Databases
StackOverflow2013
Postsdbo
POValueError: invalid literal for int() with base 10: '3"\r'
 

Note that there are some explanatory texts on larger screens.

plurals
  1. POValueError: invalid literal for int() with base 10: '3"\r'
    primarykey
    data
    text
    <p>My csv file (test.csv) content sample below: Note: My test.csv file is about 60MB.</p> <pre><code>"Position","Value" "2545600","19" "2545601","19" "2545602","19" "2545603","19" "2545604","20" "2545605","20" "2545606","21" "2545607","22" "2545608","21" "2545609","20" "2545610","21" "2545611","18" "2545612","19" "2545613","21" "2545614","21" "2545615","21" "2545616","21" "2545617","22" "2545618","25" "2545619","25" </code></pre> <p>My python code (test.py) below:</p> <pre><code>#!/usr/bin/python import sys txt = open(sys.argv[1], 'r') out = open(sys.argv[2], 'w') mil = float(sys.argv[3]) out.write('chr\tstart\tend\tfeature\t'+sys.argv[2]+'\n') for line in txt: if 'Position' not in line: line = line.strip('",\n') line = line.split('","') line[1] = str(int(line[1])/mil) out.write('gi|255767013|ref|NC_000964.3|\t'+line[0]+'\t'+line[0]+'\t\t'+line[1]+'\n') txt.close() out.close() </code></pre> <p>My command line:</p> <pre><code>python test.py test.csv test.igv 5 </code></pre> <p>After I run the command I got an error:</p> <pre><code>Traceback (most recent call last): File "test.py", line 15, in &lt;module&gt; line[1] = str(int(line[1])/mil) ValueError: invalid literal for int() with base 10: '3"\r' </code></pre> <p>However if I create a new empty csv file i.e. small.csv and copy/paste only few lines (like the sample above) from my test.csv file. Then it runs that command successfully.</p> <pre><code>python test.py small.csv small.igv 5 </code></pre> <p>Input small.csv:</p> <pre><code>"Position","Value" "2545600","19" "2545601","19" "2545602","19" "2545603","19" "2545604","20" "2545605","20" "2545606","21" "2545607","22" "2545608","21" "2545609","20" </code></pre> <p>Output small.igv:</p> <pre><code>chr start end feature small.igv gi|255767013|ref|NC_000964.3| 2545600 2545600 3.8 gi|255767013|ref|NC_000964.3| 2545601 2545601 3.8 gi|255767013|ref|NC_000964.3| 2545602 2545602 3.8 gi|255767013|ref|NC_000964.3| 2545603 2545603 3.8 gi|255767013|ref|NC_000964.3| 2545604 2545604 4.0 gi|255767013|ref|NC_000964.3| 2545605 2545605 4.0 gi|255767013|ref|NC_000964.3| 2545606 2545606 4.2 gi|255767013|ref|NC_000964.3| 2545607 2545607 4.4 gi|255767013|ref|NC_000964.3| 2545608 2545608 4.2 gi|255767013|ref|NC_000964.3| 2545609 2545609 4.0 </code></pre> <p>That's all I want. So the problem, why can't I do it on a bigger size csv file?</p>
    singulars
    1. PO
      singulars
      1. PTAnswer
    1. This table or related slice is empty.
    1. PTQuestion
    1. USStickers
    1. USStickers
    plurals
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. This table or related slice is empty.
    1. PO
      singulars
      1. PTAnswer
    2. PO
      singulars
      1. PTAnswer
    3. PO
      singulars
      1. PTAnswer
    1. VO
      singulars
      1. POValueError: invalid literal for int() with base 10: '3"\r'
      1. This table or related slice is empty.
      1. VTDownMod
    2. VO
      singulars
      1. POValueError: invalid literal for int() with base 10: '3"\r'
      1. This table or related slice is empty.
      1. VTUpMod
    1. This table or related slice is empty.
 

Querying!

 
Guidance
A row detail

Detail views are divided into sections. All the information in the data section comes from columns in the selected row. The other sections display data from other, related rows.

Related data can be related in a to-one or a to-many fashion. Captions of data related in a to-many fashion link to a list view showing a filtered view of the table.

Try moving around until you find a non-empty to-many entry and click on the label to get to one. You can move back to the root by clicking on the database name in the header.

SQuiL has stopped working due to an internal error.

If you are curious you may find further information in the browser console, which is accessible through the devtools (F12).

Reload