v0.9.16

- added version number
- added license
- added prefix option for bam2cov
- added old function names again as aliases ("plot", "comparecov")

Author: Dom Laetsch

bam2cov.py

@@ -1,13 +1,14 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 
-"""usage: blobtools bam2cov         -i FASTA -b BAM [--mq MQ] [--no_base_cov]
+"""usage: blobtools bam2cov         -i FASTA -b BAM [-o PREFIX] [--mq MQ] [--no_base_cov]
                                     [-h|--help]
 
     Options:
         -h --help                   show this
         -i, --infile FASTA          FASTA file of assembly. Headers are split at whitespaces.
         -b, --bam <BAM>             BAM file (requires samtools in $PATH)
+        -o, --output <PREFIX>       Output prefix
         --mq <MQ>                   minimum Mapping Quality (MQ) [default: 1]
         --no_base_cov               only parse read coverage (faster, but ...
                                         can only be used for "blobtools blobplot --noblobs")
@@ -65,6 +66,7 @@ def readFasta(infile):
 
 def parseFasta(infile):
     fasta_dict = {}
+    print BtLog.status_d['1'] % ("FASTA", fasta_f)
     for name, seq in readFasta(infile):
         fasta = Fasta(name, seq)
         fasta_dict[fasta.name] = fasta
@@ -124,6 +126,7 @@ def parseBam(bam_f, fasta_dict):
     return fasta_dict, reads_total, reads_mapped
 
 def writeCov(fasta_dict, reads_total, reads_mapped, out_f):
+    print BtLog.status_d['13'] % out_f
     with open(out_f, 'w') as fh:
         fh.write("# Total Reads = %s\n" % (reads_total))
         fh.write("# Mapped Reads = %s\n" % (reads_mapped))
@@ -135,10 +138,15 @@ def writeCov(fasta_dict, reads_total, reads_mapped, out_f):
 
 if __name__ == '__main__':
     args = docopt(__doc__)
-
     fasta_f = args['--infile']
     bam_f = args['--bam']
     out_f = os.path.basename(bam_f) + ".cov"
+    prefix = args['--output']
+    if (prefix):
+        if prefix.endswith("/"):
+            out_f = prefix + out_f
+        else:
+            out_f = prefix + "." + out_f
     mq = int(args['--mq'])
     no_base_cov_flag = args['--no_base_cov']
 

blobtools

@@ -5,6 +5,8 @@
 usage: blobtools <command> [<args>...] [--help]
 
 commands:
+  version       print version number
+
   create        create a BlobDB
   view          print BlobDB as a table
   blobplot      plot BlobDB as a blobplot
@@ -26,20 +28,21 @@ from docopt import docopt
 if __name__ == '__main__':
     main_dir = join(dirname(__file__), '')
     args = docopt(__doc__,
-                  version='version 0.9.13',
+                  version='blobtools v0.9.16',
                   options_first=True)
-    #print(args)
 
     argv = [args['<command>']] + args['<args>']
     if args['<command>'] == 'create':
         exit(call(['python', main_dir + 'create.py'] + argv))
     elif args['<command>'] == 'view':
         exit(call(['python', main_dir + 'view.py'] + argv))
     elif args['<command>'] == 'blobplot' or args['<command>'] == 'plot':
+        argv[0] = "blobplot"
         exit(call(['python', main_dir + 'blobplot.py'] + argv))
     elif args['<command>'] == 'bam2cov':
         exit(call(['python', main_dir + 'bam2cov.py'] + argv))
     elif args['<command>'] == 'covplot' or args['<command>'] == 'comparecov':
+        argv[0] = "blobplot"
         exit(call(['python', main_dir + 'covplot.py'] + argv))
     elif args['<command>'] == 'sumcov':
         exit(call(['python', main_dir + 'sumcov.py'] + argv))

lib/BtLog.py

@@ -80,7 +80,8 @@ def progress(iteration, steps, max_value):
     '9' : '[STATUS]\t: Reading BlobDb %s',
     '10': '[STATUS]\t: \tChecking with \'samtools flagstat\'',
     '11': '[STATUS]\t: \tMapping reads = %s, total reads = %s (mapping rate = %s)',
-    '12': '[STATUS]\t: \tChecking with \'clc_mapping_info\''
+    '12': '[STATUS]\t: \tChecking with \'clc_mapping_info\'',
+    '13': '[STATUS]\t: \tWriting %s'
 }
 
 info_d = {