Initial commit of minimal pipelines for GNU make, Nextflow and Snakemake.

alignments = set1.fasta set2.fasta set3.fasta

consensi = set1.fasta_cons.fa set2.fasta_cons.fa set3.fasta_cons.fa

%.fasta: %.fa

	clustalw -OUTPUT=FASTA -INFILE=$<

	rm *.dnd

%.fasta_cons.fa: %.fasta

	cons -sequence $< -outseq $<_cons.fa

all: $(alignments) $(consensi)

clean:

	rm *.fasta *_cons.fa

rule align:

    input:

        "{name}.fa"

    output:

        "{name}.fasta"

    run:

        shell("clustalw -OUTPUT=FASTA -INFILE={input}")

        shell("rm {wildcards.name}.dnd")

rule consensi:

    input:

        "{name}.fasta"

    output:

        "{name}.fasta_cons.fa"

    shell:

        "em_cons -sequence {input} -outseq {output}"

#!/usr/bin/env nextflow

input = Channel.fromPath('*.fa')

process ALIGN {

  publishDir "/home/lexa/pipelines"

  input:

  file x from input

  output:

  file '*.fasta' into alignment

  script:

  """

  clustalw -OUTPUT=FASTA -INFILE=${x}

  rm *.dnd

  """

}

process GET_CONSENSUS {

  publishDir "/home/lexa/pipelines"

  input:

  file a from alignment

  output:

  file '*_cons.fa'

  """

  em_cons -sequence ${a} -outseq ${a}_cons.fa 

  """

}

#!/usr/bin/env Rscript

args = commandArgs(trailingOnly=TRUE)

filename <- args[1]

filebase <- strsplit(filename,split="\\.")[[1]][1]

library(seqLogo)

library(Biostrings)

dna <- readDNAStringSet(filename)

cm <-consensusMatrix(dna)[1:4,]

sumcm <- apply(cm,2,sum)

cm[1,] <- cm[1,]/sumcm

cm[2,] <- cm[2,]/sumcm

cm[3,] <- cm[3,]/sumcm

cm[4,] <- cm[4,]/sumcm

if(length(cm[1,]) > 16) {

  cm <- cm[,1:16]

}

pwmcm <- makePWM(cm)

png(file=paste0(filebase,".png"), width=480, height=240)

seqLogo(pwmcm)

dev.off()

>Acom_chr1

CTGGATAAGGGTTTTGTGCGACCGAGTGTTTCAACTTGGGAAGCACCGGTCCTATTTGTCAAGAAGAAGGATGGATCGCTTCGCTTGCGCGTGGATTATTGTGAACTCAATAAAGTCACGATCAAGAATAAGTATCCTTTACCGAGGATTGATGATTTATTTGATCAGCTCCAGGGATCTAGGGTGTATTCTAAGATCGACTTGCAGTCGGGATACCACCAGTTGAAGATCAAGCTTGAGGATGTGTCGAAAACGGCTTTTAGAACACAGTATGGACATTATGAGTTTACAGTTATGCCGTTTGGGCTTACTAACGCCCCGGCCGCTTTTATGGATTTGATGAGCAGTGTTTTCAAGCCTTATCTAGACAGGTTCGTCGTAGTATTCATCGATGACATTTTGGTCTATTCCTGAAGTGATGCGGATCACGAGGAACACTTGAGACTTGTACTTCAAGTACTTTGGAAAAAGGAGCTCTATGCCAAATTGAAAAAGTATGAGCTTTGGCTTAGAGAGGTGGCGTTTTTGGGCCATTTGATTTTAGGATCAGGTATAGCTGTGGATCCTAGGAAGATTGAAGCTATCAAGGACTAGCCGAGGCCGACGAGTGTCACCGAGATTCGGAGTTTTCTTGGCTTAGCCGGCTACTACCGAGGGTTTGTTGAGGGATTTGCAA

>Acom_chr2

GCGTGACATTTTCTTTGTTCTTTTGAGCGGGTTCATTTTTAACTGGTATTCTCTCAATCGAATGAAGACAGTTTTTAAATCTTGGAAGAGATTTTCTTTGTTCTTTGTTTTCACAACCAAATCATTGACATAGCACTCTACTGTCTTGTGGAGTAGATCATCAAATATTCTAGTCATTACTCGCTGATATATAGCTTCGACATTCTTGAGGCCGAAAGGCATGATTTTATAACAATATATTCCAATGGGAGTTCTGAATGCAGTATGCTTCTCGTCCTCCGGTGCCATCTTGATTTTATTGTATCCTGATGACCCCATAAACGCGAATTTCTCACAACTCGATGTGTTGTCAATCATTAGTTCCGTTATTGATAATGGAAAGTCATCTTTTGGGCAAGCTTTATTTAAATCTCGAAAATCGACGCATATACAAATTTAGCTATTCTTTTTCTTGACCGGGACGATGCTAGCGATCCAATTAGCATATTTCTCCTCCCTTATAAAGCCTGCTTTAATGAGCTTTTTGGTTTTC

>Acom_chr3

AAGGCACAGTTACAAGATCTATTGGATAAAGGCTTCATTCGACCTAGTATATCGCCTTAGGGAGCACCAGTTTTGTTTGTTAAGAAAAATGACGGATCTTTTCGATCGTGTGTGGACTATCGAGAGATTAACAAGGTTACAATCAAGAATAAGTATTTGTTGCCAAAGATTGATGATTTATTCGATCAACTCCAAGGGTCAAAAGTTTATTCCAAGATTGATCTACAATCAGGTTACCATTAGCTCAAGATCAAGCCTGAGGATGTTTCTAAAATCATCTTTAGAACACGGTATGGTCATTATGAGTTCATAGTTATGCTATTTGGGCTTACTAATGCCCCGGCAGCTTTTATAGATTTAATGAACCGTGTTTTCAAGTCTTACTTGGACAGGTTTGTGGTAGTATTTATCGACGATATCCTGATCAATTCTCAAAGTGACGAAGAGCATGAAAACCATTTGAGATTGGTGTTGCAAGTATTTCCAGAAAAGAAACTGTTTGCTAAGTTAAAGAAATGCAAATTTTGGCTTCGAGAGGTAGCATTTCTAGGACATGTAATTTCAGAGGCTGGGATAGCCGTGGATCCAAAAAAAATTGAGGCAATCAAAGAATGGCCTAGGCCGACTAGTGTTGCTGCGATTCAGAGTTTTCTTGGGCTAGCAGGATACTATCGGAGATTTGTTGAGAGATTTGCTA

>Acom_CRM

AAAAAACAAGTACCCATTGCCAAGGATTGACGATTTATTCGATCAGTTGCAGGGTCAAAGGTGTATTCAAAGATTGATCTCCAATCGGGGTATCATGAACTAAAGATTAGGCCGAAGGATGTGCACAAAACGGCGTACCGTACGCGGTATGGCCATTATGAGTTCACGGTAATGCCGTTTGGGCTTACTAATGCCCCTGCAGCATTTATGTACTTGATGAATCGAGTCTTTCGGCCATTATTGGATCGATGCGTCGTGGTGTTCATTGATGATGTGTTGGTCTACTCGAAAAGTAAGGAGGAGCACGAGGAGCATTTGAGAGCCGTGCTACAGATTCTCCGACAAAAGAAGCTCTATGCTAAGCTGAAGAAATGTGGCTTTTGGCTTACGGAGGTCACATTCTTGGGCCACGTGATATCGGGCGATGGGGTCTCGGTAGATCCTAAGAAGGTGGAGGCGATCAAGGACTTGCCTCGCCCAACAAATGTAGCGGAGGTCCGCAGTTTTCTTGGACTCGCGGGCTACTACCGGCGGTTTGTGGAGGGGTTCGCTA

>Acom_Galadriel

GTAGCCTGCAATGAAACGGCGGTAGTAGTTGACGAGCCCAAGGAAAGACCGCAACTCGGACACCGTCGTTGGGGTCTCCCATTCGCAGATGGCTCGCACCTTCCGCTGGTCCATGCGAATCAGGCCCTGGCCTATCCAGTGGCCAAGGAAGTGCACCTCTTCCTTTGCGAATATACACTTCTCCTTCTTGACCAACAACTGGTTCTCCCGCAGCACTTGGAAGACGATTCGCAAGTGCTCGATGTGCTCCTACAAGGTGTTACTGTATACCATGATGTCGTCGATGTACACCACCACAAAGCGATCGAGATAGGGATGAAACAGCTTGTTCATGAGTGTGCAGAAGGTTGCCGGCGCATTTATCAAGCTGAACGGCATGACAAGGAACTCATAGGCCCCGTACCTCGTCACGCACGTGGTCTTTTCCTCATCTCCTTCCGCAATCCACACTTGG