Mercurial > repos > devteam > scatterplot
annotate scatterplot.py @ 2:53eb2c412783 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
| author | devteam |
|---|---|
| date | Fri, 18 Dec 2015 19:14:12 -0500 |
| parents | c30eeaaac86d |
| children | 1dacc8aeb452 |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
2 # Greg Von Kuster |
| 0 | 3 |
| 4 import sys | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
5 |
|
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
6 from numpy import array |
|
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
7 from rpy import r |
|
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
8 |
| 0 | 9 |
| 10 def stop_err(msg): | |
| 11 sys.stderr.write(msg) | |
| 12 sys.exit() | |
| 13 | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
14 |
| 0 | 15 def main(): |
| 16 | |
| 17 in_fname = sys.argv[1] | |
| 18 out_fname = sys.argv[2] | |
| 19 try: | |
| 20 columns = int( sys.argv[3] ) - 1, int( sys.argv[4] ) - 1 | |
| 21 except: | |
| 22 stop_err( "Columns not specified, your query does not contain a column of numerical data." ) | |
| 23 title = sys.argv[5] | |
| 24 xlab = sys.argv[6] | |
| 25 ylab = sys.argv[7] | |
| 26 | |
| 27 matrix = [] | |
| 28 skipped_lines = 0 | |
| 29 first_invalid_line = 0 | |
| 30 invalid_value = '' | |
| 31 invalid_column = 0 | |
| 32 i = 0 | |
| 33 for i, line in enumerate( file( in_fname ) ): | |
| 34 valid = True | |
| 35 line = line.rstrip( '\r\n' ) | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
36 if line and not line.startswith( '#' ): |
| 0 | 37 row = [] |
| 38 fields = line.split( "\t" ) | |
| 39 for column in columns: | |
| 40 try: | |
| 41 val = fields[column] | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
42 if val.lower() == "na": |
| 0 | 43 row.append( float( "nan" ) ) |
| 44 else: | |
| 45 row.append( float( fields[column] ) ) | |
| 46 except: | |
| 47 valid = False | |
| 48 skipped_lines += 1 | |
| 49 if not first_invalid_line: | |
| 50 first_invalid_line = i + 1 | |
| 51 try: | |
| 52 invalid_value = fields[column] | |
| 53 except: | |
| 54 invalid_value = '' | |
| 55 invalid_column = column + 1 | |
| 56 break | |
| 57 else: | |
| 58 valid = False | |
| 59 skipped_lines += 1 | |
| 60 if not first_invalid_line: | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
61 first_invalid_line = i + 1 |
| 0 | 62 |
| 63 if valid: | |
| 64 matrix.append( row ) | |
| 65 | |
| 66 if skipped_lines < i: | |
| 67 try: | |
| 68 r.pdf( out_fname, 8, 8 ) | |
| 69 r.plot( array( matrix ), type="p", main=title, xlab=xlab, ylab=ylab, col="blue", pch=19 ) | |
| 70 r.dev_off() | |
| 71 except Exception, exc: | |
|
2
53eb2c412783
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/scatterplot commit de7140295cce07e1bc1697e51dab4271c8d7a8a6
devteam
parents:
0
diff
changeset
|
72 stop_err( "%s" % str( exc ) ) |
| 0 | 73 else: |
| 74 stop_err( "All values in both columns %s and %s are non-numeric or empty." % ( sys.argv[3], sys.argv[4] ) ) | |
| 75 | |
| 76 print "Scatter plot on columns %s, %s. " % ( sys.argv[3], sys.argv[4] ) | |
| 77 if skipped_lines > 0: | |
| 78 print "Skipped %d lines starting with line #%d, value '%s' in column %d is not numeric." % ( skipped_lines, first_invalid_line, invalid_value, invalid_column ) | |
| 79 | |
| 80 r.quit( save="no" ) | |
| 81 | |
| 82 if __name__ == "__main__": | |
| 83 main() |