SEQR - SEQuence Retreival tool
Super-fast protein sequence similarity search, based on Solr.
The underlying concept of the project is based on the SEQR application, developed at NCBI, which finds similar protein sequences for a given query protein sequence by using indexes. This allows it to quickly retrieve similar sequences and makes it easy to combine with other indices like taxonomy which is useful in subsetting the data returned. Making a command line version of this algorithm has applications in many types of bioinformatics data pipelines, in a similar fashion to how BLAST and eutils are used.
For more information, please visit our wiki.
License
SEQR is released under the terms of Creative Commons 0: Public Domain.
Solr
SEQR requires a Solr backend, but it'll instantiate it's own embedded Solr server if you don't have one running. Either way, you'll need to provide either the URL of a running Solr instance, or a path to a directory where the embedded Solr can build and save indexes. Supply this as an argument to the -d option:
$ seqr search -d /path/to/solr/directory/ <fasta_file>
$ seqr index -d http://a.solr.server/ <fasta_file>usage
$ seqr -h
usage: seqr [-h] -d SOLR_URL_OR_PATH [--version] [--citation]
[-o OUTPUT_FILE] [--parse_deflines] [--html] [--lcase_masking]
[--remote] [--show_gis] [--ungapped] [--use_sw_tback]
[--import_search_strategy FILENAME]
[--export_search_strategy FILENAME] [--task TASK_NAME]
[--dbsize NUM_LETTERS] [--gilist FILENAME]
[--seqidlist FILENAME] [--negative_gilist FILENAME]
[--entrez_query ENTREZ_QUERY]
[--db_soft_mask FILTERING_ALGORITHM]
[--db_hard_mask FILTERING_ALGORITHM]
[--subject SUBJECT_INPUT_FILE] [--subject_loc RANGE]
[--evalue EVALUE] [--word_size WORD_SIZE]
[--gapopen OPEN_PENALTY] [--gapextend EXTEND_PENALTY]
[--qcov_hsp_perc QCOV_HSP_PERC] [--max_hsps MAX_HSPS]
[--xdrop_ungap XDROP_UNGAP] [--xdrop_gap XDROP_GAP]
[--xdrop_gap_final XDROP_GAP_FINAL] [--searchsp SEARCHSP]
[--sum_stats BOOL] [--seg SEG_OPTIONS]
[--soft_masking SOFT_MASKING] [--matrix MATRIX_NAME]
[--threshold THRESHOLD] [--culling_limit CULLING_LIMIT]
[--best_hit_overhang BEST_HIT_OVERHANG]
[--best_hit_score_edge BEST_HIT_SCORE_EDGE]
[--window_size WINDOW_SIZE] [--query_loc RANGE]
[--num_descriptions NUM_DESCRIPTIONS]
[--line_length LINE_LENGTH] [--max_target_seqs NUM_SEQUENCES]
[--num_threads NUM_THREADS] [--comp_based_stats COMPO] COMMAND
...
SEQR, now for shells.
optional arguments:
-h, --help show this help message and exit
-d SOLR_URL_OR_PATH, --db SOLR_URL_OR_PATH
URL of Solr server, or path to Solr directory
--version
--citation (default: false)
-o OUTPUT_FILE, --out OUTPUT_FILE
path to output directory
--parse_deflines derive metadata from FASTA deflines and comments
(default: false)
subcommands:
SEQR commands
COMMAND
search look for something
index create an index
$ seqr search -h
usage: seqr -d SOLR_URL_OR_PATH search [-h] [-n] [--solr_query SOLR_QUERY]
[--index_file INDEX_FILE] [--num_alignments NUM_ALIGNMENTS]
[--start_alignments N] [--outfmt FORMAT [FORMAT ...]]
QUERY FASTA
positional arguments:
QUERY FASTA query file for input
optional arguments:
-h, --help show this help message and exit
-n, --is_dna Input FASTA is DNA nucleotide, not protein
--solr_query SOLR_QUERY
filtering query in Solr query language
--index_file INDEX_FILE
pre-calculated index file
--num_alignments NUM_ALIGNMENTS
number of results to return
--start_alignments N begin output at the Nth result
--outfmt FORMAT [FORMAT ...]
Blast+ style output format codes are used.
Include one number from below:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = XML Blast output,
6 = tabular,
7 = tabular with comment lines,
8 = Text ASN.1,
9 = Binary ASN.1,
10 = Comma-separated values,
11 = BLAST archive format (ASN.1),
12 = JSON Seqalign output,
13 = JSON Blast output,
14 = XML2 Blast output,
15 = SAM Blast output
Optionally, include space delimited list of fields
to include in output after the number. Order
will be respected. e.g.
-outfmt "42 all_the_fish thanks_for so_long_and"
$ seqr index -h
usage: seqr -d SOLR_URL_OR_PATH index [-h] input_files [input_files ...]
positional arguments:
input_files
optional arguments:
-h, --help show this help message and exit
unused:
Unused compatibility arguments from BLASTP
--html unused (default: false)
--lcase_masking unused (default: false)
--remote unused (default: false)
--show_gis unused (default: false)
--ungapped unused (default: false)
--use_sw_tback unused (default: false)
--import_search_strategy FILENAME
unused
--export_search_strategy FILENAME
unused
--task TASK_NAME unused
--dbsize NUM_LETTERS unused
--gilist FILENAME unused
--seqidlist FILENAME unused
--negative_gilist FILENAME
unused
--entrez_query ENTREZ_QUERY
unused
--db_soft_mask FILTERING_ALGORITHM
unused
--db_hard_mask FILTERING_ALGORITHM
unused
--subject SUBJECT_INPUT_FILE
unused
--subject_loc RANGE unused
--evalue EVALUE unused
--word_size WORD_SIZE unused
--gapopen OPEN_PENALTY
unused
--gapextend EXTEND_PENALTY
unused
--qcov_hsp_perc QCOV_HSP_PERC
unused
--max_hsps MAX_HSPS unused
--xdrop_ungap XDROP_UNGAP
unused
--xdrop_gap XDROP_GAP unused
--xdrop_gap_final XDROP_GAP_FINAL
unused
--searchsp SEARCHSP unused
--sum_stats BOOL unused
--seg SEG_OPTIONS unused
--soft_masking SOFT_MASKING
unused
--matrix MATRIX_NAME unused
--threshold THRESHOLD unused
--culling_limit CULLING_LIMIT
unused
--best_hit_overhang BEST_HIT_OVERHANG
unused
--best_hit_score_edge BEST_HIT_SCORE_EDGE
unused
--window_size WINDOW_SIZE
unused
--query_loc RANGE unused
--num_descriptions NUM_DESCRIPTIONS
unused
--line_length LINE_LENGTH
unused
--max_target_seqs NUM_SEQUENCES
unused
--num_threads NUM_THREADS
unused
--comp_based_stats COMPO
unused