Commit 9375a47e authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Merge branch 'master' of...

Merge branch 'master' of ssh://git-r3lab-server.uni.lu:8022/shaman.narayanasamy/IMP_manuscript_analysis
parents c2a5022b f224ad47
#!/bin/bash -l
module load bio/SAMtools/0.1.19-goolf-1.4.10
THREADS=12
declare -a SAMPLES=("HF1" "HF2" "HF3" "HF4" "HF5")
date
for S in "${SAMPLES[@]}"
do
IMP_MG_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MG.reads.sorted.bam"
IMP_MG_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MG.reads.sorted.bam"
IGC_MG_BAM="/scratch/users/snarayanasamy/IMP_MS_data/HMP_IGC_mapping/${S}/MG_IMP_x_HMP.sorted.bam"
IMP_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MT.reads.sorted.bam"
IMP_MT_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MT.reads.sorted.bam"
IGC_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/HMP_IGC_mapping/${S}/MT_IMP_x_HMP.sorted.bam"
paste <(echo -e "${S}_MG_IMP_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) > IMP2IGC_mapping.txt
paste <(echo -e "${S}_MG_IMP-megahit_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MT_IMP_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MT_IMP-megahit_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
done
date
#!/bin/bash -l
OUTFILE="prodigal_summary.tsv"
OUTFILE="/scratch/users/snarayanasamy/IMP_MS_data/prodigal_analysis/prodigal_summary.tsv"
declare -a SAMPLES=("SM" "HF1" "HF2" "HF3" "HF4" "HF5" "WW1" "WW2" "WW3" "WW4" "BG")
echo -e "Dataset\tAssembly\tProdigal_total_genes\tProdigal_complete_genes\tProdigal_incomplete_genes" > ${OUTFILE}
......
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