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Introduced handling of Influenza-C in IRMA template and small fixes in viralrecon and exometrio #177

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merged 11 commits into from
Jan 16, 2024
Merged

Introduced handling of Influenza-C in IRMA template and small fixes in viralrecon and exometrio #177

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ef1df07
removed unnecessary line
Shettland Jan 10, 2024
a4c59c6
commented PASS_ONLY line parameter
Shettland Jan 10, 2024
032e34e
small changes in viralrecon_results script
Shettland Jan 10, 2024
fc0810f
introduced better error handling in excel_generator, now it can also …
Shettland Jan 10, 2024
e3a4be1
symbolic link for flu-C
Shettland Jan 10, 2024
f67bc19
introduced handling of flu-C in 04-irma lablog
Shettland Jan 10, 2024
7b58f45
introduced handling of flu-C in create_irma_stats.sh
Shettland Jan 10, 2024
379d912
New implementations in excel_generator.py
Shettland Jan 16, 2024
ed6beba
Changed blast symlink in viralrecon_results
Shettland Jan 16, 2024
eb8c72d
Implementations in excel_generator.py and error handling
Shettland Jan 16, 2024
75736de
No more blast folder in viralrecon_results
Shettland Jan 16, 2024
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4 changes: 2 additions & 2 deletions bu_isciii/templates/viralrecon/RESULTS/excel_generator.py
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Expand Up @@ -99,12 +99,12 @@ def excel_generator(csv_files: List[str]):
# workbook = openpyxl.Workbook(output_name)
if "nextclade" in str(file):
table = pd.read_csv(file, sep=";", header=0)
elif "illumina" in str(file) or ".tsv" in str(file):
elif "illumina" in str(file):
table = pd.read_csv(file, sep="\t", header=0)
table["analysis_date"] = pd.to_datetime(
table["analysis_date"].astype(str), format="%Y%m%d"
)
elif "assembly" in str(file):
elif "assembly" in str(file) or "tsv" in str(file) or "tab" in str(file):
table = pd.read_csv(file, sep="\t", header=0)
else:
try:
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2 changes: 1 addition & 1 deletion bu_isciii/templates/viralrecon/RESULTS/viralrecon_results
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Expand Up @@ -46,4 +46,4 @@ cd mapping_consensus; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; d
cd variants_annot; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/variants/ivar/snpeff/${arr[0]}.snpsift.txt ./${arr[0]}_${arr[1]}.snpsift.txt; done; cd -
cd assembly_spades; rsync -rlv ../../../ANALYSIS/*/*/assembly/spades/rnaviral/*.scaffolds.fa.gz .; gunzip *.scaffolds.fa.gz; cd -
cd abacas_assembly; cat ../../../ANALYSIS/*/samples_ref.txt | while read in; do arr=($in); ln -s ../../../ANALYSIS/*/*${arr[1]}*/assembly/spades/rnaviral/abacas/${arr[0]}.abacas.fasta ./${arr[0]}_${arr[1]}.abacas.fasta; done; cd -
cd blast; ln -s ../../../ANALYSIS/*/*.blast.filt.header.xlsx .; cd -
cd blast; ln -s ../../../ANALYSIS/*/all_samples_filtered_BLAST_results.xlsx . ; cd -
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Maybe for just one excel there is no need to create a blast folder, maybe you can put it on the main results folder?

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Ok!

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