8000 synteny.py：IndexError: list index out of range · Issue #748 · tanghaibao/jcvi · GitHub
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haihao999 opened this issue Feb 8, 2025 · 1 comment
Open

synteny.py：IndexError: list index out of range #748

haihao999 opened this issue Feb 8, 2025 · 1 comment

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@haihao999
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haihao999 commented Feb 8, 2025 •
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您好，请问下这个报错该如何解决？谢谢！
python -m jcvi.graphics.synteny filtered_blocks.txt \

merged.bed
layout.txt
[02/08/25 18:04:37] DEBUG Load file merged.bed base.py:36
[02/08/25 18:04:43] DEBUG Load file filtered_blocks.txt base.py:36
DEBUG Load file layout.txt base.py:36
Column 0: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 1: KDMLFL_00685 - KDMLFL_00710 (GCA_028533045_1_contig_4:3422-8752)
GCA_028533045_1_contig_4 .. 6 (5) features .. -
Column 2: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 3: CKEDOE_20530 - CKEDOE_20565 (GCA_016699655_1_contig_1:4939137-4945147)
GCA_016699655_1_contig_1 .. 8 (4) features .. +
Column 4: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 5: IPPIHO_26055 - IPPIHO_26100 (Trico_TARA_53_54_bin11_contig_1960:1281-9840)
Trico_TARA_53_54_bin11_contig_1960 .. 10 (8) features .. -
Column 6: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 7: EMIHOD_26995 - EMIHOD_27045 (Trico_eryth_IMS101_contig_1:7635217-7645377)
Trico_eryth_IMS101_contig_1 .. 11 (9) features .. -
Column 8: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 9: FGJEKF_20585 - FGJEKF_20675 (GCF_030064895_1_contig_148:21942-44576)
GCF_030064895_1_contig_148 .. 19 (14) features .. +
Column 10: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 11: KHIANG_08930 - KHIANG_09030 (GCF_000169335_1_contig_128:9004-26837)
GCF_000169335_1_contig_128 .. 21 (13) features .. +
Column 12: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 13: GIKDOD_00495 - GIKDOD_00545 (GCA_010692645_1_contig_1:123761-132221)
GCA_010692645_1_contig_1 .. 11 (7) features .. -
Column 14: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 15: OJNMIJ_43510 - OJNMIJ_43565 (GCF_020829645_1_contig_283:19942-30078)
GCF_020829645_1_contig_283 .. 12 (9) features .. +
Column 16: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 17: JFEFEL_13480 - JFEFEL_13515 (GCF_018069895_1_contig_44:168396-175118)
GCF_018069895_1_contig_44 .. 8 (4) features .. +
Column 18: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 19: MGPMNC_02360 - MGPMNC_02400 (GCA_013822265_1_contig_7:31821-39590)
GCA_013822265_1_contig_7 .. 9 (6) features .. -
Column 20: KKMGOH_16465 - KKMGOH_16565 (K2b_bin90_contig_283:2758-22047)
K2b_bin90_contig_283 .. 21 (21) features .. +
Column 21: IJKLBM_02360 - IJKLBM_02405 (GCA_016235745_1_contig_36:54136-62021)
GCA_016235745_1_contig_36 .. 10 (7) features .. -
Traceback (most recent call last):
File "", line 198, in _run_module_as_main
File "", line 88, in _run_code
File "/home/syp/biosoft/jcvi/src/jcvi/graphics/synteny.py", line 736, in
main(sys.argv[1:])
File "/home/syp/biosoft/jcvi/src/jcvi/graphics/synteny.py", line 702, in main
Synteny(
File "/home/syp/biosoft/jcvi/src/jcvi/graphics/synteny.py", line 501, in init
lo[i],
~~^^^
IndexError: list index out of range
运行文件filtered_blocks.txt:
KKMGOH_16465 . KKMGOH_16465 . KKMGOH_16465 . KKMGOH_16465 . KKMGOH_16465 >
KKMGOH_16470 KDMLFL_00700 KKMGOH_16470 . KKMGOH_16470 . KKMGOH_16470 EMIHOD_27045 >
KKMGOH_16475 KDMLFL_00710 KKMGOH_16475 . KKMGOH_16475 IPPIHO_26100 KKMGOH_16475 EMIHOD_2>
KKMGOH_16480 KDMLFL_00695 KKMGOH_16480 CKEDOE_20530 KKMGOH_16480 IPPIHO_26095 KKMGOH_16480 >
KKMGOH_16485 . KKMGOH_16485 . KKMGOH_16485 . KKMGOH_16485 . KKMGOH_16485 >
KKMGOH_16490 KDMLFL_00685 KKMGOH_16490 CKEDOE_20540 KKMGOH_16490 IPPIHO_26085 KKMGOH_16490 >
KKMGOH_16495 . KKMGOH_16495 . KKMGOH_16495 . KKMGOH_16495 . KKMGOH_16495 >
KKMGOH_16500 . KKMGOH_16500 . KKMGOH_16500 . KKMGOH_16500 . KKMGOH_16500 >
KKMGOH_16505 . KKMGOH_16505 . KKMGOH_16505 . KKMGOH_16505 . KKMGOH_16505 >
KKMGOH_16510 . KKMGOH_16510 . KKMGOH_16510 IPPIHO_26065 KKMGOH_16510 EMIHOD_27005 >
KKMGOH_16515 KDMLFL_00710 KKMGOH_16515 . KKMGOH_16515 . KKMGOH_16515 . KKMGOH_1>
KKMGOH_16520 . KKMGOH_16520 . KKMGOH_16520 . KKMGOH_16520 . KKMGOH_16520 >
KKMGOH_16525 . KKMGOH_16525 . KKMGOH_16525 IPPIHO_26080 KKMGOH_16525 EMIHOD_27020 >
KKMGOH_16530 . KKMGOH_16530 . KKMGOH_16530 . KKMGOH_16530 . KKMGOH_16530 >
KKMGOH_16535 . KKMGOH_16535 . KKMGOH_16535 IPPIHO_26070 KKMGOH_16535 EMIHOD_27010

merged.bed:
K2b_bin90_contig_1 182 1928 KKMGOH_00005 0 -
K2b_bin90_contig_1 2094 3144 KKMGOH_00010 0 -
K2b_bin90_contig_1 3625 5533 KKMGOH_00015 0 +
K2b_bin90_contig_1 5670 7086 KKMGOH_00020 0 +
K2b_bin90_contig_1 7162 7345 KKMGOH_00025 0 +
K2b_bin90_contig_1 7362 8373 KKMGOH_00030 0 +
K2b_bin90_contig_1 8379 9381 KKMGOH_00035 0 +
K2b_bin90_contig_1 9442 10276 KKMGOH_00040 0 -
K2b_bin90_contig_1 10370 11108 KKMGOH_00045 0 -
K2b_bin90_contig_1 11168 11387 KKMGOH_00050 0 -
K2b_bin90_contig_1 11390 13682 KKMGOH_00055 0 -
K2b_bin90_contig_2 38 704 KKMGOH_00060 0 -
K2b_bin90_contig_2 723 1836 KKMGOH_00065 0 -
K2b_bin90_contig_2 1865 2912 KKMGOH_00070 0 -

layout.txt :

x, y, rotation, ha, va, color, ratio, label

0.5, 1, 0, left, center, #fc8d62, 1, K2b_bin90
0.5, 0.909091, 0, left, center, #fc8d62, 1, GCA_028533045_1
0.5, 0.818182, 0, left, center, #fc8d62, 1, GCA_016699655_1
0.5, 0.727273, 0, left, center, #fc8d62, 1, Trico_TARA_53_54_bin11
0.5, 0.636364, 0, left, center, #fc8d62, 1, Trico_eryth_IMS101
0.5, 0.545455, 0, left, center, #fc8d62, 1, GCF_030064895_1
0.5, 0.454545, 0, left, center, #fc8d62, 1, GCF_000169335_1
0.5, 0.363636, 0, left, center, #fc8d62, 1, GCA_010692645_1
0.5, 0.272727, 0, left, center, #fc8d62, 1, GCF_020829645_1
0.5, 0.181818, 0, left, center, #fc8d62, 1, GCF_018069895_1
0.5, 0.0909091, 0, left, center, #fc8d62, 1, GCA_013822265_1
0.5, 0, 0, left, center, #fc8d62, 1, GCA_016235745_1

edges

e, 0, 1
e, 1, 2
e, 2, 3
e, 3, 4
e, 4, 5
e, 5, 6
e, 6, 7
e, 7, 8
e, 8, 9
e, 9, 10
e, 10, 11
@tanghaibao
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filtered_blocks.txt有22列，但是layout.txt里只规划了12条track。
多出来的那些列，JCVI不知道怎么画，所以报错。要保证列数相等。

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