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Error when dot (.) exist in filename #3

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Error when dot (.) exist in filename#3

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@atiweb
atiweb
opened on Jan 17, 2020

Im using phyloma in 20 genomes, some of them have a dot in filename, example:
pythium_insidiosum_CBS_573.85
When running busco command, the following error, rise up:
[Jan 17 12:08 AM] Loading 20 species for analysis
[Jan 17 12:14 AM] Running iterative BUSCO analysis each proteome
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_Pi-s.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_Pi-s -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_aphanidermatum_DAOM_BR444.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_aphanidermatum_DAOM_BR444 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_irregulare_DAOM_BR486.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_irregulare_DAOM_BR486 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
phytophthora_sojae_P6497.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
phytophthora_sojae_P6497 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_iwayamai_DAOM_BR242034.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_iwayamai_DAOM_BR242034 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
globisporangium_ultimum_DAOM_BR144.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
globisporangium_ultimum_DAOM_BR144 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_CR02.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_CR02 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_oligandrum_ATCC_38472_TT.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_oligandrum_ATCC_38472_TT -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
phytopythium_vexans_HF1.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
phytopythium_vexans_HF1 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_CBS_573.85.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_CBS_573 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_arrhenomanes_ATCC_12531.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_arrhenomanes_ATCC_12531 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_guiyangense_Su.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_guiyangense_Su -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_CDC_B5653.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_CDC_B5653 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_periplocum_CBS_532.74.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_periplocum_CBS_532 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_oligandrum_Po37.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_oligandrum_Po37 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_MCC_13.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_MCC_13 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
phytopythium_vexans_DAOM_BR484.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
phytopythium_vexans_DAOM_BR484 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_irregulare_CBS_494.86.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_irregulare_CBS_494 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_oligandrum_CBS_530.74.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_oligandrum_CBS_530 -c 15
CMD: /mnt/sdb/funannotate/busco-2.0.1/BUSCO.py -i
pythium_insidiosum_MTPI_04.prots.fa -m proteins -f -l
/mnt/sdb/funannotate/busco-2.0.1/lineages/fungi_odb9 -o
pythium_insidiosum_MTPI_04 -c 15
[Jan 17 12:17 AM] Parsing BUSCO results, determining shared orthologs across all genomes
BUSCO2 Results:

222 BUSCOs found in pythium_insidiosum_Pi-s
257 BUSCOs found in pythium_aphanidermatum_DAOM_BR444
231 BUSCOs found in pythium_irregulare_DAOM_BR486
264 BUSCOs found in phytophthora_sojae_P6497
239 BUSCOs found in pythium_iwayamai_DAOM_BR242034
262 BUSCOs found in globisporangium_ultimum_DAOM_BR144
174 BUSCOs found in pythium_insidiosum_CR02
268 BUSCOs found in pythium_oligandrum_ATCC_38472_TT
264 BUSCOs found in phytopythium_vexans_HF1
219 BUSCOs found in pythium_insidiosum_CBS_573.85
Traceback (most recent call last):
File "/mnt/sdb/funannotate/phyloma/bin/busco4phylogeny.py", line 283, in
with open(os.path.join(tmpdir, 'run_'+SpeciesName, SpeciesName+'.buscos.prots.fa'), 'w') as speciesout:
IOError: [Errno 2] No such file or directory: 'phylomaBUSCO_5432/run_pythium_insidiosum_CBS_573.85/pythium_insidiosum_CBS_573.85.buscos.prots.fa'

What is happening is that in busco4phylogeny.py, line 227 is:
name = os.path.basename(x).split('.',-1)[0]
I replace that line by:
name = os.path.basename(x).rsplit('.', 2)[0]

as you do in line 277 of the same file, and the issue was solved.

it may be useful to you this, or may be you have a better solution to solve this.

In other matter, is already out busco4, is posible tu update this to use busco4?
Thanks

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