How to execute command without using the do command twice in the loop-CodePudding

These are my files

KIMS2021-01_R1.fastq.gz  KIMS2021-05_R1.fastq.gz  SRR1734376_1.fastq.gz  SRR6006897_1.fastq.gz  SRR6006901_1.fastq.gz  SRR6006905_1.fastq.gz
KIMS2021-01_R2.fastq.gz  KIMS2021-05_R2.fastq.gz  SRR1734376_2.fastq.gz  SRR6006897_2.fastq.gz  SRR6006901_2.fastq.gz  SRR6006905_2.fastq.gz
KIMS2021-02_R1.fastq.gz  KIMS2021-06_R1.fastq.gz  SRR1734377_1.fastq.gz  SRR6006898_1.fastq.gz  SRR6006902_1.fastq.gz  SRR6006906_1.fastq.gz
KIMS2021-02_R2.fastq.gz  KIMS2021-06_R2.fastq.gz  SRR1734377_2.fastq.gz  SRR6006898_2.fastq.gz  SRR6006902_2.fastq.gz  SRR6006906_2.fastq.gz
KIMS2021-03_R1.fastq.gz  SRR1734374_1.fastq.gz    SRR6006895_1.fastq.gz  SRR6006899_1.fastq.gz  SRR6006903_1.fastq.gz
KIMS2021-03_R2.fastq.gz  SRR1734374_2.fastq.gz    SRR6006895_2.fastq.gz  SRR6006899_2.fastq.gz  SRR6006903_2.fastq.gz
KIMS2021-04_R1.fastq.gz  SRR1734375_1.fastq.gz    SRR6006896_1.fastq.gz  SRR6006900_1.fastq.gz  SRR6006904_1.fastq.gz
KIMS2021-04_R2.fastq.gz  SRR1734375_2.fastq.gz    SRR6006896_2.fastq.gz  SRR6006900_2.fastq.gz  SRR6006904_2.fastq.gz

To get uniform file name for each pair i got this answer from my previous question which is this

for i in $(echo *.fastq*.gz); do echo ${i%_*}; done | uniq

My final command which i want to use after I get uniform file name

for i in $(ls *.fastq*.gz); do echo ${i%_*}; done | uniq; do STAR --runMode alignReads --outSAMtype BAM SortedByCoordinate --runThreadN 30 --genomeDir /run/media/punit/data3/Santosh_star_index --readFilesIn  <(gunzip -c ${i}_R1.fastq.gz ${i}_R2.fastq.gz ) --outFileNamePrefix ${i%};done

Now i understand i can;t use do twice in a loop

How to pass the uniform file name to my command without using do twice

CodePudding user response：

from my previous question which is this

For starters let's fix it! Do not do:

for i in $(anything); do

Just do:

for i in *.fastq*.gz; do

How to pass the uniform file name to my command

Shell most importantly works with pipes |. The output of one command is input to another - like in your pipe, the output of for loop is the input of uniq.

Read the output of uniq.

for i in *.fastq*.gz; do echo "${i%_*}"; done |
   uniq |
   while IFS= read -r file; do stuff with "$file"; done

Check your scripts with shellcheck.net . See https://mywiki.wooledge.org/BashFAQ/001

as a biologist its a pain for me do dig the basic nuances of the scripting my simple solution would be if i run the them as two sets

Sure! I do that when interactive scripting a lot.

tmp=$( for i in *.fastq*.gz; do echo "${i%_*}"; done )
tmp=$( uniq <<<"$tmp" )   # or tmp=$( echo "$tmp" | uniq )
tmp=$( echo "$tmp" | while IFS= read -r file; do stuff with "$file"; done )
echo "$tmp"

Remember about qoutes "! <<<"stuff" works like <file - inputs the content of "stuff" to the input of the command, does the same as echo "$tmp" |.