a python utility to subset multisequence file based on identifiers from external text file
usage: SubsetSeq [-h] -i INPUT -s SEARCH -t TYPE [-m MATCH] [-u UNMATCH]
[-f INPUT_FORMAT] [-F OUTPUT_FORMAT] [-v Y/y or N/n] [-V]
Subset multisequence based on identifiers from text file
Citation: Singh, Abhijeet. SubsetSeq: a python utility to multisequence file based on
identifiers from external text file. ResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.34956.59528,
Available at GitHub: https://github.com/abhijeetsingh1704/SubsetSeq
required arguments:
-i INPUT, --input INPUT
┆
└─ input file
-s SEARCH, --search SEARCH
┆
└─ text file with identifiers to query input file
-t TYPE, --type TYPE
┆
└─ identifier type to match in input file
┆
└─ 1 = id (sequence identifier before first empty character)
┆
└─ 2 = description (complete description of sequence according to input file)
options:
-h, --help show this help message and exit
-m MATCH, --match_out MATCH
┆
└─ output file with matched sequences (default: <time>-MATCH_<input_file>)
-u UNMATCH, --unmatch_out UNMATCH
┆
└─ output file with unmatched sequences (default: <time>-UNMATCH_<input_file>)
-f INPUT_FORMAT, --input_format INPUT_FORMAT
┆
└─ format of input file (default: 1 (fasta))
┆
└─ 1 = fasta
┆
└─ 2 = genbank
-F OUTPUT_FORMAT, --output_format OUTPUT_FORMAT
┆
└─ format of output file (default: 1 (interleaved fasta))
┆
└─ 1 = interleaved fasta
┆
└─ 2 = fasta-2line
┆
└─ 3 = tab-delimited
-v Y/y or N/n, --verbose Y/y or N/n
┆
└─ print progress to the terminal (default: verbose)
-V, --version show program's version number and exit
Singh, Abhijeet. SubsetSeq: a python utility to multisequence file based on identifiers from external text file. ResearchGate 2022, http://dx.doi.org/10.13140/RG.2.2.34956.59528, Available at GitHub: https://github.com/abhijeetsingh1704/SubsetSeq