Shell scripts and grep, awk command
Dear all,
I have a scripts like the following, but it always reported grep: .pep: No such file or directory when I running the script directly. And I am also confused with the awk command line as well as the paste command line in this script, if anyone could help me to clarify the meaning...
ls *BGI* | while read pipeline
do
grep '>' ${line}.pep | sed 's/>//g' > ${line}.modify.seqid
awk '{if($3 =="gene"){a=index($0,"~~");b=index($0,";");print substr($0,a+2,b-a-2)}}' > ${line}.origin.seqid
paste -d '\t' ${line}.origin.seqid ${line}.modify.seqid > ${line}_coress.seqid
done
Also, here are the related files and what they looks like:
- Prunella_fulvescens_BGI.pep
- Prunella_himalayana_BGI.pep
grep '>' Prunella_fulvescens_BGI.pep.fa | sed 's/>//g' > Prunella_fulvescens_BGI.modify.seqid
It will creat a file Prunella_fulvescens_BGI.modify.seqid like this:
PRUFUL_R14685 [mRNA] locus=scaffold1534:862:1958:- [translate_table: standard]
PRUFUL_R05501 [mRNA] locus=scaffold10:6068:6277:- [translate_table: standard]
PRUFUL_R10205 [mRNA] locus=scaffold1726:12292:22891:+ [translate_table: standard]
PRUFUL_R07295 [mRNA] locus=scaffold2643:33509:34789:+ [translate_table: standard]
PRUFUL_R07296 [mRNA] locus=scaffold2643:7708:8886:+ [translate_table: standard]
PRUFUL_R10726 [mRNA] locus=scaffold1079:172399:200680:- [translate_table: standard]
PRUFUL_R13095 [mRNA] locus=scaffold1079:16827:27665:+ [translate_table: standard]
PRUFUL_R13096 [mRNA] locus=scaffold1079:111918:114560:+ [translate_table: standard]
PRUFUL_R14411 [mRNA] locus=scaffold1079:153277:155466:+ [translate_table: standard]
PRUFUL_R07297 [mRNA] locus=scaffold2912:21167:49513:+ [translate_table: standard]
I will be appreciated if you could help combine the scritps and explain a little bit...:)
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it seems like your ${line} is empty. Try echo your ${line} in for loop first
Yes, exactly!! When I give up the loop and use
grep '>' Prunella_fulvescens_BGI.pep.fa | sed 's/>//g' > Prunella_fulvescens_BGI.modify.seqiddirectly, this step works well. But if you know how to echo the ${line} to make it work well in the loop....I am very new to the scripts etc....:(This line in your script is looking for files ending with
.pepwhereas they seem to have.pep.faending. That is first issue. There are likely others.At a minimum modify that bit to
and see if that helps.
Note: Please post text sample snippets instead of screen shots. People can't use the data for example purposes when posted as images.
Thank you so much for the guidance, I tried to change ".pep" to ".pep.fa" but still the same error....:(