ogilo-array 0.0.2

Automated construction of oligo library sequences for oligo array synthesis.

⛓️ ogilo

Automating construction of oligo library sequences for oligo array synthesis.

ogilo takes your table of sequences (such as a library of guide RNAs) and concatenates them
with any other nucleotide sequences you provide, Type IIS restriction sites, and PCR handles.

If your table of sequences contains a column indicating subsets or groups, you can use this column to instruct ogilo to add distinct PCR handles to each group. This allows you to order multiple libraries as one oligo pool and selectively PCR each one as needed.

Installation

The easy way

Install the pre-compiled version from PyPI:

pip install ogilo-array

From source

Clone the repository, then cd into it. Then run:

pip install -e .

Usage

Call ogilo with a set of sequence directives and other options:

ogilo file:guide-rnas.csv:sequence:guide_name:essentiality seq:ATCGGGC:spacer re:BsmBI:f --format CSV

You tell ogilo which sequences to concatenate using the following directive format:

[@]<type>:<value>[:<f1>[:<f2>[:<f3>]]]

For example, file:oligos.csv:2 would instruct ogilo to take sequences from column 2 of the file oligos.csv, and seq:ATCCCGAGAG:spacer would add the sequence ATCCCGAGAG and include "spacer" in the oligo name.

If you prepend the directive with @, then reverse complement sequences will be automatically generated.

The allowed values of <type> are as follows.

Files

[@]file:<filename>[:<seq_col>[:<name_col>[:<group_col>]]]

Take sequences from file <filename>. If <seq_col> is provided, ogilo will use this column, otherwise assumes column 1.

<seq_col>, <name_col>, <group_col> can be column names (in which case, the first line will be skipped) or integers (in which case, the first line will be included).

Do not mix column names and integers. If your file has a header, use column names. If <group_col> is provided, and PCR handles are requested, then different PCR handles will be added to each group.

For example:

file:guide-rnas.tsv:sequence:guide_name:essentiality

would load sequences from the file guide-rnas.tsv, using column sequence for sequences, guide_name for the names, and essentiality for the groups (if you want different PCR handles for each group).

Constant sequences

[@]seq:<sequence>[:<name>]

An explicit sequence given in <sequence>, optionally with a <name>.

For example:

@seq:ATCGGGC:spacer

Type IIS restriction enzyme sites

[@]re:<enzyme_name>

A named Type IIS restriction enzyme site. This does not take care of overhangs for you; these can be added as a seq component.

For example:

re:BsmBI

Output

The output is a TSV-formatted table with the following columns:

• group: The group of oligos sharing the same PCR handles.
• pcr_handles: The name of the PCR handle pair used (if any).
• length: Total oligo length.
• mnemonic: Adjective-noun mnemonic of oligo sequence.
• restriction_sites: Type IIS restriction sites which happen to be in the oligo even though they weren't requested.
• oligo_name: Name for the oligo, constricted by concatenating the names of the sequence components.
• oligo_sequence: Sequence for the oligo. Each concatenated section alternates case to allow visual checks.

Examples

Simple example showing parts being concatenated. Note that group and pcr_handles columns are empty.

$ ogilo seq:ATCG:s1 re:BsmBI seq:GGCCTTAA:main @re:BsaI seq:CATG:s2
group pcr_handles length mnemonic restriction_sites oligo_name                oligo_sequence
                   28    immense_memo               s1-BsmBI_f-main-BsaI_r-s2 ATCGcgtctcGGCCTTAAgagaccCATG

You can ask for a seqment to be reverse complemented by prepending the directive with @.

$ ogilo @seq:ATCG:s1 re:BsmBI seq:GGCCTTAA:main @re:BsaI seq:CATG:s2
group pcr_handles length mnemonic restriction_sites oligo_name                oligo_sequence
                   28    immense_memo               s1-BsmBI_f-main-BsaI_r-s2 CGATcgtctcGGCCTTAAgagaccCATG

You can request PCR handles. These are the outermost sections of the sequence.

$ ogilo seq:ATCG:s1 re:BsmBI seq:GGCCTTAA:main @re:BsaI seq:CATG:s2 --pcr_handles
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        sans18a 68      defeated_active         s1-BsmBI_f-main-BsaI_r-s2       AGGCACTTGCTCGTACGACGatcgCGTCTCggccttaaGAGACCcatgATGTGGGCCCGGCACCTTAA

You can specify the subset of PCR handles to use. The current options are illumina for P5/P7 or NextEra i5/i7 primers, or sanson2018 for the primers used in Sanson et al., Nat. Commun., 2018. Here, we request illumina, and ogilo detects the extra BbsI site in the P5/P7 PCR handles.

$ ogilo seq:ATCG:s1 re:BsmBI seq:GGCCTTAA:main @re:BsaI seq:CATG:s2 --pcr_handles --handle_set illumina
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        p5p7    69      vivid_stereo    BbsI    s1-BsmBI_f-main-BsaI_r-s2       AATGATACGGCGACCACCGAatcgCGTCTCggccttaaGAGACCcatgTCAAGCAGAAGACGGCATACG

ogilo will check for other spurious Type IIS restriction sites that emerge after sequences have been concatenated. It ignores the ones you've requested.

$ ogilo seq:ATCG:s1 re:BsmBI seq:ACCTGC:quasi_paqCI @re:BsaI seq:CATG:s2 --pcr_handles --handle_set illumina
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        p5p7    67      muddy_method    BbsI;PaqCI      s1-BsmBI_f-quasi_paqCI-BsaI_r-s2        AATGATACGGCGACCACCGAatcgCGTCTCacctgcGAGACCcatgTCAAGCAGAAGACGGCATACGA

Files containing sequences can also be used, so long as you specify which column the sequence is coming from.

$ ogilo re:BsmBI seq:AATTA:s1 file:test/guides-RLC12_mapped-tiny.tsv:guide_sequence seq:ATGCG:s2 @re:BsmBI --pcr_handles
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        sans18a 84      festive_enigma          BsmBI_f-s1-1-s2-BsmBI_r AGGCACTTGCTCGTACGACGcgtctcAATTAaacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 83      tipsy_classic           BsmBI_f-s1-2-s2-BsmBI_r AGGCACTTGCTCGTACGACGcgtctcAATTAacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
       ...
        sans18a 79      tidy_isotope            BsmBI_f-s1-19-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAaacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 78      wistful_liquid          BsmBI_f-s1-20-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA

ogilo interprets the .csv or .tsv file extnsion to indicate that your file is either comma- or tab-delimited, but if the file extension is misleading you can force to read either CSV or TSV instead with the --format option.

$ ogilo re:BsmBI seq:AATTA:s1 file:test/guides-RLC12_mapped-tiny.txt:guide_sequence seq:ATGCG:s2 @re:BsmBI --pcr_handles --format CSV
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        sans18a 84      festive_enigma          BsmBI_f-s1-1-s2-BsmBI_r AGGCACTTGCTCGTACGACGcgtctcAATTAaacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 83      tipsy_classic           BsmBI_f-s1-2-s2-BsmBI_r AGGCACTTGCTCGTACGACGcgtctcAATTAacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
       ...
        sans18a 79      tidy_isotope            BsmBI_f-s1-19-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAaacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 78      wistful_liquid          BsmBI_f-s1-20-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA

Optionally, a column to take names from can be specified. Here, we're using the column called pam_offset.

$ ogilo re:BsmBI seq:AATTA:s1 file:test/guides-RLC12_mapped-tiny.tsv:guide_sequence:pam_offset seq:ATGCG:s2 @re:BsmBI --pcr_handles
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
        sans18a 84      festive_enigma          BsmBI_f-s1-25-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAaacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 83      tipsy_classic           BsmBI_f-s1-25-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
       ...
        sans18a 79      tidy_isotope            BsmBI_f-s1-58-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAaacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA
        sans18a 78      wistful_liquid          BsmBI_f-s1-58-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAacactggtgcgcgataATGCGgagacgATGTGGGCCCGGCACCTTAA

A column to indicate grouping for different PCR handles can also be specified in addition. Here, we're using the column called ann_gene_biotype. The different values in this column are matched with a different PCR handle pair.

$ ogilo re:BsmBI seq:AATTA:s1 file:test/guides-RLC12_mapped-tiny.tsv:guide_sequence:pam_offset:ann_gene_biotype seq:ATGCG:s2 @re:BsmBI --pcr_handles
group   pcr_handles     length  mnemonic        restriction_sites       oligo_name      oligo_sequence
rRNA    sans18a 84      festive_enigma          BsmBI_f-s1-25-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAaacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
rRNA    sans18a 83      tipsy_classic           BsmBI_f-s1-25-s2-BsmBI_r        AGGCACTTGCTCGTACGACGcgtctcAATTAacccaaacactccctttggaaATGCGgagacgATGTGGGCCCGGCACCTTAA
        ...
tRNA    sans18b 79      good_iceberg            BsmBI_f-s1-58-s2-BsmBI_r        GTGTAACCCGTAGGGCACCTcgtctcAATTAaacactggtgcgcgataATGCGgagacgGTCGAGAGCAGTCCTTCGAC
tRNA    sans18b 78      damp_index              BsmBI_f-s1-58-s2-BsmBI_r        GTGTAACCCGTAGGGCACCTcgtctcAATTAacactggtgcgcgataATGCGgagacgGTCGAGAGCAGTCCTTCGAC

Command line options

usage: ogilo [-h] [--input INPUT] [--pcr_handles] [--column COLUMN] [--pcr_group PCR_GROUP] [--format {TSV,CSV}] [--output OUTPUT] [inputs ...]

Automated construction of oligo library sequences for oligo array synthesis.

positional arguments:
  inputs                Further input(s). Format is <type>:<value>:<seq_col>[:<name_col>:<group_col>], for example file:oligos.csv:2 seq:ATCGTAT.

options:
  -h, --help            show this help message and exit
  --input INPUT         Single input file. Default: STDIN
  --pcr_handles, -p     Requests PCR handles to be added either side of final sequences.
  --column COLUMN, -c COLUMN
                        Column number to take from input as sequence. Default: 1
  --pcr_group PCR_GROUP, -g PCR_GROUP
                        Column heading containing groups to give different PCR handles to.
  --format {TSV,CSV}, -f {TSV,CSV}
                        Format of files. Default: TSV
  --output OUTPUT, -o OUTPUT
                        Output file. Default: STDOUT

Documentation

Available at ReadTheDocs.