Using pandas and sqldf and getting a nondescript error

Question

I decided to use Pandas for some of my data analysis and to use the combined sqldf library that uses sqlite3 syntax. The problem is I'm getting a non discript error. I assume it's my sql syntax but nothing is glaring out at me.

Error:

Error on sql  SELECT u.chromosome, u.transcript_affected, u.ensembl_gene_id, u.gene_name ,u.strand, s.transcript_affected, s.ensembl_gene_id, s.gene_name FROM utr_file u INNER JOIN ssm_file s ON u.chromosome= s.chromosome AND u.strand = s.chromosome_strand WHERE s.chromosome_start BETWEEN u.start AND u.end ORDER BY u.chromosome;

SQL line (also in the error above):

 q = ''' SELECT u.chromosome, u.transcript_affected, u.ensembl_gene_id, u.gene_name ,u.strand, s.transcript_affected, s.ensembl_gene_id, s.gene_name FROM utr_file u INNER JOIN ssm_file s ON u.chromosome= s.chromosome AND u.strand = s.chromosome_strand WHERE s.chromosome_start BETWEEN u.start AND u.end ORDER BY u.chromosome;'''

 qsubset= sqldf(q,globals())

Goal: I'm trying to determine where mutations in ssm_file (by location) match in utr_file (between start and end). I also need to match by chromosome and strand first.

Sample utr-file:

  chromosome     start       end                              gene_name strand  
0       chr1  67208778  67210768    NM_032291_utr3_24_0_chr1_67208779_f   +
1       chr1  48998526  48999844     NM_032785_utr3_0_0_chr1_48998527_r   -
2       chr1  16785385  16786584     NM_018090_utr3_7_0_chr1_16785386_f   +
3       chr1  33585783  33585995    NM_052998_utr3_11_0_chr1_33585784_f   +
4       chr1  16785385  16786584  NM_001145278_utr3_7_0_chr1_16785386_f   +

Sample ssm_file:

  chromosome  chromosome_start  chromosome_strand transcript_affected  \
0       chr1         100951090                  +     ENSG00000079335   
1       chr1         100951090                  +     ENSG00000079335   
2       chr1         100951090                  +     ENSG00000079335   
3       chr1         100951090                  +     ENSG00000079335   
4       chr1         100951090                  +     ENSG00000079335   

   ensembl_gene_id gene_name  
0  ENST00000544534    CDC14A  
1  ENST00000542213    CDC14A  
2  ENST00000370125    CDC14A  
3  ENST00000361544    CDC14A  
4  ENST00000336454    CDC14A

qxjit · Accepted Answer · 2013-06-08 18:32:56Z

2

It looks like you have some column location issues. I don't have Pandas installed, but this query worked against temp tables created in sqlite:

SELECT u.chromosome, u.gene_name ,u.strand, s.transcript_affected, 
s.ensembl_gene_id, s.gene_name FROM utr_file u INNER JOIN ssm_file s ON u.chromosome=
s.chromosome AND u.strand = s.chromosome_strand
WHERE s.chromosome_start BETWEEN u.start AND u.end ORDER BY u.chromosome;

I've removed u.ensembl_gene_id and u.transcript_affected from the select since those columns only appear in ssm_file.

answered Jun 8, 2013 at 18:32

qxjit

361 bronze badge

Sign up to request clarification or add additional context in comments.

Collectives™ on Stack Overflow

Using pandas and sqldf and getting a nondescript error

1 Answer 1

Comments

Your Answer

Hot Network Questions

Collectives™ on Stack Overflow

1 Answer 1

Comments

Your Answer

Sign up or log in

Post as a guest

Related