https://github.com/abhijeetsingh1704/subsetseq

a python utility to subset multisequence file based on identifiers from external text file
https://github.com/abhijeetsingh1704/subsetseq

fasta genbank sequence subset

Last synced: 7 months ago
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a python utility to subset multisequence file based on identifiers from external text file

• Host: GitHub
• URL: https://github.com/abhijeetsingh1704/subsetseq
• Owner: abhijeetsingh1704
• License: gpl-3.0
• Created: 2022-05-28T16:10:35.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-05-30T13:48:53.000Z (over 3 years ago)
• Last Synced: 2025-01-26T12:09:48.310Z (8 months ago)
• Topics: fasta, genbank, sequence, subset
• Language: Python
• Homepage:
• Size: 34.2 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

          
# SubsetSeq

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: -MATCH_)

                        

  -u UNMATCH, --unmatch_out UNMATCH

                        ┆

                        └─ output file with unmatched sequences (default: -UNMATCH_)

                        

  -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

                        

```

# 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