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Concatenates FASTA files, imputes dummy sequences, and prints a partition table

License: GNU General Public License v3.0

Python 100.00%

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concatfasta's Issues

UnboundLocalError: local variable 'head' referenced before assignment

Hello,
When trying to use ConcatFasta with the code below:

python /n/home10/tlvieira/ConcatFasta.py --dir /n/holyscratch01/davis_lab/tlvieira/raw-data-target-dec-8/231130_A00794_0971_BHV5NWDSX7_SUB14926/fastq/clean_reads_cutted_dedup/Alignments_trimmed --suffix trim.aln.fa --out /n/holyscratch01/davis_lab/tlvieira/raw-data-target-dec-8/231130_A00794_0971_BHV5NWDSX7_SUB14926/fastq/clean_reads_cutted_dedup/IQtree/concat.fasta --nexus

It outputs the following:

ConcatFasta v2.0
Traceback (most recent call last):le
File "/n/home10/tlvieira/ConcatFasta.py", line 293, in
main()
File "/n/home10/tlvieira/ConcatFasta.py", line 78, in main
datalist[file] = readfasta(args.dir+"/"+file, args.delim)
File "/n/home10/tlvieira/ConcatFasta.py", line 199, in readfasta
data[head] += re.sub(" ","",line)
UnboundLocalError: local variable 'head' referenced before assignment

Any ideas of what is going on?

Best,
Tiago

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