implements changes by @sidd in issue #329 in a separate new PR

KwanLab · Jul 31, 2023 · a2ae5d7 · a2ae5d7
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commit a2ae5d7
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diff --git a/workflows/autometa-large-data-mode.sh b/workflows/autometa-large-data-mode.sh
@@ -241,10 +241,10 @@ then
         set -x
         grep ">" $kingdom_fasta | \
             sed 's/^>//' | \
-            sed 's/$/_/' | \
-            cut -f1 -d" " > $orf_prefixes
+            cut -f1 -d" " | \
+            sed 's/$/_/' > $orf_prefixes
         # Retrieve ORF IDs from contig IDs
-        grep -f $orf_prefixes $orfs | sed 's/^>//' | cut -f1 -d" " > $orf_ids
+        grep -f $orf_prefixes $orfs | cut -f1 -d" " | sed 's/^>//'  > $orf_ids  
         # Retrieve ORF seqs from ORF IDs
         seqkit grep \
             --pattern-file $orf_ids \

diff --git a/workflows/autometa.sh b/workflows/autometa.sh
@@ -231,10 +231,10 @@ then
         set -x
         grep ">" $kingdom_fasta | \
             sed 's/^>//' | \
-            sed 's/$/_/' | \
-            cut -f1 -d" " > $orf_prefixes
+            cut -f1 -d" " | \
+            sed 's/$/_/' > $orf_prefixes
         # Retrieve ORF IDs from contig IDs
-        grep -f $orf_prefixes $orfs | sed 's/^>//' | cut -f1 -d" " > $orf_ids
+        grep -f $orf_prefixes $orfs | cut -f1 -d" " | sed 's/^>//'  > $orf_ids
         # Retrieve ORF seqs from ORF IDs
         seqkit grep \
             --pattern-file $orf_ids \