add new -m8Cr option for raw scores, update documentation

wrpearson · Nov 14, 2022 · bd53d2a · bd53d2a
1 parent af03795
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diff --git a/doc/README_v36.3.8i.md b/doc/README_v36.3.8i.md
@@ -79,6 +79,8 @@ Changes in **fasta-36.3.8i** Nov, 2022
 
 4. changes to annotation scripts for Pfam shutdown; new ann_pfam_www.py, ann_pfam_sql.py
 
+5. a new option, `r` for `-m 8CB` that displays the raw optimal alignment score (typically Smith-Waterman).
+
 Changes in **fasta-36.3.8i** Sept, 2021
 
 1. Enable translation table -t 9 for Echinoderms.  This bug has existed

diff --git a/doc/fasta_guide.tex b/doc/fasta_guide.tex
@@ -906,11 +906,15 @@ \subsubsection{Command line options}
   \texttt{-m 8CBd} adds a new field with
   the raw domain coordinate information for the query and subject, with \texttt{DX/XD} used to indicate the domains.
   \texttt{-m 8CBL} provides both query/subject lengths and raw domain information.
+
+
 \begin{verbatim}
   |DX:3-82;C=C.Thio|DX:105-201;C=C.GST_C|XD:3-82;C=C.Thio|XD:105-201;C=C.GST_C
 \end{verbatim}
 
-  These \texttt{-m 8CB} options, \texttt{'l/L'}, \texttt{'s'}, \texttt{'d'} can be combined in any order.
+  \texttt(-m 8CBr) (v36.3.8i release, 14-Nov-2022) adds a new field with the raw optimal alignment score (typically Smith-Waterman for proteins).
+
+  These \texttt{-m 8CB} options, \texttt{'l/L'}, \texttt{'s'}, \texttt{'d'}, and \texttt{'r'} can be combined in any order.
 
 \item[\texttt{-m 9}] display alignment coordinates and scores with the
   best score information.  \texttt{-m 9i} provides alignment length,

diff --git a/doc/readme.v36 b/doc/readme.v36
@@ -16,6 +16,12 @@ because clan information is not yet available (or I do not know how to
 get it).  In addition, ann_pfam_sql.py is available, which largely
 replaces ann_pfam_sql.pl.
 
+>>Nov 14, 2022
+[defs.h, initfa.c, mshowbest.c]
+
+Add option 'r' to -m8CB to display raw optimal score in BLAST tabular
+output, e.g "-m8Cr"  or "-m8CBlr".
+
 >>Nov 7, 2022
 [doinit.c/initenv()]
 Check string size for query and library file names, and abort if they
@@ -82,7 +88,7 @@ Format (PEFF) files (http://www.psidev.info/peff).
 
 >>June 2, 2020
 [src/scaleswn.c]
-Modifiy line describing query in -R .res file.
+Modify line describing query in -R .res file.
 Add line to report ave_n1, sample_fract, zs_off in -R .res file.
 Add line to report properties of library to -R .res file.
 

diff --git a/src/defs.h b/src/defs.h
@@ -158,6 +158,7 @@
 #define MX_RES_ALIGN_SCORE (1<<20)  /* show residue alignment score, not alignment */
 #define MX_M8_BTAB_LEN  (1<<21) /* show query/subject seq. lens in -m 8 output */
 #define MX_M8_BTAB_SIM  (1<<22) /* show similarity + identity in -m 8 output */
+#define MX_M8_BTAB_RAW  (1<<23) /* show raw score */
 
 /* codes for -m 9, -m 8C? */
 #define SHOW_CODE_ID	1	/* identity only */

diff --git a/src/doinit.c b/src/doinit.c
@@ -938,6 +938,9 @@ parse_markx(char *optarg, struct markx_str *this) {
     if (strchr(stmp,'s')) {
       this->markx |= MX_M8_BTAB_SIM;
     }
+    if (strchr(stmp,'r')) {
+      this->markx |= MX_M8_BTAB_RAW;
+    }
     if (strchr(stmp,'d')) {
       this->show_code |= SHOW_CODE_DOMINFO;
     }

diff --git a/src/mshowbest.c b/src/mshowbest.c
@@ -250,18 +250,39 @@ void showbest (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
     /* line below copied from BLAST+ output */
     if (m_msp->markx & MX_M8_BTAB_LEN) {  /* yes qslen */
       if (m_msp->markx & MX_M8_BTAB_SIM) {  /* yes similarity */
-	fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% similar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+
+	if (m_msp->markx & MX_M8_BTAB_RAW) {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% similar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, raw score");
+	}
+	else {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% similar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	}
       }
       else { /* no similarity */
-	fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	if (m_msp->markx & MX_M8_BTAB_RAW) {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, raw score");
+	}
+	else {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	}
       }
     }
     else {  /* no qslen */
       if (m_msp->markx & MX_M8_BTAB_SIM) {  /* yes similarity */
-	fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% simlar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	if (m_msp->markx & MX_M8_BTAB_RAW) {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% simlar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, raw score");
+	}
+	else {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, %% simlar, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	}
       }
       else { /* no similarity */
-	fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	if (m_msp->markx & MX_M8_BTAB_RAW) {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score, raw score");
+	}
+	else {
+	  fprintf(fp,"# Fields: query id, query length, subject id, subject length, %% identity, alignment length, mismatches, gap opens, q. start, q. end, s. start, s. end, evalue, bit score");
+	}
       }
     }
 
@@ -635,6 +656,10 @@ void showbest (FILE *fp, unsigned char **aa0, unsigned char *aa1save, int maxn,
 		    zs_to_E(lzscore,n1,ppst->dnaseq,ppst->zdb_size,m_msp->db),
 		    lbits);
 
+	    if (m_msp->markx & MX_M8_BTAB_RAW) {
+	      fprintf(fp,"\t%d",cur_ares_p->sw_score);
+	    }
+
 	    if (ppst->zsflag > 20) {
 	      fprintf(fp,"\t%.2g",zs_to_E(lzscore2, n1, ppst->dnaseq, ppst->zdb_size, m_msp->db));
 	    }