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