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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,109 @@ | ||
| #!/bin/bash | ||
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| ############################################################ | ||
| # For Referee, 09.19 | ||
| # Takes a sorted BAM file and runs through the steps to | ||
| # split and run mpileup on the file. | ||
| ############################################################ | ||
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| display_usage() { | ||
| # Usage message for -h | ||
| echo "Usage:" | ||
| echo | ||
| echo "tab_split.sh -f <A bgzipped pileup or ANGSD output file> -r <1> -h" | ||
| echo | ||
| echo "Options:" | ||
| echo "-i: (required) A bgzipped, tab delimited file with scaffold in column 1 and position in column 2. Both pileup and ANGSD output files fit these criteria." | ||
| echo "-r: The number of processors to use. If > 1, GNU Parallel (https://www.gnu.org/software/parallel/) is required. Default: 1." | ||
| echo "-h: Display this help message." | ||
| echo | ||
| echo "Dependencies:" | ||
| echo "01: tabix (required; https://sourceforge.net/projects/samtools/files/tabix/)" | ||
| echo "02: GNU parallel (required for multiprocessing; https://www.gnu.org/software/parallel/)" | ||
| echo | ||
| echo "This script will create the following directories and files:" | ||
| echo "01: tabsplit-scaffold-list.txt -> A list of scaffolds in the input file." | ||
| echo "02: tabsplit/ -> A directory to which the split files will be written." | ||
| echo "03: referee-input.txt -> This file file will have the paths to the split files for Referee's -i flag." | ||
| echo "===========================================================================" | ||
| exit 0 | ||
| } | ||
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| ########## | ||
| # Invalid input option message | ||
| invalid_opt() { | ||
| echo "Error 1: Invalid option: $1" | ||
| echo "===========================================================================" | ||
| exit 1 | ||
| } | ||
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| ########## | ||
| # Invalid run mode message | ||
| invalid_file(){ | ||
| echo "Error 2: A pileup or ANGSD output file must be provided (-i)" | ||
| echo "===========================================================================" | ||
| exit 1 | ||
| } | ||
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| ############################################################ | ||
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| echo | ||
| echo "===========================================================================" | ||
| echo " Workflow script to split a tabbed pileup or ANGSD output file for Referee" | ||
| echo | ||
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| input=false | ||
| scafffile="tabsplit-scaffold-list.txt" | ||
| procs=1 | ||
| # Defaults | ||
|
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| while getopts ":i:r:h" arg; do | ||
| case $arg in | ||
| h) display_usage;; | ||
| i) input=$OPTARG;; | ||
| r) procs=$OPTARG;; | ||
| \?) invalid_opt $OPTARG ;; | ||
| esac | ||
| done | ||
| # Parse input options | ||
|
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| if [ "$input" == false ]; then | ||
| invalid_file | ||
| fi | ||
| # Check to make sure a file has been provided. | ||
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| echo | ||
| echo "STEP 01: INDEXING INPUT FILE" | ||
| tabix -s 1 -b 2 -e 2 $input | ||
| # Index the input file | ||
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| echo "STEP 02: GETTING LIST OF ALL SCAFFOLDS IN INPUT TAB FILE: tabsplit-scaffold-list.txt" | ||
| tabix -l $input | grep -v "*" > $scafffile | ||
| # Get a list of all scaffolds in the BAM file | ||
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| echo "STEP 03: SPLITTING INPUT FILE" | ||
| mkdir "tabsplit" | ||
| if [ $procs == 1 ]; then | ||
| while read scaff; do | ||
| echo "SPLIT: " $scaff | ||
| tabix -s 1 -b 2 -e 2 $input $scaff > tabsplit/$scaff.tab | ||
| done < "$scafffile" | ||
| # Serial | ||
| else | ||
| echo | ||
| echo "SPLITTING INPUT FILE WITH GNU PARALLEL" | ||
| echo | ||
| cat $scafffile | parallel --progress --eta -j $procs "tabix -s 1 -b 2 -e 2 $input {.} > tabsplit/{.}.tab" | ||
| fi | ||
| # Parallel | ||
| # Split the input file | ||
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| echo "-> GENERATING referee-input.txt" | ||
| ls -d -1 "$PWD/tabsplit/"*.tab > referee-input.txt | ||
| # Create the referee input file. | ||
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| echo | ||
| echo "DONE! Please confirm that all your output files were created successfully." | ||
| echo "You can now use referee-input.txt as your -i input to Referee." | ||
| echo "===========================================================================" | ||
| echo |