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Fix generation of dict_proteinId_assemblyIds for Entrez download #3

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merged 5 commits into from
Jan 27, 2022
Merged

Fix generation of dict_proteinId_assemblyIds for Entrez download #3

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f5a339d
Fix generation of dict_proteinId_assemblyIds for download
skrakau Dec 23, 2021
cdb275c
Update CHANGELOG
skrakau Dec 23, 2021
46d7a3e
Update CHANGELOG.md
AntoniaSchuster Jan 10, 2022
181eec2
Merge branch 'dev' into fix_protein_entities
AntoniaSchuster Jan 26, 2022
725cff4
Update CHANGELOG.md
AntoniaSchuster Jan 27, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -28,6 +28,7 @@ Initial release of nf-core/metapep, created with the [nf-core](https://nf-co.re/

- [#41](https://github.com/skrakau/metapep/pull/41) - Allow `assembly` input without weights
- [#53](https://github.com/skrakau/metapep/pull/53) - Add buffering of predictions and chunk-wise merging to avoid sbatch error due to too many input files [#52](https://github.com/skrakau/metapep/issues/52)
- [#3](https://github.com/nf-core/metapep/pull/3) - Fix generation of `entities_proteins.entrez.tsv` for Entrez download

### `Dependencies`

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9 changes: 2 additions & 7 deletions bin/download_proteins_entrez.py
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Expand Up @@ -204,18 +204,13 @@ def main(args=None):
sys.exit("Entrez elink download failed!")

### for each nucleotide sequence get list of protein ids
dict_proteinId_assemblyIds = {}
dict_proteinId_assemblyIds = defaultdict(lambda : set())
for nucleotide_record in protein_results:
seqId = nucleotide_record["IdList"][0]
assemblyIds = dict_seqId_assemblyIds[seqId]
if len(nucleotide_record["LinkSetDb"]) > 0:
for protein_record in nucleotide_record["LinkSetDb"][0]["Link"]:
if protein_record["Id"] not in dict_proteinId_assemblyIds:
dict_proteinId_assemblyIds[protein_record["Id"]] = assemblyIds
else:
for i in assemblyIds:
if i not in dict_proteinId_assemblyIds[protein_record["Id"]]:
dict_proteinId_assemblyIds[protein_record["Id"]].append(i)
dict_proteinId_assemblyIds[protein_record["Id"]].update(assemblyIds)

# NOTE:
# some proteins, such as 487413233, occur within multiple sequences of the assembly!
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