This script prepares data for use by the atram.py script. It takes fasta or fastq files of paired-end (or single-end) sequence reads and creates a set of atram databases.
You need to prepare the sequence read archive files so that the header lines contain only a sequence ID with the optional paired-end suffix at the end of the header line. The separator for the optional trailing paired-end suffix may be a space, a slash "/", a dot ".", or an underscore "_".
For example:
>DBRHHJN1:427:H9YYAADXX:1:1101:10001:77019/1
GATTAA...
>DBRHHJN1:427:H9YYAADXX:1:1101:10001:77019/2
ATAGCC...
>DBRHHJN1:427:H9YYAADXX:1:1101:10006:63769/2
CGAAAA...
-h, --help
Show this help message and exit.
--version
Show program's version number and exit.
--end-1 FASTA/Q [FASTA/Q ...], -1 FASTA/Q [FASTA/Q ...]
Sequence read archive files that have only end 1 sequences. The sequence names do not need an end suffix, we will assume the suffix is always 1. The files are in fasta or fastq format. You may enter more than one file or you may use wildcards.
If there are end 2 sequences in the file then you will want to use the
--mixed-ends argument instead.
--end-2 FASTA/Q [FASTA/Q ...], -2 FASTA/Q [FASTA/Q ...]
Sequence read archive files that have only end 2 sequences. The sequence names do not need an end suffix, we will assume the suffix is always 2. The files are in fasta or fastq format. You may enter more than one file or you may use wildcards.
If there are end 1 sequences in the file then you will want to use the
--mixed-ends argument instead.
--mixed-ends FASTA/Q [FASTA/Q ...], -m FASTA/Q [FASTA/Q ...]
Sequence read archive files that have a mix of both end 1 and end 2 sequences (or single ends). The files are in fasta or fastq format. You may enter more than one file or you may use wildcards.
The sequence names must have a sequence end suffix like "/1" or "_2".
--single-ends FASTA/Q [FASTA/Q ...], -0 FASTA/Q [FASTA/Q ...]
Sequence read archive files that have only unpaired sequences. Any sequence suffix will be ignored. The files are in fasta or fastq format. You may enter more than one file or you may use wildcards.
This option will ignore any sequence ends in the in the sequence name.
-b DB, --blast-db DB, --db DB
This is the prefix of all of the blast database files. So you can identify different blast database sets. You may include a directory as part of the prefix. The default is "./atram_<today's date>".
For example, if you want to keep you data base in a directory called:
/home/my_dir/atram_db/. And you want to identify that these sequences are for
Canis lupus. Then you might prefix this database with
/home/my_dir/atram_db/canis_lupus. aTRAM will create a bunch a file in that
directory with names starting with 'canis_lupus'. Like
'canis_lupus.001.blast.nhr' or 'canis_lupus.sqlite.db', etc. This allows you to
keep many aTRAM databases in the same directory.
--cpus CPUS, --processes CPUS, --max-processes CPUS
Number of CPU threads to use. On this machine the default is to use the number of processes on your computer minus 4. More threads can improve the speed but if you use too many you will slow down the computer for any other use.
-t DIR, --temp-dir DIR
Place temporary files in this directory. All files will be deleted after aTRAM completes. The directory must exist.
Sometimes using the system temporary directory is not the right option because
aTRAM is filling up that disk or it is too slow or you want to debug issues.
Note: If you want to keep the temporary files around for debugging then you
should also use the --keep-temp-dir option.
--keep-temp-dir
This flag will keep the temporary files in the --temp-dir around for debugging.
-l LOG_FILE, --log-file LOG_FILE
Log file (full path). The default is to use the DB and program name to come up with a name like "_atram_preprocessor.log".
-s SHARDS, --shards SHARDS, --number SHARDS
Number of blast DB shards to create. The default is to have each shard contain roughly 250MB of sequence data.
--path PATH
If makeblastdb is not in your $PATH then use this to prepend directories to
your path. For instance, if you installed makeblastdb in
/home/my_dir/bin/makeblastdb, you could use this option to find it.
--fasta
Are these fasta files? If you do not specify either --fasta or --fastq then aTRAM will guess the file type by looking at the last character of the file name. This option is most useful when you are dealing with compressed files which will defeat aTRAM's FASTA/Q format guessing algorithm.
--fastq
Are these fastq files? If you do not specify either --fasta or --fastq then aTRAM will guess the file type by looking at the last character of the file name. This option is most useful when you are dealing with compressed files which will defeat aTRAM's FASTA/Q format guessing algorithm.
--gzip
Are these gzip files? aTRAM does not try to guess if the file is compressed.
--bzip
Are these bzip files? aTRAM does not try to guess if the file is compressed.