ORSON: workflow for prOteome and tRanScriptome functiOnal aNnotation.
This mirror of ORSON workflow on Github is no longer supported and will soon be deleted.
Please go to: https://gitlab.ifremer.fr/bioinfo/workflows/orson
Workflow for prOteome and tRanScriptome functiOnal aNnotation. CAUTION : project has moved to Gitlab.
Home Page: https://gitlab.ifremer.fr/bioinfo/workflows/orson
License: MIT License
ORSON: workflow for prOteome and tRanScriptome functiOnal aNnotation.
This mirror of ORSON workflow on Github is no longer supported and will soon be deleted.
Please go to: https://gitlab.ifremer.fr/bioinfo/workflows/orson
Hello,
here is a correction for script IPRScanXMLmerge.sh which doesn't work on test data.
*.xml
-> *results.xml
and I correct error badly placed "
#!/usr/bin/env bash
###############################################################################
## ##
## Purpose of script: Merge multiple InterProScan XML files ##
## ##
###############################################################################
# var settings
args=("$@")
MERGED_XML=${args[0]}
QUERY_TYPE=${args[1]}
# Run InterProScan XML merging
CMD="sed -i '1d' *results.xml;
sed -i '\$d' *results.xml;
cat *results.xml > $MERGED_XML;"
if [ "$QUERY_TYPE" = "p" ]
then
CMD=$CMD . " sed -i '1 i\<?xml version=\"1.0\" encoding=\"UTF-8\"?><protein-matches xmlns=\"http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5\" interproscan-version=\"5.51-85.0\">' $MERGED_XM
L;
echo '</protein-matches>' >> $MERGED_XML"
else
CMD=$CMD . " sed -i '1 i\<?xml version=\"1.0\" encoding=\"UTF-8\"?><nucleotide-sequence-matches xmlns=\"http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5\" interproscan-version=\"5.51-85.0\">
' $MERGED_XML;
echo '</nucleotide-sequence-matches>' >> $MERGED_XML"
fi
eval $CMD
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