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genotoul-bioinfo
metagWGS
Commits
6b2f2dda
Commit
6b2f2dda
authored
Dec 16, 2021
by
Jean Mainguy
Browse files
add sort to faciliate functional testing.
parent
0ff60cf3
Changes
1
Hide whitespace changes
Inline
Side-by-side
bin/aln2taxaffi.py
View file @
6b2f2dda
...
...
@@ -511,10 +511,10 @@ def main():
accessions_unfound_in_mapping_prot
=
accessions_unfound_in_mapping
&
hit_accessions
if
acessions_with_unfound_taxid_prot
:
outdisc
.
write
(
f
"
{
protein_id
}
\t
No taxid in taxdump
\t
{
','
.
join
(
acessions_with_unfound_taxid_prot
)
}
\n
"
)
outdisc
.
write
(
f
"
{
protein_id
}
\t
No taxid in taxdump
\t
{
','
.
join
(
sorted
(
acessions_with_unfound_taxid_prot
)
)
}
\n
"
)
if
accessions_unfound_in_mapping_prot
:
outdisc
.
write
(
f
"
{
protein_id
}
\t
No protid correspondance file
\t
{
','
.
join
(
accessions_unfound_in_mapping_prot
)
}
\n
"
)
outdisc
.
write
(
f
"
{
protein_id
}
\t
No protid correspondance file
\t
{
','
.
join
(
sorted
(
accessions_unfound_in_mapping_prot
)
)
}
\n
"
)
consensual_contig_taxid
=
get_taxid_consensus
(
contig_collate_hits
,
main_ranks
)
count_rank_affiliation_contig
[
taxid2rank
[
consensual_contig_taxid
]]
+=
1
...
...
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