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2018pipeline [2018/09/11 15:32]
david [Pipeline script]
2018pipeline [2018/09/11 15:44] (current)
david [Pipeline script]
Line 471: Line 471:
 # pipeline.sbatch - Perform grep on a GFF file, then run faFrag to extract DNA for  # pipeline.sbatch - Perform grep on a GFF file, then run faFrag to extract DNA for 
 # each line returned by grep. # each line returned by grep.
- + 
 +annotations=chr_wormbase.gff 
 + 
 +if [ ! -e "​$annotations"​ ] 
 +then 
 +    echo "Need to supply an annotation file" >&​2 
 +    exit 1 
 +fi 
    
 # Specify Gene list file  # Specify Gene list file 
Line 479: Line 486:
    
 # Perform grep -f on Gene list file to get annotation lines from the GFF # Perform grep -f on Gene list file to get annotation lines from the GFF
-grep -f $gene_lst ​chr_wormbase.gff ​| grep five_prime_utr > tmpfile.gff+grep -f $gene_lst ​$annotations ​| grep five_prime_utr > tmpfile.gff
 echo "​temporary file contains $(wc -l tmpfile.gff) lines" echo "​temporary file contains $(wc -l tmpfile.gff) lines"
 # #
Line 508: Line 515:
    ​out_fasta="​$gene_id_trimmed.fa"​    ​out_fasta="​$gene_id_trimmed.fa"​
    ###########​ run the command! #############​    ###########​ run the command! #############​
-   ​faFrag $in_fasta $chrom_start $chrom_end $out_fasta ||  echo ">>>>>>>>>>>>>>>​>>>>>>>>>>>​There was a problem with: '​$line'​<<<<<<<<<<<<<<<<<<<<<<<​<<<<<<<<<<<<<<<"​+   echo "​Running faFrag on $gene_id_trimmed"​ 
 +   faFrag $in_fasta $chrom_start $chrom_end $out_fasta ||  echo ">>>>>>>>>>>​There was a problem with: '​$line'<<<<<<<<<<<<<<<"​
    
 done < tmpfile.gff done < tmpfile.gff
2018pipeline.1536701558.txt.gz · Last modified: 2018/09/11 15:32 by david