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Verified Commit fa7de5ce authored by Laurent Modolo's avatar Laurent Modolo
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switch fastq file to fasta file for kmdiff

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data/sample_mbelari.csv
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View file @ fa7de5ce
female1: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fastq.gz female1: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/1_S1_L001_R2_001.fasta.gz
female2: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fastq.gz female2: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/2_S2_L001_R2_001.fasta.gz
female3: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fastq.gz female3: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/3_S3_L001_R2_001.fasta.gz
female4: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fastq.gz female4: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/4_S4_L001_R2_001.fasta.gz
female5: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fastq.gz female5: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/5_S5_L001_R2_001.fasta.gz
female6: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fastq.gz female6: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/6_S6_L001_R2_001.fasta.gz
female7: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fastq.gz female7: /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mbelari_females/MRDR5_R2.fasta.gz
male1: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fastq.gz male1: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R1_001.fasta.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/JU2817_males_S11_L002_R2_001.fasta.gz
male2: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fastq.gz male2: //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R1.fasta.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mbelari_males/MRDR6_R2.fasta.gz
data/sample_mlongespiculosa.csv
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View file @ fa7de5ce
female1: /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fastq.gz female1: /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R1.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_females/MRDR3_R2.fasta.gz
male1: //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fastq.gz male1: //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mlongespiculosa_males/MRDR4_R1.fasta.gz
data/sample_mspiculigera.csv
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View file @ fa7de5ce
female1: /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fastq.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fastq.gz female1: /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R1_001.fasta.gz ; /scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_females/AF72-females_BIS_S8_L002_R2_001.fasta.gz
male1: //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fastq.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fastq.gz male1: //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R1_001.fasta.gz ; //scratch/Bio/lmodolo/kmer_diff/data/Mspiculigera_males/AF72-males_S7_L002_R2_001.fasta.gz
src/kmdiff.sh
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View file @ fa7de5ce
...@@ -4,13 +4,23 @@ docker push lbmc/kmdiff:1.0.1 ...@@ -4,13 +4,23 @@ docker push lbmc/kmdiff:1.0.1
# build charliecloud image # build charliecloud image
ch-image pull -s /Xnfs/abc/charliecloud/ lbmc/kmdiff:1.0.1 ch-image pull -s /Xnfs/abc/charliecloud/ lbmc/kmdiff:1.0.1
ch-image pull -s /Xnfs/abc/charliecloud quay.io/biocontainers/seqtk:1.3--ha92aebf_0
update_ch_image.sh update_ch_image.sh
alias kmdiff="ch-run -b /scratch /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff" alias kmdiff="ch-run -b /scratch -c $PWD /Xnfs/abc/charliecloud/img/lbmc%kmdiff+1.0.1 -- kmdiff"
alias seqtk="ch-run -b /scratch -c $PWD /Xnfs/abc/charliecloud/img/quay.io%biocontainers%seqtk+2.3--ha92aebf_0 -- seqtk"
WORK=$(pwd) WORK=$(pwd)
mkdir results/ mkdir results/
# convert fastq into fasta
fd ".*fastq" data \
| sed 's|.fastq.gz||' \
| awk '{system("ch-run -b /scratch -c $PWD /Xnfs/abc/charliecloud/img/quay.io%biocontainers%seqtk+1.3--ha92aebf_0 -- seqtk seq -a "$0".fastq.gz > "$0".fasta")}'
fd ".*fasta" data --exec gzip -v9 {}
# kmdiff count # kmdiff count
kmdiff count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32 kmdiff count -f ${WORK}/data/sample_mbelari.csv -d ${WORK}/results/mbelari_counts/ -t 32
kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32 kmdiff count -f ${WORK}/data/sample_mlongespiculosa.csv -d ${WORK}/results/mlongespiculosa_counts/ -t 32
......
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