Loop in bwa commands

Kax · 11-24-2019, 05:31 PM

Hiya,

I'm trying to loop multiple input files with matching prefixes and different file types in bwa sampe ; here's the general structure:

Code:

bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna H2_S16_L001_read1.sai H2_S16_L001_read2.sai \
H2_S16_L001_R1_001.fastq.gz H2_S16_L001_R2_001.fastq.gz > aln_H2_S16_L001.sam

I'm trying to make a loop like:

Code:

for i in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/ \
do bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
$i\-read1.sai $i\-read2.sai $i\-R1_001.fastq.gz $i\-R2_001.fastq.gz > $i\-aln.sam; done

Does anyone have suggestions for what I am missing? Like perhaps I need to create a list of the prefix file names? I would greatly appreciate any advice. Thanks!

abedkurdi · 07-08-2020, 12:30 AM

You can do the following:
for f in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/*.fastq.gz; do
name=$(basename $f _L001_R1_001.fastq.gz)
bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \
${name}_L001_read1.sai ${name}_L001_read2.sai \
${name}_L001_R1_001.fastq.gz ${name}_L001_R2_001.fastq.gz > ${name}_aln.sam
done

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11-24-2019, 05:31 PM	#1
Kax Junior Member Location: Utah Join Date: Nov 2019 Posts: 1	Loop in bwa commands Hiya, I'm trying to loop multiple input files with matching prefixes and different file types in bwa sampe ; here's the general structure: Code: bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna H2_S16_L001_read1.sai H2_S16_L001_read2.sai \ H2_S16_L001_R1_001.fastq.gz H2_S16_L001_R2_001.fastq.gz > aln_H2_S16_L001.sam I'm trying to make a loop like: Code: for i in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/ \ do bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \ $i\-read1.sai $i\-read2.sai $i\-R1_001.fastq.gz $i\-R2_001.fastq.gz > $i\-aln.sam; done Does anyone have suggestions for what I am missing? Like perhaps I need to create a list of the prefix file names? I would greatly appreciate any advice. Thanks!

07-08-2020, 12:30 AM	#2
abedkurdi Junior Member Location: Beirut, Lebanon Join Date: Sep 2016 Posts: 2	You can do the following: for f in /Users/xxx/Desktop/Index_align/Fastq/fastq_run4/*.fastq.gz; do name=$(basename $f _L001_R1_001.fastq.gz) bwa sampe /Users/xxx/Desktop/Index_align/GRCh37_latest_genomic.fna \ ${name}_L001_read1.sai ${name}_L001_read2.sai \ ${name}_L001_R1_001.fastq.gz ${name}_L001_R2_001.fastq.gz > ${name}_aln.sam done