search

aweimann / traitar

GNU General Public License v3.0
21 stars 25 forks source link

TypeError: expected string or buffer #63

Open Katterinne opened 7 years ago

Katterinne commented 7 years ago

Dear Aaron Weimann,

Thank you for develop Traitar, I think this program would be very useful to better understand the biological meaning of our data.

I have a issue that I can not understand when I run traitar. I have succefully installed traitar using python2.7 virtualenv. But when I run traitar I get the following...

traitar phenotype genus_in genus_sample-file from_nucleotides genus_out

Traceback (most recent call last): File "/lustre/groups/cbi/ecastron/Katterinne/Psychrobacter_glacincola/Traitar/pyc1traitar/bin/traitar", line 492, in <module> args.func(args) File "/lustre/groups/cbi/ecastron/Katterinne/Psychrobacter_glacincola/Traitar/pyc1traitar/bin/traitar", line 32, in phenolyze p = Traitar(args.input_dir, args.output_dir, args.sample2file, args.cpus, args.rearrange_heatmap, args.heatmap_format, args.no_heatmap_phenotype_clustering, args.no_heatmap_sample_clustering, args.gene_gff_type, args.primary_models, args.secondary_models) File "/lustre/groups/cbi/ecastron/Katterinne/Psychrobacter_glacincola/Traitar/pyc1traitar/bin/traitar", line 71, in __init__ self.s2f = self.parse_sample_f() File "/lustre/groups/cbi/ecastron/Katterinne/Psychrobacter_glacincola/Traitar/pyc1traitar/bin/traitar", line 133, in parse_sample_f if not self._special_match(i): File "/lustre/groups/cbi/ecastron/Katterinne/Psychrobacter_glacincola/Traitar/pyc1traitar/bin/traitar", line 111, in _special_match return not bool(search(strg)) TypeError: expected string or buffer

I hope this can be fixed and be useful for other users.

Thank you very much!

abremges commented 7 years ago

Thank you, @Katterinne – I believe Aaron will look into this once he's back.

Katterinne commented 7 years ago

Thank you @abremges ! Meantime I'm testing traitor in Mac OS, it seems to work well.

aweimann commented 7 years ago

Dear @Katterinne, Thanks for your interest in Traitar and for reporting this issue! It might be a problem with your sample table. Make sure you use tabs to separate your output. Please let me know if that works. Just to be sure, do you mean you don't observe that problem with Mac OS?

Cheers, Aaron