in flair.py correct, no data read into splice junctions when junctions file has strand '0'

[alfredsimkin]

Hello,

I used STAR to align reads to the dm6.fa genome, followed by samtools view to convert the output bam file over to sam, followed by junctions_from_sam.py so that I could use the -j option. I'm not getting any errors (only a warning: RuntimeWarning: line buffering (buffering=1) isn't supported in binary mode, the default buffer size will be used
self.stderr = io.open(errread, 'rb', bufsize) but the output file is empty. Further querying with print statements added to ssCorrect.py reveals that none of the splice junctions from my input file are being utilized.

My tab delimited file lists splice junctions, but always lists column[3] as 0. Incidentally, the file is output with the .bed suffix, but it seems to be more akin to junc.tab formatted file of the sort I might expect to see from STAR (there are only 5 columns, and the last column does not end in '+' or '-'.

In the file ssCorrect.py, it looks like line 121 interprets the file type as junc.tab (because column[3]=='0'), but then line 150 reads in the fact that column[3] is not '1' or '2' and executes 'continue' for every line of the junctions file, resulting in an empty output file.

I am looking into STAR and other upstream programs to attempt to get strand information in my junctions files (column[3]==1 or 2, or a true bed formatted output file) from my mapped short reads, but in the meantime, I thought it might be useful if modify ssCorrect.py could be altered so that it either has the ability to analyze non-stranded splice junction annotations (rather than 'continue' on these lines) or gives the user an informative error stating that non-stranded junction files are not supported.

Does ssCorrect have support for non-stranded junction files, and do you have any insight into how these non-stranded junction files were created by junctions_from_sam.py?

[diekhans]

related to #273