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61 eukaryotic evaluation has completeness and contamination as strings #62

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merged 5 commits into from
Nov 18, 2024
Merged

61 eukaryotic evaluation has completeness and contamination as strings #62

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274f2f8
add .gitignore
mbthornton-lbl Nov 18, 2024
a65b9ae
update parse_eucc
mbthornton-lbl Nov 18, 2024
198dcad
cast as floats
mbthornton-lbl Nov 18, 2024
79d7aac
increment version.txt
mbthornton-lbl Nov 18, 2024
3ef4994
update docker image and sha256 hash
Nov 18, 2024
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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
.idea/
2 changes: 1 addition & 1 deletion Docker/Dockerfile
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Expand Up @@ -2,7 +2,7 @@ FROM doejgi/mbin:v1.0.1
## python 3.9.12

LABEL maintainer="[email protected]"
LABEL version="1.0.3"
LABEL version="1.0.4"
LABEL software="NMDC_MAG_Pipeline"
LABEL tags="bioinformatics"

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8 changes: 4 additions & 4 deletions Docker/mbin_stats.py
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Expand Up @@ -76,17 +76,17 @@ def parse_eukcc(file, bin_list):
if 'completeness' not in line:
content = line.rstrip().split("\t")
binname = content[0].replace('.fa','')
eukcc[binname]['completeness'] = content[1]
eukcc[binname]['contamination'] = content[2]
eukcc[binname]['completeness'] = float(content[1])
eukcc[binname]['contamination'] = float(content[2])
eukcc[binname]['ncbi_lineage_tax_ids'] = content[3]
eukcc[binname]['ncbi_lineage'] = content[4]

for bin in bin_list:
if bin['bin_name'] in eukcc:
if 'eukaryotic_evaluation' not in bin:
bin['eukaryotic_evaluation']= dict()
bin['eukaryotic_evaluation']['completeness'] = eukcc[bin['bin_name']]['completeness']
bin['eukaryotic_evaluation']['contamination'] = eukcc[bin['bin_name']]['contamination']
bin['eukaryotic_evaluation']['completeness'] = float(eukcc[bin['bin_name']]['completeness'])
bin['eukaryotic_evaluation']['contamination'] = float(eukcc[bin['bin_name']]['contamination'])
bin['eukaryotic_evaluation']['ncbi_lineage_tax_ids'] = eukcc[bin['bin_name']]['ncbi_lineage_tax_ids']
bin['eukaryotic_evaluation']['ncbi_lineage'] = eukcc[bin['bin_name']]['ncbi_lineage']
update_bin_list.append(bin)
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2 changes: 1 addition & 1 deletion mbin_nmdc.wdl
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Expand Up @@ -24,7 +24,7 @@ workflow nmdc_mags {
String checkm_db="/refdata/checkM_DB/checkm_data_2015_01_16"
String eukcc2_db="/refdata/EUKCC2_DB/eukcc2_db_ver_1.2"
String package_container = "microbiomedata/nmdc_mbin_vis:0.7.0"
String container = "microbiomedata/nmdc_mbin@sha256:49e218e9de783d3f307740dd02c9e0213bfaff0b8095abc89eb111a962388430"
String container = "microbiomedata/nmdc_mbin@sha256:2d9d79740eef27b2959d00c34fa5816ff911ec7c4dc80fedb110ab170ce0b868"
}
call stage {
input:
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2 changes: 1 addition & 1 deletion version.txt
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@@ -1 +1 @@
v1.3.11
v1.3.12
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