Question

I am using Python 2.7.3 btw

Hi all,

I have a little problem. The problem is that I keep running into trouble with the starred line below. (Sorry, kinda new to Python)

So here is my code so far:

with open('parsedChr','w') as fout, open('heartLungClassU.gtf','r') as filein:

    average = 0
    difference = 0
    position = ''
    bp = 0

    for line in filein:
      **chrom,cuff,exon,start,end,dot,sign,dots,gene,tranid,exonid,rest = line.split('\t',11)**
      ## notice 12 variables here so I tried to unpack with value 11

    ##more code after

I keep getting this error:

Traceback (most recent call last):
  File "parse.py", line 11, in <module>
    chrom,cuff,exon,start,end,dot,sign,dots,gene,tranid,exonid,rest = line.split('\t',11)
ValueError: need more than 9 values to unpack

I don’t understand why though — note that there are 12 variables I am splitting the line into. Why would python complain about needing more than 9 values to unpack? I’ve had code before where I had to split into 6 variables and so used 5 in line.split (5 cuts into 6 pieces, as I understood it), but I don’t understand why similar logic doesn’t work here.

EDIT: here is a portion of the file:

chr1    Cufflinks   exon    14765607    14765689    .   +   .   gene_id "XLOC_000018";  transcript_id   "TCONS_00001260";   exon_number "1";    oId "CUFF.68.1";    class_code  "u";    tss_id  "TSS40";
chr1    Cufflinks   exon    14766604    14767199    .   +   .   gene_id "XLOC_000018";  transcript_id   "TCONS_00001260";   exon_number "2";    oId "CUFF.68.1";    class_code  "u";    tss_id  "TSS40";
chr1    Cufflinks   exon    21156530    21156632    .   +   .   gene_id "XLOC_000028";  transcript_id   "TCONS_00002433";   exon_number "1";    oId "CUFF.88.1";    class_code  "u";    tss_id  "TSS69";

EDIT: Meh. Figured it out. Thanks for the help everyone.

Answer 1

To see what the exact line number where the error is do this:

for i, line in enumerate(filein):
    try:
        chrom,cuff,exon,start,end,dot,sign,dots,gene,tranid,exonid,rest = line.split('\t',11)
    except ValueError:
        print "ValueError on line", i+1
        print "line", repr(line)
        raise

In your comment you provided a link to your text file. I don’t find any line with less than 11 tabs:

>>> for i, line in enumerate(urllib.urlopen('http://dl.dropbox.com/u/108419362/file.gtf')):
...     if line.count('\t') < 11:
...         print i+1, repr(line)
...         break
...
>>>

Double check that you are really opening the file you think you are opening.