santiagosnchez / concatfasta

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

ConcatFasta.py

note: ConcatFasta has now been updated for Python3

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

This is a Python version of concat_fasta.pl. It is more portable and expandable than its Perl predecessor and will be updated more regularly.

Concatenates FASTA files given a suffix present in all target files (e.g. "XXX.fasta"). Labels for the same "taxon" should be the same on all FASTA files, but can be unordered. The number of sequences on each file can also be different. In this case, an empty sequence will be added (e.g. "???.."). It will also print a layout of the partitions to the screen with the -p/--part flag. Sequences can be wrapped at 100 characters with the -w/--wrap option.

The program now can export as NEXUS or PHYLIP formats by switching the --nexus/-n or --phylip/-p arguments. Partition blocks will be added to the NEXUS file or a file written for PHYLIP with the --part/-q argument.

Downloading the program

wget https://raw.githubusercontent.com/santiagosnchez/ConcatFasta/master/ConcatFasta.py

Running the code

Use the -h flag for more details:

python ConcatFasta.py -h
usage: ConcatFasta.py [-h] [--files [FASTA_FILE [FASTA_FILE ...]]]
                  [--dir [DIR]] [--suffix [SUFFIX]] [--outfile [OUTFILE]]
                  [--part ] [--wrap ] [--nexus ] [--phylip ]

Concatenates FASTA files into a single file.

optional arguments:
  -h, --help            show this help message and exit
  --files [FASTA_FILE [FASTA_FILE ...]], -f [FASTA_FILE [FASTA_FILE ...]]
                        file to concatenate in FASTA format.
  --dir [DIR], -d [DIR]
                        directory where FASTA files to concatenate are
                        (default: .).
  --suffix [SUFFIX], -s [SUFFIX]
                    suffix for FASTA files.
  --outfile [OUTFILE], -o [OUTFILE]
                    name for output file (default: concat.fasta).
  --part [], -q []      will print a partition table.
  --wrap [], -w []      sequences will be wrapped every 100 characters.
  --nexus [], -n []     export in NEXUS format.
  --phylip [], -p []    export in PHYLIP format.

Files can be sepcified one by one with --files or by specifying a directory
--dir with the files. Additionally, a --suffix suffix can be combined with
--dir to filter out other files.

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