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2018pipeline
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| Both sides previous revision Previous revision Next revision | Previous revision | ||
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2018pipeline [2018/09/11 15:32] david [Pipeline script] |
2018pipeline [2018/09/11 15:44] david [Pipeline script] |
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| 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.txt · Last modified: 2018/09/11 15:44 by david
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