Commit 1e99f76f authored by Olivier Rue's avatar Olivier Rue
Browse files

curation real its1 complete

parent f1ec2546
Pipeline #42624 passed with stage
in 14 seconds
......@@ -127,6 +127,35 @@ scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABA
#scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/multiaff.tsv REAL_MEAT/RPB2_multiaff.tsv
```
```{bash}
### GET DATA FROM GENOTOUL
scp orue@genotoul.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/affiliation.biom .
scp orue@genotoul.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/REAL/results/DADA2_FROGS/RPB2/filters.fasta .
##########################
otu_filters.py --input-biom affiliation.biom --input-fasta filters.fasta --contaminant /db/frogs_databanks/assignation/Unite_Fungi_8.2_20200204/Unite_Fungi_8.2_20200204.fasta --output-biom 1.biom --output-fasta 1.fasta --nb-cpus 4
otu_filters.py --input-biom 1.biom --input-fasta 1.fasta --contaminant /db/frogs_databanks/assignation/SILVA_132_LSU/SILVA_132_LSU.fasta --nb-cpus 4 --output-biom 2.biom --output-fasta 2.fasta
otu_filters.py --input-biom 2.biom --input-fasta 2.fasta --contaminant /db/frogs_databanks/assignation/silva_138_SSU/silva_138_SSU.fasta --nb-cpus 4 --output-biom 3.biom --output-fasta 3.fasta
otu_filters.py --input-biom 3.biom --input-fasta 3.fasta --contaminant /db/frogs_databanks/assignation/Unite_Euka_8.2_20200204/Unite_Euka_8.2_20200204.fasta --output-biom 4.biom --output-fasta 4.fasta --nb-cpus 4
biom_to_tsv.py --input-biom 4.biom --output-tsv 4.tsv
head -n 1 4.tsv > 4-2.tsv
sed "s/no data/NA;NA;NA;NA;NA;NA;NA/" 4.tsv |sed "s/no data/0/g" | grep 'FROGS_combined' >> 4-2.tsv
tsv_to_biom.py --input-tsv 4-2.tsv --output-biom 4-2.biom
affiliation_filters.py --input-fasta 4.fasta --input-biom 4-2.biom --min-blast-identity 0.1 --delete
biom_to_tsv.py --input-biom affiliation-filtered.biom --output-tsv affiliation-filtered.tsv
affiliation_OTU.py --input-fasta affiliation-filtered.fasta --input-biom affiliation-filtered.biom --nb-cpus 8 --output-biom affiliation.biom --summary affiliation.html --reference D1D2.fasta
biom_to_tsv.py --input-biom affiliation.biom --output-tsv affiliation.tsv
head -n 1 4.tsv > final.tsv
awk -F'\t' '{ if ($4 < 80 && $5 > 95 && length($8 > 400)) { print } }' affiliation.tsv >> final.tsv
awk -F'\t' '{print $8}' <(grep -v "^#" final.tsv) > to_keep.lst
head -n 1 4.tsv > affiliation-filtered-final.tsv
grep -f to_keep.lst affiliation-filtered.tsv >> affiliation-filtered-final.tsv
```
## Analysis of raw BIOM files
```{r, eval=T}
......@@ -250,10 +279,11 @@ scp orue@genologin.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABA
```{bash}
### GET DATA FROM GENOTOUL
scp orue@genotoul.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/filters.[bf]* .
scp orue@genotoul.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/affiliation.biom .
scp orue@genotoul.toulouse.inra.fr:/work/frogsfungi/FungiPubli/Real_mock/METABARFOOD/CHEESE_REAL/results/DADA2_FROGS/RPB2/filters.fasta .
##########################
otu_filters.py --input-biom filters.biom --input-fasta filters.fasta --contaminant /db/frogs_databanks/assignation/Unite_Fungi_8.2_20200204/Unite_Fungi_8.2_20200204.fasta --output-biom 1.biom --output-fasta 1.fasta --nb-cpus 4
otu_filters.py --input-biom affiliation.biom --input-fasta filters.fasta --contaminant /db/frogs_databanks/assignation/Unite_Fungi_8.2_20200204/Unite_Fungi_8.2_20200204.fasta --output-biom 1.biom --output-fasta 1.fasta --nb-cpus 4
otu_filters.py --input-biom 1.biom --input-fasta 1.fasta --contaminant /db/frogs_databanks/assignation/SILVA_132_LSU/SILVA_132_LSU.fasta --nb-cpus 4 --output-biom 2.biom --output-fasta 2.fasta
otu_filters.py --input-biom 2.biom --input-fasta 2.fasta --contaminant /db/frogs_databanks/assignation/silva_138_SSU/silva_138_SSU.fasta --nb-cpus 4 --output-biom 3.biom --output-fasta 3.fasta
otu_filters.py --input-biom 3.biom --input-fasta 3.fasta --contaminant /db/frogs_databanks/assignation/Unite_Euka_8.2_20200204/Unite_Euka_8.2_20200204.fasta --output-biom 4.biom --output-fasta 4.fasta --nb-cpus 4
......@@ -264,11 +294,14 @@ tsv_to_biom.py --input-tsv 4-2.tsv --output-biom 4-2.biom
affiliation_filters.py --input-fasta 4.fasta --input-biom 4-2.biom --min-blast-identity 0.1 --delete
biom_to_tsv.py --input-biom affiliation-filtered.biom --output-tsv affiliation-filtered.tsv
affiliation_OTU.py --input-fasta affiliation-filtered.fasta --input-biom affiliation-filtered.biom --nb-cpus 8 --output-biom affiliation.biom --summary affiliation.html --reference D1D2.fasta
biom_to_tsv.py --input-biom affiliation.biom --output-tsv affiliation.tsv
head -n 1 4.tsv > final.tsv
awk -F'\t' '{ if ($4 < 80 && $5 > 95 && length($8 > 400)) { print } }' affiliation.tsv >> final.tsv
awk -F'\t' '{print $8}' <(grep -v "^#" final.tsv) > to_keep.lst
head -n 1 4.tsv > affiliation-filtered-final.tsv
grep -f to_keep.lst affiliation-filtered.tsv >> affiliation-filtered-final.tsv
```
......
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