print messages more explicit

rigdenlab · Feb 18, 2017 · 604d0ca · 604d0ca
1 parent a8d5290
commit 604d0ca
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Showing 4 changed files with 22 additions and 17 deletions.
diff --git a/scripts/conkit.msatool b/scripts/conkit.msatool
@@ -34,13 +34,13 @@ def main():
     plot = args.msafile.rsplit('.', 1)[0] + '.png'
     conkit.plot.SequenceCoverageFigure(hierarchy, file_name=plot)
 
-    logging.info('Input MSA File:                   {0}'.format(args.msafile))
-    logging.info('Input MSA Format:                 {0}'.format(args.msaformat))
-    logging.info('Sequence Identity Threshold:      {0}'.format(args.id))
-    logging.info('Length of the Target Sequence:    {0}'.format(seq_len))
-    logging.info('Total Number of Sequences:        {0}'.format(nseqs))
-    logging.info('Number of Effective Sequences:    {0}'.format(meff))
-    logging.info('Sequence Coverage Plot:           {0}'.format(plot))
+    logging.info('Input MSA File:                            {0}'.format(args.msafile))
+    logging.info('Input MSA Format:                          {0}'.format(args.msaformat))
+    logging.info('Pairwise Sequence Identity Threshold:      {0}'.format(args.id))
+    logging.info('Length of the Target Sequence:             {0}'.format(seq_len))
+    logging.info('Total Number of Sequences:                 {0}'.format(nseqs))
+    logging.info('Number of Effective Sequences:             {0}'.format(meff))
+    logging.info('Sequence Coverage Plot:                    {0}'.format(plot))
 
     return 0
 

diff --git a/scripts/conkit.plot b/scripts/conkit.plot
@@ -185,8 +185,8 @@ For more specific descriptions, call each subcommand's help menu directly.
         if args.interchain:
             logging.info('This script is experimental for inter-chain contact plotting')
 
-        logging.info('Distance to neighbors: {0}'.format(args.dtn))
-        logging.info('Contact list cutoff factor: {0}'.format(args.dfactor))
+        logging.info('Min sequence separation for contacting residues: {0}'.format(args.dtn))
+        logging.info('Contact list cutoff factor: {0} * L'.format(args.dfactor))
 
         seq = conkit.io.read(args.seqfile, args.seqformat)[0]
         con = conkit.io.read(args.confile, args.conformat)[0]
@@ -248,8 +248,8 @@ For more specific descriptions, call each subcommand's help menu directly.
                                             dpi=args.dpi)
 
     elif args.which == 'contact_map_chord':
-        logging.info('Distance to neighbors: {0}'.format(args.dtn))
-        logging.info('Contact list cutoff factor: {0}'.format(args.dfactor))
+        logging.info('Min sequence separation for contacting residues: {0}'.format(args.dtn))
+        logging.info('Contact list cutoff factor: {0} * L'.format(args.dfactor))
 
         seq = conkit.io.read(args.seqfile, args.seqformat)[0]
         con = conkit.io.read(args.confile, args.conformat)[0]
@@ -268,8 +268,8 @@ For more specific descriptions, call each subcommand's help menu directly.
         if args.interchain:
             logging.info('This script is experimental for inter-chain contact plotting')
 
-        logging.info('Distance to neighbors: {0}'.format(args.dtn))
-        logging.info('Contact list cutoff factor step: {0}'.format(args.cutoff_step))
+        logging.info('Min sequence separation for contacting residues: {0}'.format(args.dtn))
+        logging.info('Contact list cutoff factor: {0} * L'.format(args.dfactor))
 
         seq = conkit.io.read(args.seqfile, args.seqformat)[0]
         con = conkit.io.read(args.confile, args.conformat)[0]

diff --git a/scripts/conkit.precision b/scripts/conkit.precision
@@ -46,14 +46,15 @@ def main():
     con.sequence = seq
     con.assign_sequence_register()
 
-    logging.info('Distance to neighbors: {0}'.format(args.dtn))
-    con.remove_neighbors(min_distance=args.dtn, inplace=True)
+    logging.info('Min sequence separation for contacting residues: {0}'.format(args.dtn))
+    logging.info('Contact list cutoff factor: {0} * L'.format(args.dfactor))
 
+    con.remove_neighbors(min_distance=args.dtn, inplace=True)
     ncontacts = int(seq.seq_len * args.dfactor)
-    logging.info('Max number of contacts: {0}'.format(ncontacts))
     con.sort('raw_score', reverse=True, inplace=True)
     con_sliced = con[:ncontacts]
 
+
     con_matched = con_sliced.match(pdb)
     precision = con_matched.precision
 

diff --git a/scripts/conkit.predict b/scripts/conkit.predict
@@ -146,7 +146,8 @@ def main():
     logging.info('Final alignment file: {0}'.format(jon_fname))
     msa_h = conkit.io.read(jon_fname, 'jones')
     logging.info('|- Total Number of sequences: {0}'.format(msa_h.nseqs))
-    logging.info('|- Number of effective sequences: {0}'.format(msa_h.calculate_meff()))
+    logging.info('|- Pairwise Sequence Identity Threshold: {0}'.format(0.7))
+    logging.info('|- Number of effective sequences: {0}'.format(msa_h.calculate_meff(identity=0.7)))
     freq_plot_fname = os.path.join(args.wdir, args.prefix + 'freq.pdf')
     conkit.plot.SequenceCoverageFigure(msa_h, file_name=freq_plot_fname)
     logging.info('|- Plotted sequence coverage: {0}'.format(freq_plot_fname))
@@ -177,12 +178,15 @@ def main():
     contact_map_fname = os.path.join(args.wdir, args.prefix + 'cmap.pdf')
     conkit.plot.ContactMapFigure(cmap, file_name=contact_map_fname)
     logging.info('Plotted contact map: {0}'.format(contact_map_fname))
+    logging.info('|- Min sequence separation for contacting residues: {0}'.format(args.dtn))
+    logging.info('|- Contact list cutoff factor: {0} * L'.format(args.dfactor))
 
     # Use the ccmpred parser to write a contact file
     casprr_fname = os.path.join(args.wdir, args.prefix + '.rr')
     conkit.io.convert(matrix_fname, 'ccmpred', casprr_fname, 'casprr')
     logging.info('Final prediction file: {0}'.format(casprr_fname))
 
+
     return 0