Makefile

DATA = SRR013437

# Allowed errors for primers and barcodes
# Even reads containing errors in these may still be usuable.
BCDE_ERS = 2
PRMR_ERS = 3

# Nucleotides differences to cluster sequences
DIFF = 4

# Mothur trim opts
TRIMOPTS = bdiffs=$(BCDE_ERS), pdiffs=$(PRMR_ERS), minlength=$(LENGTH), processors=$(PS)

# Expected number of clusters
EXPCT = 23

all: .$(DATA).read_accurate.tab.xz.uploaded

%.read_accurate.tab: %.accurate.txt %.inaccurate.txt
  sed 's/$$/ 0/' $*.accurate.txt >  [email protected]
	sed 's/$$/ 1/' $*.inaccurate.txt >> [email protected]
	echo 'read bad.read' > $@
	sort [email protected] >> $@
	rm [email protected]

%.inaccurate.txt: %.accurate.txt %.unique.names
	cut -f 2 $(lastword $^) | tr ',' '\n' | sort | comm -2 -3 - $< > $@

%.accurate.txt: %.correct.txt %.unique.names
	join $^ | cut -f 2 -d ' ' | tr ',' '\n' | sort > $@

# Identify the unique sequences corresponding to the original reads
# The number of lines in this file should match the expectation
%.correct.txt: %.align.fasta
	mothur '#pre.cluster(fasta=$<, name=$*.unique.names, diffs=$(DIFF))' > /dev/null
	cut -f 1 $*.align.precluster.names | sort > $@
	rm mothur.*.logfile $*.align.precluster.*

# Align the top (expected*2) unique sequences
%.align.fasta: %.counts.tab %.unique.names
	head -n `echo '$(EXPCT) * 2' | bc` $< | cut -f 1 -d ' ' | xargs -I {} egrep -A 1 '{}$$' $*.unique.fasta | mafft - > $@ 2> /dev/null

# Count the number of reads mapping to each unique sequence
%.counts.tab: ./bin/count-reads %.unique.names
	$^ | sort -r -n -k 2,2 > $@

%.unique.names: %.processed.fasta
	mothur '#unique.seqs(fasta=$<)' > /dev/null
	mv $*.processed.unique.fasta $*.unique.fasta
	cat $*.processed.names | sort > $@
	rm mothur.*.logfile $*.processed.names

# Remove barcode and filter sequences on length and errors
# Then trim sequences down to required length
%.processed.fasta: %.filtered.fasta primers.txt
	mothur '#trim.seqs(fasta=$<,oligos=$(lastword $^),$(TRIMOPTS))' > /dev/null
	fastx_trimmer -i $(basename $<).trim.fasta -o $@ -l $(LENGTH)
	rm mothur.*.logfile $(basename $<).groups $(basename $<).trim.fasta

%.filtered.fastq: %.filtered.fastq.xz
	xz --decompress $<

primers.txt: primers.txt.xz
	xz --keep --decompress $<

primers.txt.xz:
	$(INPUT_DATA)$@

include ../Makefile