| annotate |
-ano |
<name> <location> [strand] [qualifiers] [regex_pattern] |
Add a feature (annotation) to selected sequences. |
| ave_seq_length |
-asl |
['clean'] |
Find the average length of all sequences in an input file |
| back_translate |
-btr |
None |
Convert amino acid sequences into codons. Select mode/species with -p flag [{'random', 'optimized'}] [{'human', 'mouse', 'yeast', 'ecoli'}] |
| bl2seq |
-bl2s |
None |
All-by-all blast among sequences using bl2seq. Only Returns top hit from each search |
| blast |
-bl |
<BLAST database> |
BLAST your sequence file using common blast settings, return the hits from blastdb |
| clean_seq |
-cs |
['strict'] [replacement character] |
Strip out non-sequence characters, such as stops (*) and gaps (-) |
| complement |
-cmp |
None |
Return complement of nucleotide sequence |
| concat_seqs |
-cts |
['clean'] |
Concatenate a bunch of sequences into a single solid string |
| count_codons |
-cc |
['concatenate'] |
Return codon frequency statistics. |
| count_residues |
-cr |
None |
Generate a table of sequence compositions. |
| delete_features |
-df |
<regex> [regex ...] |
Remove specified features from all records |
| delete_large |
-dlg |
<threshold (int)> |
Delete sequences with length above threshold |
| delete_metadata |
-dm |
None |
Remove meta-data from file (only IDs are retained) |
| delete_records |
-dr |
<regex> [regex ...] [path] [cols (int)] |
Remove records from a file (deleted IDs are sent to stderr) |
| delete_repeats |
-drp |
[scope {'all', 'ids', 'seqs'}] [columns (int)] |
Strip out repeat records (ids and/or identical sequences) |
| delete_small |
-dsm |
<threshold (int)> |
Delete sequences with length below threshold |
| extract_regions |
-er |
<positions (str)> [positions] ... |
Pull out sub-sequences |
| find_CpG |
-fcpg |
None |
Predict regions under strong purifying selection based on high CpG content |
| find_pattern |
-fp |
<regex> [regex ...] ['ambig'] |
Search for sub-sequences, returning match start positions. |
| find_repeats |
-frp |
[columns (int)] |
Identify whether a file contains repeat sequences and/or sequence ids |
| find_restriction_sites |
-frs |
[enzymes {'commercial', 'all', <specific>} ...] [min cuts (int)] [max cuts (int)] [order {'position', 'alpha'}] |
Returns a dictionary of all of the restriction sites and their indices for each sequence in the file |
| group_by_prefix |
-gbp |
[Split Pattern [Split pattern ...]] [length (int)] [out dir] |
Sort sequences into separate files based on prefix |
| group_by_regex |
-stf |
<regex> [regex ...] [Out dir (path)] |
Group sequences by ID into new files based on some search criteria |
| guess_alphabet |
-ga |
None |
Return the alphabet type found in the input file |
| guess_format |
-gf |
None |
Guess the flatfile format of the input file |
| hash_seq_ids |
-hsi |
[hash length (int)] |
Rename all identifiers to random hashes |
| insert_seq |
-is |
<sequence> <location {front, rear, index (int)}> |
Insert a sequence at the desired location |
| isoelectric_point |
-ip |
None |
Calculate isoelectric points |
| list_features |
-lf |
None |
Print a pretty list of sequence annotations |
| list_ids |
-li |
[columns (int)] |
Output list of sequence identifiers in one (default) or more columns |
| lowercase |
-lc |
None |
Convert sequences to lowercase |
| make_ids_unique |
-miu |
[separator (string)] [padding (int)] |
Add a number at the end of replicate ids to make them unique |
| map_features_nucl2prot |
-fn2p |
None |
Transfer annotations from cDNA/mRNA sequences onto protein sequences |
| map_features_prot2nucl |
-fp2n |
None |
Transfer annotations from protein sequences onto cDNA/mRNA sequences |
| merge |
-mrg |
None |
Group a sequence files together |
| molecular_weight |
-mw |
None |
Computes the molecular weight of each sequence |
| num_seqs |
-ns |
None |
Counts how many sequences are present |
| order_features_alphabetically |
-ofa |
['rev'] |
Change the output order of sequence features, based on sequence position |
| order_features_by_position |
-ofp |
['rev'] |
Change the output order of sequence features, based on sequence position |
| order_ids |
-oi |
['rev'] |
Sort all sequences by id in alpha-numeric order (reverse with 'rev') |
| order_ids_randomly |
-oir |
None |
Randomly reorder the position of records in the file |
| pull_random_record |
-prr |
[number (int)] |
Extract random sequence(s) |
| pull_records |
-pr |
<regex> [regex ...]['full'][path] |
Get all the records with ids containing a given string |
| pull_record_ends |
-pre |
<amount (int)> |
Get the ends of all sequences |
| purge |
-prg |
<Max BLAST bit-score (int)> |
Delete sequences with high similarity |
| rename_ids |
-ri |
<regex> <subs (str)> [num] ['store'] |
Replace a pattern in IDs with a new string |
| replace_subseq |
-rs |
<regex> [regex ...] [replacement] |
Replace a sequence pattern with something new |
| reverse_complement |
-rc |
None |
Return reverse complement of nucleotide sequences |
| reverse_transcribe |
-r2d |
None |
Convert RNA sequences to DNA |
| screw_formats |
-sf |
<new format> |
Change the file format to something else |
| select_frame |
-sfr |
<frame {1, 2, 3}> |
Change the reading frame of sequences by deleting characters from the front |
| shuffle_seqs |
-ss |
None |
Randomly reorder primary sequence |
| translate |
-tr |
None |
Convert coding sequences into amino acid sequences |
| translate6frames |
-tr6 |
None |
Translate nucleotide sequences into all six reading frames |
| transcribe |
-d2r |
None |
Convert DNA sequences to RNA |
| transmembrane_domains |
-tmd |
[Job ID] |
Identify and annotate transmembrane domains using the TOPCONS web service |
| uppercase |
-uc |
None |
Convert sequences to uppercase |
