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BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.
GNU General Public License v3.0
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NameError: global name 'AllSeqsToPrint' is not defined #2

Closed olli0601 closed 8 years ago

olli0601 commented 8 years ago

Hi all, Just pulled the latest version (Feb-1), and I call phylotypes.py with the command

"/Users/Oliver/git/phylotypes/phylotypes.py 1 2 "ptyr1_bam.txt" "ptyr1_ref.txt" -Q1 18 -Q2 2 -P -W 1000,1060 --alignment-of-other-refs /Users/Oliver/Library/R/3.1/library/phyloscan/HIV1_compendium_C_B_CPX.fasta --ref-for-rooting R0_CPX_AF460972_read_1_count_0 -T --keep-overhangs --x-raxml raxml --x-mafft mafft"

which gives

Now processing window 1000-1060 Warning: bam file R3_res021_S94_L001 has no reads in window 175-235 Warning: bam file R6_RES666_S34_L001 has no reads in window 175-235 Traceback (most recent call last): File "/Users/Oliver/git/phylotypes/phylotypes.py", line 782, in SampleReadCounts, RefSeqs = ReadFastaOfReadsIntoDicts(FileForReads) File "/Users/Oliver/git/phylotypes/phylotypes.py", line 562, in ReadFastaOfReadsIntoDicts AllSeqsToPrint.append(seq) NameError: global name 'AllSeqsToPrint' is not defined

Thank you, olli

PS: The same command with modifications on -W runs fine with the previous version.

ChrisHIV commented 8 years ago

Fixed! Ta