From b9d01cc5ba1512e0595613dc83064a37c7a6e6f4 Mon Sep 17 00:00:00 2001
From: vinuesa <vinuesa@ccg.unam.mx>
Date: Sun, 29 Oct 2023 12:11:43 -0600
Subject: [PATCH] fix_FASTA_headers4blastdb.sh v0.1_2023-10-29; first commit

---
 fix_FASTA_headers4blastdb.sh | 63 ++++++++++++++++++++++++++++++++++++
 1 file changed, 63 insertions(+)
 create mode 100755 fix_FASTA_headers4blastdb.sh

diff --git a/fix_FASTA_headers4blastdb.sh b/fix_FASTA_headers4blastdb.sh
new file mode 100755
index 0000000..bbee123
--- /dev/null
+++ b/fix_FASTA_headers4blastdb.sh
@@ -0,0 +1,63 @@
+#!/usr/bin/bash -
+
+#: progname: compute_RBH_clusters.sh
+#: Author: Pablo Vinuesa, CCG-UNAM, @pvinmex, https://www.ccg.unam.mx/~vinuesa/
+#
+#: AIM: Edit FASTA header of proteomes not fetched from standard databases (sp|tr ...)
+#:      This is a companion script for compute_RBH_clusters.sh
+#: - for example, for ACAC3.faa, >FUN_000001-T1 FUN_000001 is transformed to: 
+#: 			      >lcl|FUN_000001-T1_ACAC3 FUN_000001
+#----------------------------------------------------------------------------------------
+#: LICENSE: GPL v3.0. See https://github.com/vinuesa/get_phylomarkers/blob/master/LICENSE
+#----------------------------------------------------------------------------------------
+#: DISCLAIMER 
+#: THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+#: APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+#: HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+#: OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+#: THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+#: PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+#: IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+#: ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+#----------------------------------------------------------------------------------------
+#: GitHub repo: you can fetch the latest version of the script from:
+#   https://github.com/vinuesa/TIB-filoinfo/blob/master/compute_blastp_RBH_orthologous_clusters.sh
+# wget -c https://raw.githubusercontent.com/vinuesa/TIB-filoinfo/master/fix_FASTA_headers4blastdb.sh
+#----------------------------------------------------------------------------------------
+
+
+# set Bash's unofficial strict mode
+# http://redsymbol.net/articles/unofficial-bash-strict-mode/
+set -euo pipefail
+IFS=$'\n\t'
+
+progname=${0##*/}
+vers='0.1_2023-10-28'  # first commit 
+
+
+function print_help {
+
+   cat << HELP
+
+   Usage: $progname <fasta2edit>
+   
+   * AIM: Edit FASTA header of proteomes not fetched from standard databases (sp|tr ...)
+          This is a companion script for compute_RBH_clusters.sh
+     - for example, for ACAC3.faa, >FUN_000001-T1 FUN_000001 is transformed to: 
+                                   >lcl|FUN_000001-T1_ACAC3 FUN_000001
+   
+   # To process specific files, list them in a for loop like shown below:
+   for f in ACAC3.faa Neff2.faa; do $progname \$f; done
+
+   # To process all *.faa files, list them in a for loop like shown below:
+   for f *.faa; do $progname \$f; done
+
+HELP
+
+   exit 1
+
+}
+
+[ $# -ne 1 ] && print_help
+
+perl -pe 'if(/^>(\S+)\s+(.*)?$/){ $id1=$1; $id2=$2; $f=(split(/\./, $ARGV))[0]; s/>.*$/>lcl|$id1\_$f $id2/}' $1 > ${1%.*}ed.faa