error while running BlockInfo.
Error

(base) [nawazk@login509-02-l W6-48549-006]$ wgdi -bi bi_total.conf
blast  =  SG_A_vs_SB_B.blast
gff1  =  SG_A.gff
gff2  =  SG_B.gff
lens1  =  SG_A.lens
lens2  =  SG_B.lens
collinearity  =  SG_A_vs_SB_B.list
score  =  100
evalue  =  1e-5
repeat_number  =  20
position  =  order
ks  =  ks file
ks_col  =  ks_NG86
savefile  =  block information (*.csv)
/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/block_info.py:74: FutureWarning: In a future version of pandas, a length 1 tuple will be returned when iterating over a groupby with a grouper equal to a list of length 1. Don't supply a list with a single grouper to avoid this warning.
  index = [group.sort_values(by=11, ascending=False)[:repeat_number].index.tolist()
Traceback (most recent call last):
  File "/home/nawazk/.conda/envs/mamba/bin/wgdi", line 10, in <module>
    sys.exit(main())
  File "/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/run.py", line 163, in main
    module_to_run(arg, value)
  File "/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/run.py", line 122, in module_to_run
    run_subprogram(program, conf, name)
  File "/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/run.py", line 87, in run_subprogram
    r.run()
  File "/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/block_info.py", line 121, in run
    collinearity = self.auto_file(gff1, gff2)
  File "/home/nawazk/.conda/envs/mamba/lib/python3.10/site-packages/wgdi/block_info.py", line 164, in auto_file
    return collinearity
UnboundLocalError: local variable 'collinearity' referenced before assignment

Can you check the files attached?
SG_A_vs_SB_B.blast.txt
SG_A_vs_SB_B.collinearit_pair.txt
SG_A.gff.txt
SG_A.lens.txt
SG_B.gff.txt
SG_B.lens.txt

[SunPengChuan]

collinearity = SG_A_vs_SB_B.list
This file is the result of the -c Subprogram of WGDI, and it could also be the output of MCScanX or JCVI. It’s not a gene pair.

savefile = block information (*.csv)
The savefile has not been modified; it is an output file.