Multiple bugs encountered

[pliang64]

Hi Simo,

I wanted to try your tool, but encountered multiple issues as listed below. It would be great if you can provide a new working version.

Thanks, Ping Liang

python ~/labbin/AGOUTI/agouti.py --version[pliang@cop33 AGOUTI]$ Traceback (most recent call last): File "/home/pliang/labbin/AGOUTI/agouti.py", line 20, in from src import agouti_update as agUPDATE File "/gwork/lianglab/bin/AGOUTI/src/agouti_update.py", line 346 print oriPath ^ SyntaxError: Missing parentheses in call to 'print'

[pliang@cop33 AGOUTI]$ 2017-10-23 12:00:12,293 - INFO - SHREDDER PROGRESS - [BEGIN] Shredding assembly 2017-10-23 12:00:12,338 - INFO - SHREDDER PROGRESS - # processed | Current sequence ID | Elapsed Time Traceback (most recent call last): File "/home/pliang/labbin/AGOUTI/agouti.py", line 288, in main() File "/home/pliang/labbin/AGOUTI/agouti.py", line 285, in main args.func(args) File "/home/pliang/labbin/AGOUTI/agouti.py", line 174, in run_shredder minGap, minCtgLen) File "/gwork/lianglab/bin/AGOUTI/src/agouti_shred.py", line 269, in agouti_shred_main dHeader2Intervals = shred_assembly(assemblyFile, breakerProgress, prefix, minGaps, minCtgLen) File "/gwork/lianglab/bin/AGOUTI/src/agouti_shred.py", line 292, in shred_assembly for header, seq in agSeq.read_fasta(assemblyFile): File "/gwork/lianglab/bin/AGOUTI/src/agouti_sequence.py", line 56, in read_fasta header = header.next()[1:].strip().split()[0] AttributeError: 'itertools._grouper' object has no attribute 'next'

[svm-zhang]

Hello Ping,

Thanks for using AGOUTI.

From what I see here, are you using Python 3?

Simo

[svm-zhang]

Close now. Reopen if issue persists.