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Diffstat (limited to 'academic/pyCRAC/test_slack.sh')
-rw-r--r-- | academic/pyCRAC/test_slack.sh | 121 |
1 files changed, 121 insertions, 0 deletions
diff --git a/academic/pyCRAC/test_slack.sh b/academic/pyCRAC/test_slack.sh new file mode 100644 index 0000000000000..0606665d69e20 --- /dev/null +++ b/academic/pyCRAC/test_slack.sh @@ -0,0 +1,121 @@ +#!/usr/bin/env bash +echo +echo "##### testing all pyCRAC tools #####" +echo +echo "# pyBarcodeFilter.py..." +echo "...demultiplexing illumina indexes" +pyBarcodeFilter.py -f test_f.fastq -r test_r.fastq -b indexes.txt -i -m 1 +echo "...demultiplexing illumina indexes on compressed files" +pyBarcodeFilter.py -f test_f.fastq.gz -r test_r.fastq.gz -b indexes.txt -i -m 1 --file_type=fastq.gz +echo "...demultiplexing random barcodes in 5' adapter" +pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1 +echo "...demultiplexing random barcodes in 5' adapter on compressed data and compressing output files" +pyBarcodeFilter.py -f test_f_dm.fastq -r test_r_dm.fastq -b barcodes.txt -m 1 --gz +echo "# pyReadCounters..." +echo "...range 300 and deletions only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...same as above but counting hits for introns only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s intron -o test_intron -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...same as above but now counting hits in exons only" +pyReadCounters.py -f test.novo -m 10000 -r 300 --mutations=delsonly --discarded=pyReadCounters_discarded.txt --rpkm -a protein_coding --hittable -s exon -o test_exon -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyClusterReads..." +pyClusterReads.py -f test_count_output_reads.gtf -r 300 --cic=5 --ch=5 --co=5 --mutsfreq=10 -o test_count_output_clusters.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...counting overlap between clusters and genomic features" +pyReadCounters.py -f test_count_output_clusters.gtf --file_type=gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyMotif..." +echo "...with range setting" +pyMotif.py -f test_count_output_clusters.gtf -r 300 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with annotation = protein_coding" +pyMotif.py -f test_count_output_clusters.gtf -a protein_coding -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyBinCollector..." +echo "...with annotation = protein_coding" +pyBinCollector.py -f test_count_output_clusters.gtf -a protein_coding -n 50 -o test_count_output_protein_coding_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with all annotations" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 -o test_count_output_all_50.pileup -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with --binoverlap flag" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --binoverlap 1 5 -o test_count_output_selected_1_5.gtf -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "...with --outputall flag" +pyBinCollector.py -f test_count_output_clusters.gtf -n 50 --outputall -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyPileup..." +echo "...with genes list" +pyPileup.py -f test.novo -g genes.list --limit=1000 --discarded=pyPileup_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with genes list and removal of duplicates" +pyPileup.py -f test.novo -g genes.list --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with chromosome coordinates" +pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with chromosome coordinates and removal of duplicates" +pyPileup.py -f test.novo --chr test_coordinates.txt --limit=1000 --blocks -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyReadAligner..." +echo "...with chromosome coordinates" +pyReadAligner.py -f test.novo --chr test_coordinates.txt --limit=1000 --discarded=pyReadAligner_discarded.txt -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "...with genes list and mutation filtering" +pyReadAligner.py -f test.novo -g genes.list --limit=500 --mutations=delsonly -v --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf --tab=../db/Saccharomyces_cerevisiae.EF2.59.1.0.fa.tab +echo "# pyCalculateFDRs..." +pyCalculateFDRs.py -f test_count_output_reads.gtf -r 200 -o test_count_output_FDRs_005.gtf -v -m 0.05 --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyCalculateMutationFrequencies..." +pyCalculateMutationFrequencies.py -i test_count_output_FDRs_005.gtf -r test_count_output_reads.gtf -o test_count_output_FDRs_005_with_muts.gtf --mutsfreq=20 -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo +echo "##### testing pyCRAC scripts #####" +echo +echo "# pyFastqJoiner.py..." +pyFastqJoiner.py -f test_f.fastq test_r.fastq -c "|" -o test_joined.fastq +echo "...with compressed data and output compression" +pyFastqJoiner.py -f test_f.fastq.gz test_r.fastq.gz --file_type=fastq.gz -c "|" --gz -o test_joined_compressed.fastq +echo "...with reverse-complementing the reverse read" +pyFastqJoiner.py -f test_f.fastq test_r.fastq --reversecomplement -c "|" -o test_reverse_joined.fastq +echo "# pyFastqDuplicateRemover.py..." +echo "...with single-end data" +pyFastqDuplicateRemover.py -f test_f.fastq -o test_f.fasta +echo "...with paired-end data" +pyFastqDuplicateRemover.py -f test_f.fastq -r test_r.fastq -o test +echo "# pyFastqSplitter.py..." +pyFastqSplitter.py -f test_joined.fastq -c "|" -o test_splitted +echo "...with compressed data" +pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted +echo "...with compressed data and compressing output" +pyFastqSplitter.py -f test_joined_compressed.fastq.gz --file_type=fastq.gz -c "|" -o test_compressed_splitted --gzip +echo "# pyCheckGTFfile.py..." +pyCheckGTFfile.py --gtf=test.gtf -o test_corrected.gtf +echo "# pyGetGTFSources.py..." +pyGetGTFSources.py --gtf=test.gtf -o test_gtf_sources.txt --count +echo "# pyGetGeneNamesFromGTF.py..." +pyGetGeneNamesFromGTF.py --gtf=test.gtf -a gene_name -o test_gtf_gene_names.txt --count +echo "# pyNormalizeIntervalLengths with various flags..." +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --fixed 20 -o test_count_output_FDRs_fixed_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --min 20 -o test_count_output_FDRs_min_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addboth 20 -o test_count_output_FDRs_addboth_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addleft 20 -o test_count_output_FDRs_addleft_20.gtf -v +pyNormalizeIntervalLengths.py -f test_count_output_FDRs_005.gtf -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt --addright 20 -o test_count_output_FDRs_addright_20.gtf -v +echo "# pyAlignment2Tab.py..." +pyAlignment2Tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test.tab +echo "# pyExtractLinesFromGTF.py..." +pyExtractLinesFromGTF.py --gtf=test.gtf -g genes.list -o test_snR17A.gtf -a gene_name +echo "# pyGTF2bed.py..." +pyGTF2bed.py --gtf=test_count_output_reads.gtf -o test.bed -n test_gtf -d test_gtf --color red +echo "# pyGTF2bedGraph.py..." +echo "...default settings" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...normalized to hits per million" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -t reads -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...start positions" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...end positions" +pyGTF2bedGraph.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -n test_gtf -d test_gtf -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyGTF2sgr.py..." +echo "...default settings" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...normalized to hits per million" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm --permillion -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...start positions" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_5end --permillion -t startpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "...end positions" +pyGTF2sgr.py --gtf=test_count_output_reads.gtf -o test_out_norm_3end --permillion -t endpositions -v -c ../db/Saccharomyces_cerevisiae.EF2.59.1.0_chr_lengths.txt +echo "# pyFilterGTF.py..." +pyFilterGTF.py -f test_count_output_reads.gtf -o test_sense_filtered_reads.gtf -a protein_coding --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pybed2GTF.py..." +pybed2GTF.py --bed=test.bed -o test_bed2gtf.gtf --gtf=../db/Saccharomyces_cerevisiae.EF2.59.1.3.gtf +echo "# pyFasta2tab.py..." +pyFasta2tab.py -f sense-reads_SNR17A_genomic_test.fasta -o sense-reads_SNR17A_genomic_test_f2a.tab +echo +echo "##### tests finished #####" +echo |