Error in using phaser_gene_ae.py about phaser

[secastel]

Hmmm, not sure what is going on here. Could you provide both full input files (wm82a2.gene.bed, F12_1_output.haplotypic_counts.txt) so I can try to reproduce the error?

[c-nabokov]

Hmmm, not sure what is going on here. Could you provide both full input files (wm82a2.gene.bed, F12_1_output.haplotypic_counts.txt) so I can try to reproduce the error?

Of course. Thank you very much for your reply and help.

I have uploaded the file to the following link.

https://github.com/c-nabokov/Test-files

Thanks for your help again.

[lintingyi2014]

I am also encountering this error

[lint6@cn4287 SCRIPTS]$ phaser_gene_ae.py --haplotypic_counts phaser_test.haplotypic_counts.txt --features gencode.v26.GRCh38.genes.bed.gz --o phaser_test_case_gene_ae.txt

##################################################
Welcome to phASER Gene AE v1.2.0
Author: Stephane Castel ([email protected])
##################################################

#1 Loading features...
Traceback (most recent call last):
File "/usr/local/bin/phaser_gene_ae.py", line 241, in
main();
File "/usr/local/bin/phaser_gene_ae.py", line 47, in main
start = int(columns[1]);
IndexError: list index out of range

[lintingyi2014]

somehow it needed to be re-tabbed

It works with:
zcat gencode.v26.GRCh38.genes.bed.gz | sed 's/^I/\t/g' | awk 'BEGIN{OFS="\t"} {if(NF==4) print $0; else print "Invalid line:", $0}' > re_tabbed_file.bed

[secastel]

When I try this I am not seeing any lines come up as "Invalid". Are you? If so can you please share which? When you say it is now working, are you using the ".bed" file you generated with the above code as input, or are you gzipping it again?

[netwon123]

Hellow, Could you solved this bug?