merge with Dale Kreitler's pa_sg_res_cut -- HJB

Author: Herbert Bernstein

README.md

@@ -1,7 +1,27 @@
 pa_sg_res
     by Wuxian Shi, 13 Feb 2017
     adapted to keyword arguments by H. J. Bernstein
+    window args added by D. Kreitler
+    merged with ps_sg_res_cut by H. J. Bernstein
 
-pa_sg_res [-r<reslow>] [-R<reshigh>] [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]
-  "infile defaults to XDS_ASCII.HKL, oufile to aimless.mtz
+pa_sg_res [-1<first_frame>] [-N<frame_cutoff>] [-R<reslow>] [-r<reshigh>]
+   [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]
+
+ -h produces a short help messaage< --help produces this help message
+
+pa_sg_res is a bash shell script wrapper for aimless and pointless, for
+the downstream processing of fast_dp output. This script allows for trimming
+integrated reflection files (from XDS) based on resolution and frame number
+in addition to spacegroup assignment/enforcement.
+
+Caveat: The impact of crystal misalignment and/or unreliable indexing in the
+first few frames of data collection may still be present even if those frames
+are excluded from pointless/aimless. In such cases re-running fast_dp is
+recommended.
+
+Input arg variables match those of fast_dp (where overlap occurs)
+Input arg variables changed to match pa_sg_res_cut (N for f, swap r and R)
+
+infile defaults to XDS_ASCII.HKL, outfile to aimless.mtz
+logfile in pa_sg_res.log
 

pa_sg_res

@@ -3,7 +3,11 @@
 #  pa_sg_res
 #    By Wuxian Shi, 13 Feb 2017
 #    adapted to keyword arguments by H. J. Bernstein
-#
+#    window args added by D. Kreitler
+#    merged with ps_sg_res_cut by H. J. Bernstein
+if [ "$CCP4"XX == XX ]; then
+  . /usr/local/crys-local/ccp4-7.0/bin/ccp4.setup-sh
+fi
 
 tempfiles=( )
 cleanup() {
@@ -46,16 +50,39 @@ tempfiles+=( "/tmp/aimless$$.log" )
 
 if [ XX$1 == "XX--help" ]
   then
-  echo "pa_sg_res [-r<reslow>] [-R<reshigh>] [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]" >&2
-  echo "infile defaults to XDS_ASCII.HKL, oufile to aimless.mtz" >&2
+  echo "pa_sg_res [-1<first_frame>] [-N<frame_cutoff>] [-R<reslow>] [-r<reshigh>]" >&2
+  echo "   [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]" >&2
+  echo "" >&2
+  echo " -h produces a short help messaage< --help produces this help message" >&2
+  echo "" >&2
+  echo "pa_sg_res is a bash shell script wrapper for aimless and pointless, for" >&2
+  echo "the downstream processing of fast_dp output. This script allows for trimming" >&2
+  echo "integrated reflection files (from XDS) based on resolution and frame number" >&2
+  echo "in addition to spacegroup assignment/enforcement." >&2
+  echo "" >&2
+  echo "Caveat: The impact of crystal misalignment and/or unreliable indexing in the" >&2
+  echo "first few frames of data collection may still be present even if those frames" >&2
+  echo "are excluded from pointless/aimless. In such cases re-running fast_dp is" >&2
+  echo "recommended." >&2
+  echo "" >&2
+  echo "Input arg variables match those of fast_dp (where overlap occurs)" >&2
+  echo "Input arg variables changed to match pa_sg_res_cut (N for f, swap r and R)" >&2
+  echo "" >&2
+  echo "infile defaults to XDS_ASCII.HKL, outfile to aimless.mtz" >&2
   exit -1
 fi
 
-while getopts ":r:R:S:h:o:l:" opt; do
+while getopts "1:f:N:R:r:S:ho:l:" opt; do
   case $opt in
-    r) reslow="$OPTARG"
+    1) first_frame="$OPTARG"
+    ;;
+    f) frame_cutoff="$OPTARG"
+    ;;
+    N) frame_cutoff="$OPTARG"
     ;;
-    R) reshigh="$OPTARG"
+    R) reslow="$OPTARG"
+    ;;
+    r) reshigh="$OPTARG"
     ;;
     S) spacegroup="$OPTARG"
     ;;
@@ -66,8 +93,11 @@ while getopts ":r:R:S:h:o:l:" opt; do
     l) logfile="$OPTARG"
     ;;
     h)
-       echo "pa_sg_res [-r<reslow>] [-R<reshigh>] [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]" >&2
-       echo "file defaults to XDS_ASCII.HKL" >&2
+       echo "pa_sg_res [-1<first_frame>] [-N<frame_cutoff>][-R<reslow>] [-r<reshigh>] \\" >&2
+       echo "          [-S<spacegroup>] [-i<infile>] [-o<outfile>] [-l<logfile>]" >&2
+       echo "infile defaults to XDS_ASCII.HKL" >&2
+       echo " -h produces this message" >&2
+       echo " --help produces a longer messages" >&2
        exit -1
     ;;
     \?) echo "Invalid option -$OPTARG" >&2
@@ -97,6 +127,7 @@ if [ "${spacegroup}XX" == "XX" ]
     spacegroup_arg=${spacegroup}
 fi 
 
+
 resolution_arg="resolution low $reslow high $reshigh"
 if [ "${reslow}XX" == "XX" ]
   then
@@ -108,7 +139,21 @@ if [ "${reslow}XX" == "XX" ]
 elif [ "${reshigh}XX" == "XX" ]
   then
     resolution_arg="resolution low $reslow"
-fi 
+elif (( $(echo "${reslow} <  ${reshigh}" |bc -l) )); then
+  resolution_arg="resolution low $reshigh high $reslow"
+fi
+
+frame_cutoff_arg="exclude batch $frame_cutoff TO 1000000"
+if [ "${frame_cutoff}XX" == "XX" ]
+  then
+    frame_cutoff_arg=${frame_cutoff}
+fi
+
+first_frame_arg="exclude batch 1 to $first_frame"
+if [ "${first_frame}XX" == "XX" ]
+  then
+    first_frame_arg=${first_frame}
+fi
 
 
 
@@ -118,6 +163,8 @@ lla
 
 aimless hklin /tmp/pa_sg_res_pointless$$.mtz hklout $outfile << eof | tee /tmp/aimless$$.log
 $resolution_arg
+$frame_cutoff_arg
+$first_frame_arg
 onlymerge
 eof