SB Guess format - mendessoares/BuddySuite GitHub Wiki

--guess_format, -gf

Description

Auto-detect and return the file format of input files. The following formats are currently supported: fasta, genbank, embl, phylip, nexus, stockholm, seqxml, and fastq.

Example

Input directory:

$: ls ~/test_files
>>> Mnemiopsis_cds.gb    Dre.nex          align.phy    temp.seqs
    Mnemiopsis_cds.fa    N-terms.gb       fastq.txt    temp
    Mnemiopsis_pep.gb    N-terms_pep.txt  stock.st

Usage example

$: sb ~/test_files/* -gf

Output

Mnemiopsis_cds.gb   -->  gb
Mnemiopsis_cds.fa   -->  fasta
Mnemiopsis_pep.gb   -->  gb
Dre.nex	            -->  nexus
N-terms.gb	        -->  gb
N-terms_pep.txt	    -->  gb
align.phy	        -->  phylip-relaxed
fastq.txt	        -->  fastq
stock.st	        -->  stockholm
temp.seqs	        -->  fasta
temp	            -->  gb