Commit 0f74906f authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
Browse files

Change output stuffs

parent 5906e192
#!/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"
......@@ -13,16 +16,12 @@ IMP_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/
IMP_MT_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${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"
echo "IGC and IMP MG total reads"
sort <(samtools view -f 2 $IMP_MG_BAM | cut -f1) <(samtools view -f 2 $IGC_MG_BAM | cut -f1) | uniq | wc -l
echo "IGC and IMP-megahit MG total reads"
sort <(samtools view -f 2 $IMP_MG_MEGAHIT_BAM | cut -f1) <(samtools view -f 2 $IGC_MG_MEGAHIT_BAM | cut -f1) | uniq | wc -l
paste <(echo -e "${S}_MG_IMP_IGC\t") <(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
echo "IGC and IMP MT total reads"
sort <(samtools view -f 2 $IMP_MT_BAM | cut -f1) <(samtools view -f 2 $IGC_MT_BAM | cut -f1) | uniq | wc -l
paste <(echo -e "${S}_MG_IMP-megahit_IGC\t") <(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
echo "IGC and IMP-megahit MT total reads"
sort <(samtools view -f 2 $IMP_MT_MEGAHIT_BAM | cut -f1) <(samtools view -f 2 $IGC_MT_MEGAHIT_BAM | cut -f1) | uniq | wc -l
<(echo -e "${S}_MT_IMP_IGC\t") <(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\t") <(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
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