70 lines
2.7 KiB
Bash
Executable file
70 lines
2.7 KiB
Bash
Executable file
#!/bin/bash
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set -e
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# Metadata files edited:
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# rpob: remove positions above 1151
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# embb: remove positions above 1054
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#=======================================================================
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#https://www.biostars.org/p/336891/
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#python Mutate.py -v -o /path/to/output.fasta mutation_map_file.csv input.fasta
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#=======================================================================
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DATA_DIR="/home/tanu/git/Data"
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echo "Processing Mutation Files"
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echo "-------------------------"
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echo
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while read -r gene drug; do
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echo "vvvvvvvvvvvvvvvvvvvvv"
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echo "gene: $gene drug: $drug";
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echo "Source File: ${DATA_DIR}/${drug}/output/${gene}_metadata.csv"
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MSA_MAP=${DATA_DIR}/${drug}/output/${gene}_msa_map.csv
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wc -l ${DATA_DIR}/${drug}/output/${gene}_metadata.csv
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cat ${DATA_DIR}/${drug}/output/${gene}_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | uniq -c > ${DATA_DIR}/${drug}/output/${gene}_metadata_mut_count.csv
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cat ${DATA_DIR}/${drug}/output/${gene}_metadata.csv | rev| cut -d, -f1 |rev | tail -n +2 |sort | sed -e 's/"//g' > $MSA_MAP
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echo "Output to: $MSA_MAP"
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sed -i "s/^/${gene},/" $MSA_MAP
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wc -l $MSA_MAP
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echo "^^^^^^^^^^^^^^^^^^^^^"
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echo
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echo "Running mutate.py on data file $MSA_MAP"
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python3 mutate.py -v -o ${DATA_DIR}/${drug}/output/${gene}_msa_interim.csv $MSA_MAP $DATA_DIR/${drug}/input/${gene}_f2.fasta
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echo "mutate.py completed"
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sed -E 's/>.*//g;/^$/d' ${DATA_DIR}/${drug}/output/${gene}_msa_interim.csv > ${DATA_DIR}/${drug}/output/${gene}_msa.csv
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wc -l ${DATA_DIR}/${drug}/output/${gene}_msa.csv
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echo
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done < gene_targets_names.txt
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# Stop here so we don't run the examples below :)
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exit
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########################################################################
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#
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########################################################################
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# make sure there is no new line at the end of the mutation file (snps.csv)
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# check
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cat output/gid_metadata.csv | rev | cut -d, -f1 |rev | tail -n +2 |sort | head
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cat output/gid_metadata.csv | rev | cut -d, -f1 |rev | tail -n +2 |sort | uniq -c > output/gid_metadata_mut_count.csv
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cat output/gid_metadata.csv | rev | cut -d, -f1 |rev | tail -n +2 |sort > gid_msa_snp.csv
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sed -i 's/^/gid,/' gid_msa_snp.csv
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#cp gid_msa_snp.csv gid_mut_map.csv
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#%%
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# Date: 16/01/22
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# pre processing
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sed 's/"//g' gene_msa_snp.csv > gid_mut_map.csv
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# mut prefix for mutation map file MUST match fasta file header
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python3 mutate.py -v -o /home/tanu/git/Data/streptomycin/output/TEST2.csv /home/tanu/git/Data/streptomycin/output/gid_mut_map.csv /home/tanu/git/Data/streptomycin/input/gid2.fasta
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wc -l TEST2.csv
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# post processing
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sed -E 's/>.*//g' TEST2.csv | sed '/^$/d' > TEST3.csv
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wc -l TEST3.csv
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#==============================================
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