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Makefile
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Makefile
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# ######################
# Makefile
#
# amadis.pages@upf.edu
# amadis.pages@crg.eu
# ######################
include mks/mkdefs.makefile
include mks/mkparams.makefile
# Fast and accurate discovery and characterization of processed small non-coding RNAs by SeRPeNT
# - Figure 1
# - Supplementary Figure 1
# - Supplementary Figure 2
# - Supplementary Figure 3
# - Supplementary Figure 4
# - Supplementary Table 1
benchmarking:
@echo "[LOG] Downloading data"
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile annotation # Download Gencode annotation
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile benchmarking # Download Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile diffprocbnm # Download Diffproc Benchmarking data
@echo "[LOG] Executing SeRPeNT"
@make -B -w -s --no-print-directory -f mks/mkprofiles.makefile benchmarking # Execute SeRPeNT profiler for Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkprofiles.makefile diffprocbnm # Execute SeRPeNT profiler for Diffproc Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkannotation.makefile benchmarking # Execute SeRPeNT annotator for Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkannotation.makefile diffprocbnm # Execute SeRPeNT annotator for Diffproc Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkdiffproc.makefile diffprocbnm # Execute SeRPeNT diffproc for Diffproc Benchmarking data
@echo "[LOG] Generating accuracy stats"
@make -B -w -s --no-print-directory -f mks/mkbenchmarking.makefile benchmarking # Generate accuracy stats for Benchmarking data
@make -B -w -s --no-print-directory -f mks/mkbenchmarking.makefile diffprocbnm # Generate accuracy stats for Diffproc Benchmarking data
@echo "[LOG] Generating figures, tables and data"
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig1 # Figure 1
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig1 # Supplementary Figure 1
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig2 # Supplementary Figure 2
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig3 # Supplementary Figure 3
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig4 # Supplementary Figure 4
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile tab1 # Supplementary Table 1
# An extended annotation of processed small non-coding RNAs in human
# - Figure 2a
# - Figure 2b
# - Figure 2c
# - Figure 4a
# - Figure 4b
# - Figure 4c
# - Supplementary Figure 5
# - Supplementary Figure 7
# - Supplementary Figure 8
# - Supplementary Figure 9
# - Supplementary Table 2
# - Supplementary Table 3
# - Supplementary Table 4
# - Supplementary Table 6
# - Supplementary Data 1
annotation:
@echo "[LOG] Downloading data"
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile annotation # Download Gencode annotation
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile lines # Download ENCODE cell lines data
@make -B -w -s --no-print-directory -f mks/mkdownload.makefile genome # Download human genome assembly
@echo "[LOG] Executing SeRPeNT"
@make -B -w -s --no-print-directory -f mks/mkprofiles.makefile lines # Execute SeRPeNT profiler for ENCODE cell lines data
@make -B -w -s --no-print-directory -f mks/mkannotation.makefile lines # Execute SeRPeNT annotator for ENCODE cell lines data
@echo "[LOG] Generating accuracy stats"
@make -B -w -s --no-print-directory -f mks/mkbenchmarking.makefile lines # Generate accuracy stats for ENCODE cell lines data
@echo "[LOG] Generating extended annotation"
@make -B -w -s --no-print-directory -f mks/mkannotation.makefile extended # Calculates entropy of predictions across ENCODE cell lines data
@make -B -w -s --no-print-directory -f mks/mkvalidation.makefile extended # Validate prediction of novel predicted profiles with Rfam db, Friedlander and DASHR
@make -B -w -s --no-print-directory -f mks/mkvalidation.makefile knockdown # Calculate differential expression between AGO-loaded and DICER-knockdown
@echo "[LOG] Generating figures, tables and data"
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig2a # Figure 2a
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig2b # Figure 2b
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig2c # Figure 2c
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig4a # Figure 4a
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig4b # Figure 4b
@make -B -w -s --no-print-directory -f mks/mkmain.makefile fig4c # Figure 4c
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig5 # Supplementary Figure 5
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig7 # Supplementary Figure 7
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig8 # Supplementary Figure 8
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile fig9 # Supplementary Figure 9
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile tab2 # Supplementary Table 2
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile tab3 # Supplementary Table 3
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile tab4 # Supplementary Table 4
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile tab6 # Supplementary Table 6
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile dat1 # Supplementary Data 1
@make -B -w -s --no-print-directory -f mks/mksupplementary.makefile dat2 # Supplementary Data 2
# Differential processing of sRNAs among ENCODE cell compartments
# - Figure 3a
# - Figure 3b
# - Figure 3c
# - Supplmentary Figure 6
# - Supplementary Table 5
# - Supplementary Data 2
diffproc:
@echo "[LOG] Downloading data"
@make -w -s --no-print-directory -f mks/mkdownload.makefile annotation # Download Gencode annotation
@make -w -s --no-print-directory -f mks/mkdownload.makefile compartments # Download ENCODE cell compartments data
@echo "[LOG] Executing SeRPeNT"
@make -w -s --no-print-directory -f mks/mkprofiles.makefile compartments # Execute SeRPeNT profiler for ENCODE cell compartments data
@make -w -s --no-print-directory -f mks/mkannotation.makefile compartments # Execute SeRPeNT annotator for ENCODE cell compartments data
@make -w -s --no-print-directory -f mks/mkdiffproc.makefile compartments # Execute SeRPeNT diffproc for ENCODE cell compartments data
@echo "[LOG] Generating figures, tables and data"
@make -w -s --no-print-directory -f mks/mkmain.makefile fig3a # Figure 3a
@make -w -s --no-print-directory -f mks/mkmain.makefile fig3b # Figure 3b
@make -w -s --no-print-directory -f mks/mkmain.makefile fig3c # Figure 3c
@make -w -s --no-print-directory -f mks/mksupplementary.makefile fig6 # Supplementary Figure 6
@make -w -s --no-print-directory -f mks/mksupplementary.makefile tab5 # Supplementary Table 5
@make -w -s --no-print-directory -f mks/mksupplementray.makefile dat3 # Supplementary Data 3
# Rule for cleaning benchmarking data
cleanb:
@rm -rf bnm/a549
@rm -rf bnm/ag04450
@rm -rf bnm/bj
@rm -rf bnm/gm12878
@rm -rf bnm/h1hesc
@rm -rf bnm/helas3
@rm -rf bnm/hepg2
@rm -rf bnm/mcf7
@rm -rf bnm/sknsh
@rm -rf bnm/normal/*.dat
@rm -rf bnm/normal/*.bed
@rm -rf bnm/tumour/*.dat
@rm -rf bnm/tumour/*.bed
@rm -rf bnm/profiles.bed
@rm -rf dfp/a549vsmcf7
@rm -rf dfp/ag04450vsbj
@rm -rf dfp/ag04450vsh1hesc
@rm -rf dfp/ag04450vshepg2
@rm -rf dfp/bjvsh1hesc
@rm -rf dfp/bjvshepg2
@rm -rf dfp/gm12878vshelas3
@rm -rf dfp/h1hescvshelas3
@rm -rf dfp/helas3vshepg2
@rm -rf dfp/normalvstumour
@rm -rf dfp/a549vssknsh
@rm -rf dfp/ag04450vsgm12878
@rm -rf dfp/ag04450vshelas3
@rm -rf dfp/bjvsgm12878
@rm -rf dfp/bjvshelas3
@rm -rf dfp/gm12878vsh1hesc
@rm -rf dfp/gm12878vshepg2
@rm -rf dfp/h1hescvshepg2
@rm -rf dfp/mcf7vssknsh
# Rule for cleanning annotation data
cleana:
@rm -rf dat/a549
@rm -rf dat/gm12878
@rm -rf dat/helas3
@rm -rf dat/hepg2
@rm -rf dat/imr90
@rm -rf dat/k562
@rm -rf dat/mcf7
@rm -rf dat/nhek
@rm -rf dat/sknsh
@rm -rf dat/serpent_annotation_novel.fa
@rm -rf dat/serpent_annotation_novel.hits
@rm -rf fig/supp/supplementary_data_1.tab
# Rule for cleaning compartments
cleanc:
@rm -rf dat/chromatin/*
@rm -rf dat/cytosol/*
@rm -rf dat/nucleolus/*
@rm -rf dat/nucleoplasm/*
# Rule for cleaning knockdown data
cleank:
@rm -f dat/wild/*.dat
@rm -f dat/wild/*.bed
@rm -f dat/wild/*.neWick
@rm -f dat/dicer/*.dat
@rm -f dat/dicer/*.bed
@rm -f dat/dicer/*.neWick
@rm -f dat/drosha/*.dat
@rm -f dat/drosha/*.bed
@rm -f dat/drosha/*.neWick
@rm -f dfp/wtvsdcr/*
@rm -f dfp/wtvsdrsh/*