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DoaneAS / rseqc

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cdsStart=int(fields[6]) ValueError: invalid literal for int() with base 10: '1.7e+07' #24

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. read_distribution.py -i some.bam -r refGenes.bed

What is the expected output? What do you see instead?
processing refGenes.bed ...Traceback (most recent call last):
  File "/usr/local/bin/read_distribution.py", line 5, in <module>
    pkg_resources.run_script('RSeQC==2.3.6', 'read_distribution.py')
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 499, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 1235, in run_script
    execfile(script_filename, namespace, namespace)
  File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.3.6-py2.7-linux-x86_64.egg/EGG-INFO/scripts/read_distribution.py", line 298, in <module>
main()
  File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.3.6-py2.7-linux-x86_64.egg/EGG-INFO/scripts/read_distribution.py", line 187, in main
    intergenic_down1kb_base,intergenic_down5kb_base,intergenic_down10kb_base) = process_gene_model(options.ref_gene_model)
  File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.3.6-py2.7-linux-x86_64.egg/EGG-INFO/scripts/read_distribution.py", line 71, in process_gene_model
    utr_3 = obj.getUTR(utr=3)
  File "/usr/local/lib/python2.7/dist-packages/RSeQC-2.3.6-py2.7-linux-x86_64.egg/qcmodule/BED.py", line 427, in getUTRcdsStart=int(fields[6])                                                       ValueError: invalid literal for int() with base 10: '1.7e+07'

What version of the product are you using? On what operating system?
2.3.6

Please provide any additional information below.
R> summary(refGenes[,7])
     Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
     6010  26830000  54800000  70380000 107200000 249200000

Original issue reported on code.google.com by andreas....@gmail.com on 19 Jun 2013 at 10:44

Attachments:

GoogleCodeExporter commented 9 years ago 
I've had the same problem, if you remove all spaces (blanks) in the gene ID's 
in your
refGenes.bed file, it should work.

E.g.
chr11   102314959   102319748   GPALPHA 
IIB 0   -   102317122   102318902   255,0,0 7   2355,117,120,144,393,80,93  0,2584,3319,353
9,3814,4467,4696
changed to:
chr11   102314959   102319748   GPALPHA_IIB 0   -   102317122   102318902   255,0,0 7   2355,117
,120,144,393,80,93  0,2584,3319,3539,3814,4467,4696

Martin
--
Martin Reczko

Original comment by mrec...@googlemail.com on 10 Feb 2015 at 1:59