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sema4-research zhengxinchang cschin

pgr-tk-notebooks's Issues

Cannot get ROI_seq

Hi, @cschin

I am following the pgrtk-notebook to build Arabidopsis pangenome. But the code have throw an error:

thread '<unnamed>' panicked at 'assertion failed: self.ctg_lens.contains_key(&key)', pgr-db/src/agc_io.rs:111:9
---------------------------------------------------------------------------
PanicException                            Traceback (most recent call last)
Cell In[15], line 5
      3 padding = 10000
      4 ROI_len = ROI_b - ROI_e
----> 5 ROI_seq = sdb.get_sub_seq(ref_file_name, ROI_chr, ROI_b-padding, ROI_e+padding)

PanicException: assertion failed: self.ctg_lens.contains_key(&key)

Here is the code I used.

agc create -i fn.txt -t 12 TAIR10_chr.fa > Atha_pan.agc
echo "Atha_pan.agc" > input.fn
pgr-mdb input.fn Atha_pan.agc
import pgrtk

# lazy load an agc file of the reference without any SHIMMER index
ref_db =pgrtk.AGCFile("Atha_pan.agc")
sdb = pgrtk.SeqIndexDB()
sdb.load_from_agc_index("Atha_pan")

ref_file_name, ROI_chr, ROI_b, ROI_e = 'TAIR10_chr.fa', 'TAIR10_Chr3', 16000000,16400000
padding = 10000
ROI_len = ROI_b - ROI_e
ROI_seq = sdb.get_sub_seq(ref_file_name, ROI_chr, ROI_b-padding, ROI_e+padding)

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