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Added new isON_pipeline.sh script and already updated isONform version
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aljpetri
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Jan 24, 2024
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,186 @@ | ||
| #!/bin/bash | ||
| set -e | ||
| #the pipeline can be run in different modes: | ||
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| ####ONT data | ||
| # ont_with_pychopper: the full pipeline is run in addition to pychopper (pychopper, isONclust,isONcorrect,isONform) | ||
| # ont_no_pychopper: only the isONpipeline is run without pychopper (isONclust,isONcorrect, isONform) | ||
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| ####PACBIO data | ||
| # pacbio: for PacBio data runs isONclust and isONform | ||
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| ###### test modes (only for internal use) | ||
| # analysis: analysis of ont data: isONclust,isONcorrect and isONform are run (e.g. analyses on the paper) | ||
| # only_isonform: only isONform is run | ||
| #!/bin/bash | ||
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| programname=$0 | ||
| function usage { | ||
| echo "" | ||
| echo "Runs the full isON pipeline. Please make sure that the input file has been preprocessed with pychopper for ONT data " | ||
| echo "" | ||
| echo "usage: $programname --raw_reads string --outfolder string --num_cores integer --isONform_folder string --iso_abundance integer --mode string" | ||
| echo "" | ||
| echo " --raw_reads absolute path to the input file (in fastq format)" | ||
| echo " (example: /home/user/Rawdata/raw_reads.fq)" | ||
| echo " --outfolder absolute path to the output folder (the folder in which all outputs are stored)" | ||
| echo " (example: /home/user/analysis_output)" | ||
| echo " --num_cores the number of processors the pipeline may use" | ||
| echo " (example: 8)" | ||
| echo " --isONform_folder the absolute path to the isONform installation on your machine (leave empty if you have installed isONform via pip)" | ||
| echo " (example: /home/user/isONform )" | ||
| echo " --iso_abundance threshold which denotes the minimum read support neccessary for an isoform to be called (also minimum number of reads per cluster in isONclust)" | ||
| echo " (example: 5)" | ||
| echo " --mode Run mode of the pipeline, possible modes are 'ont_no_pyc' and 'ont_with_pc' for ont data and 'pacbio' for pacbio data" | ||
| echo " (example: ont_no_pychopper/ont_with_pychopper/pacbio)" | ||
| echo " For ONT data: use 'ont_no_pychopper' if you want to run the isON pipeline and pychopper, use 'ont_with_pychopper' if you only want to run the isON pipeline. Please run pychopper yourself before running the pipeline." | ||
| echo "" | ||
| } | ||
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| while [ $# -gt 0 ]; do | ||
| # Check if the current argument is "--help" | ||
| if [[ $1 == "--help" ]]; then | ||
| # Call the usage function and exit with status code 0 | ||
| usage | ||
| exit 0 | ||
| # Check if the current argument is an option starting with "--" | ||
| elif [[ $1 == "--"* ]]; then | ||
| # Extract the option name by removing the leading dashes | ||
| v="${1/--/}" | ||
| # Check if the argument for this option was left empty (then we would have the next argument name as next entry) | ||
| if [[ $2 == "--"* ]]; then | ||
| # The argument was left empty therefore we leave the argument for the option empty | ||
| declare "$v"='' | ||
| else | ||
| #The argument was not left empty, therefore we properly set the argument as the value for option | ||
| declare "$v"="$2" | ||
| #We have to shift only in this case | ||
| shift | ||
| fi | ||
| fi | ||
| #This is the shift we have to perform each time | ||
| shift | ||
| done | ||
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| if [[ -z $raw_reads ]]; then | ||
| usage | ||
| die "Missing parameter --raw_reads" | ||
| elif [[ -z $outfolder ]]; then | ||
| usage | ||
| die "Missing parameter --outfolder" | ||
| elif [[ -z $mode ]]; then | ||
| usage | ||
| die "Missing parameter --mode" | ||
| #elif [[ -z $isONform_folder ]]; then | ||
| # isONform_folder='' | ||
| #TODO set isONform folder to '' if not given | ||
| fi | ||
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| echo "Running `basename $0` raw reads: '$raw_reads' outfolder: '$outfolder' num_cores: '$num_cores' isONform_folder:'$isONform_folder' iso_abundance: '$iso_abundance' mode: '$mode'" | ||
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| mkdir -p $outfolder | ||
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| if [ $mode == "ont_with_pychopper" ] | ||
| then | ||
| echo | ||
| echo "Will run pychopper (cdna_classifier.py), isONclust, isONcorrect and isONform. Make sure you have these tools installed." | ||
| echo "For installation see: https://github.com/ksahlin/isONcorrect#installation and https://github.com/aljpetri/isONform" | ||
| echo | ||
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| echo | ||
| echo "Running pychopper" | ||
| echo | ||
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| pychopper $raw_reads $outfolder/full_length.fq -t $num_cores | ||
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| echo | ||
| echo "Finished pychopper" | ||
| echo | ||
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| fi | ||
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| if [ $mode != "only_isonform" ] # this if statement prevents isONclust and isONcorrect from being run | ||
| then | ||
| echo | ||
| echo "Running isONclust" | ||
| echo | ||
| if [ $mode == "ont_with_pychopper" ] | ||
| then | ||
| /usr/bin/time -v isONclust --t $num_cores --ont --fastq $outfolder/full_length.fq \ | ||
| --outfolder $outfolder/clustering | ||
| /usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \ | ||
| --fastq $outfolder/full_length.fq --outfolder $outfolder/clustering/fastq_files | ||
| elif [ $mode == "ont_no_pychopper" ] | ||
| then | ||
| /usr/bin/time -v isONclust --t $num_cores --ont --fastq $raw_reads \ | ||
| --outfolder $outfolder/clustering | ||
| /usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \ | ||
| --fastq $raw_reads --outfolder $outfolder/clustering/fastq_files | ||
| elif [ $mode == "pacbio" ] | ||
| then | ||
| /usr/bin/time -v isONclust --t $num_cores --isoseq --fastq $raw_reads \ | ||
| --outfolder $outfolder/clustering | ||
| /usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \ | ||
| --fastq $raw_reads --outfolder $outfolder/clustering/fastq_files | ||
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| else #[ $mode != "pacbio" ] && [ $mode != "'ont'" ] | ||
| /usr/bin/time -v isONclust --t $num_cores --fastq $raw_reads \ | ||
| --outfolder $outfolder/clustering | ||
| /usr/bin/time -v isONclust write_fastq --N $iso_abundance --clusters $outfolder/clustering/final_clusters.tsv \ | ||
| --fastq $raw_reads --outfolder $outfolder/clustering/fastq_files | ||
| #This is the pacbio mode | ||
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| fi | ||
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| echo | ||
| echo "Finished isONclust" | ||
| echo | ||
| #conda activate isON311 | ||
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| if [ $mode != "pacbio" ] | ||
| then | ||
| echo | ||
| echo "Running isONcorrect" | ||
| echo | ||
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| /usr/bin/time -v python3.11 run_isoncorrect --t $num_cores --fastq_folder $outfolder/clustering/fastq_files --outfolder $outfolder/correction/ | ||
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| echo | ||
| echo "Finished isONcorrect" | ||
| echo | ||
| fi | ||
| fi | ||
| echo | ||
| echo "Merging reads back to single file. Corrected reads per cluster are still stored in: " $outfolder/correction/ | ||
| echo | ||
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| echo | ||
| echo "Running isONform" | ||
| echo | ||
| if [ -n "$isONform_folder" ] #the user has given a path to isONform (cloned from github) | ||
| then | ||
| if [ $mode != "pacbio" ] #i.e. we run in ONT mode | ||
| then | ||
| /usr/bin/time -v $isONform_folder/isONform_parallel --t $num_cores --fastq_folder $outfolder/correction/ --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches --delta_iso_len_3 30 --delta_iso_len_5 50 | ||
| else #we run isONform in pacbio mode (adding the keyword clustered to the command) | ||
| /usr/bin/time -v $isONform_folder/isONform_parallel --t $num_cores --fastq_folder $outfolder/clustering/fastq_files --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches --delta_iso_len_3 30 --delta_iso_len_5 50 --clustered | ||
| fi | ||
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| else #the user has not given a path to isONform (pip installation | ||
| if [ $mode != "pacbio" ] #i.e. we run in ONT mode | ||
| then | ||
| /usr/bin/time -v isONform_parallel --t $num_cores --fastq_folder $outfolder/correction/ --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches --delta_iso_len_3 30 --delta_iso_len_5 50 | ||
| else #we run isONform in pacbio mode (adding the keyword clustered to the command) | ||
| /usr/bin/time -v isONform_parallel --t $num_cores --fastq_folder $outfolder/clustering/fastq_files --exact_instance_limit 50 --k 20 --w 31 --xmin 14 --xmax 80 --max_seqs_to_spoa 200 --delta_len 10 --outfolder $outfolder/isoforms --iso_abundance $iso_abundance --split_wrt_batches --delta_iso_len_3 30 --delta_iso_len_5 50 --clustered | ||
| fi | ||
| fi | ||
| echo | ||
| echo "Finished isONform" | ||
| echo | ||
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| echo | ||
| echo "Finished with pipeline and wrote corrected reads into: " $outfolder | ||
| echo |
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