Expand the range of PCR handles

.github/workflows/python-package.yml

@@ -13,12 +13,12 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
@@ -33,8 +33,11 @@ jobs:
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest ogilo --doctest-modules --junitxml=tests/test-results.xml --cov=com --cov-report=xml --cov-report=html
     - name: Upload pytest test results
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
           name: pytest-results-${{ matrix.python-version }}
           path: junit/test-results-${{ matrix.python-version }}.xml

.github/workflows/python-publish.yml

@@ -21,12 +21,12 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.11"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python
-      uses: actions/setup-python@v3
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

ogilo/__init__.py

@@ -0,0 +1,3 @@
+from importlib.metadata import version
+
+__version__ = version("ogilo-array")

ogilo/cli.py

@@ -9,6 +9,7 @@
 
 import streq as sq
 
+from . import __version__
 from .io import extract_col, write_constructs 
 from .types import Input, Oligo, Seq
 from .utils import _get_pcr_handles, grouping_key
@@ -144,9 +145,11 @@ def _assemble(args: argparse.Namespace) -> None:
     constructs = _generate_combos(constructs)
 
     if args.pcr_handles:
-        constructs = _add_pcr_handles(constructs, 
-                                      handle_set=args.handle_set, 
-                                      grouped=True)
+        constructs = _add_pcr_handles(
+            constructs, 
+            handle_set=args.handle_set, 
+            grouped=True,
+        )
 
     write_constructs(constructs, args.output)
 
@@ -185,7 +188,7 @@ def main() -> None:
             Sequence for the oligo.
 
     For example:
-    $ ogilo re:BsmBI:f file:test/guides-RLC12_mapped-tiny.tsv:guide_sequence:Name:ann_gene_biotype re:BsmBI:r -p
+    $ ogilo re:BsmBI file:test/guides-RLC12_mapped-tiny.tsv:guide_sequence:Name:ann_gene_biotype @re:BsmBI -p
     group   pcr_handles   length  mnemonic     restriction_sites  oligo_name                                    oligo_sequence
     rRNA    sans18a         74      brief_nadia             BsmBI_f-_up-rrs-1471818-ultimate_parody-BsmBI_r  AGGCACTTGCTCGTACGACGcgtctcAACCCAAACACTCCCTTTGGAAgagacgATGTGGGCCCGGCACCTTAA
     rRNA    sans18a         73      rancid_kayak            BsmBI_f-_up-rrs-1471818-nostalgic_sonata-BsmBI_r AGGCACTTGCTCGTACGACGcgtctcACCCAAACACTCCCTTTGGAAgagacgATGTGGGCCCGGCACCTTAA
@@ -225,7 +228,7 @@ def main() -> None:
     parser.add_argument('--handle_set', '-s', 
                         type=str,
                         default='all',
-                        help='Which set of PCR handles to use. Either "all", "sanson2018", "illumina", or '
+                        help='Which set of PCR handles to use. Either "all", "sanson2018", "illumina", "subramanian2018", "winston2022", or '
                              'a path to a CSV with column headings pcr_handle_id, pcr_handle_f, pcr_handle_r. '
                              'Default: %(default)s')
     parser.add_argument('--format', '-f', 

ogilo/data/handles/raw/subramanian2018.csv

@@ -0,0 +1,168 @@
+# https://doi.org/10.1093/synbio/ysx008
+pcr_handle_id,is_forward,to_reverse_complement,sequence
+1,yes,no,AAACACGTGGCAAACATTCC
+2,yes,no,AAACCGGAGCCATACAGTAC
+3,yes,no,AAAGCACTCTTAGGCCTCTG
+4,yes,no,AAAGGGGCCGTCAATATCAG
+5,yes,no,AAATAAGACGACGACCCTCG
+6,yes,no,AACGATGATGCTCACTCTCG
+7,yes,no,AAGAATTACTGACCCCTCGG
+8,yes,no,AAGACGATCCGAGCCATTAC
+9,yes,no,AAGGAACTATGGCATCGAGC
+10,yes,no,AAGGACTGCATACCAGGTTG
+11,yes,no,AAGGATATGTAGACACCGCC
+12,yes,no,AAGGCCCAGAAGGATACAAC
+13,yes,no,AAGGCGCTCGGATAATACTC
+14,yes,no,AAGGTATGTATAGCGACCGC
+15,yes,no,AATAGGAACCTCTTACGCGG
+16,yes,no,AATATCACGCAAAAGCACCG
+17,yes,no,AATCAGTTTCTTTGGCAGCC
+18,yes,no,AATGCAAAGCTATTAGCGCG
+19,yes,no,AATGCGTCATTTTACACGGC
+20,yes,no,AATGTCCTTAGGCAGTCGTC
+21,yes,no,ACAACGAGCAGACCGAATAG
+22,yes,no,ACAAGGAGTCGGCATATCAC
+23,yes,no,ACAGAACGAACAGGCACTAC
+24,yes,no,ACAGGAAGCAAGGTATACGC
+25,yes,no,ACAGGGTATATTGAGTGCCC
+26,yes,no,ACATAAGCGATCCCAAGGTC
+27,yes,no,ACATCGCATACCAGAACAGG
+28,yes,no,ACATTAAATTTCGCCGTGGC
+29,yes,no,ACCACAGGTCAAGATTCACG
+30,yes,no,ACCCGTATCGCATAAGGATG
+31,yes,no,ACGAGATGATGCACCGATAG
+32,yes,no,ACGATGGGGACATAGAACAC
+33,yes,no,ACGGAGCCCTTATTGTAACC
+34,yes,no,ACGTATGGGGAACACTACAC
+35,yes,no,ACGTGAAACTGTATCGAGCC
+36,yes,no,ACGTTCAGTTTTCCAATGGC
+37,yes,no,ACTAGATTAGCAAGGCACCC
+38,yes,no,ACTGGACCCAATAAAAGGCC
+39,yes,no,ACTTCGATTGGCAAGGACTG
+40,yes,no,AGAACATAGCATTCACGGGG
+41,yes,no,AGACAACAATCTGAGGCTGG
+42,yes,no,AGACAAGCCTTAACCGTAGG
+43,yes,no,AGACACAAGGCTGATTCCAG
+44,yes,no,AGACATGGGATTGACCACAC
+45,yes,no,AGAGAGGCATGATTGACCTC
+46,yes,no,AGAGTTGCACCTAGAATCCG
+47,yes,no,AGATAGATGCTCCGTCAAGC
+48,yes,no,AGATAGTCACGCACAAGACC
+49,yes,no,AGATTAGCCGACTTTCCTGG
+50,yes,no,AGATTAGCTGCCGATACTGG
+51,yes,no,AGATTGTTACTCCGACGGAC
+52,yes,no,AGATTTCCGACGAGATTCCC
+53,yes,no,AGCATCCGTCTAAATCTCGG
+54,yes,no,AGCTATAAGAATTGCCGGGC
+55,yes,no,AGCTATGATCCCGGTGTAAC
+56,yes,no,AGCTCAATCTAACAGTGGGG
+57,yes,no,AGGACACCAGACCAATGAAG
+58,yes,no,AGGGCTAATTACCATCAGCG
+59,yes,no,AGGTGATCTGACGAATGTCC
+60,yes,no,AGTAAAGCATAGTGCCCAGC
+61,yes,no,AGTAGTATCCGAATCGCTGC
+62,yes,no,AGTATCTCAGCAAGGGCAAC
+63,yes,no,AGTATTAGGCGTCAAGGTCC
+64,yes,no,AGTATTCTTACAGCCAGCCG
+65,yes,no,AGTATTGCCGGACTAAACCC
+66,yes,no,AGTCCCAAGTTCAGACGTAC
+67,yes,no,AGTCCGACACAATGTGACAC
+68,yes,no,AGTGAACTGACCGAATCCTC
+69,yes,no,AGTGGTCTGTAAACCGTACC
+70,yes,no,AGTGTTTTCCATTTTCCGCG
+71,yes,no,AGTTATAAGGGTCCGATGCC
+72,yes,no,AGTTGCAGTATCTAACCCGC
+73,yes,no,AGTTGTAATATCACCCGCGC
+74,yes,no,ATACGTGGCTAGCATGAGAC
+75,yes,no,ATACTGTAAGAACCACGCGG
+76,yes,no,ATAGATCATGTCGGCAGTCG
+77,yes,no,ATAGATGGTGCCTACATGCG
+78,yes,no,ATCACAACAAAGGACGGGTC
+79,yes,no,ATCAGACAACACAGAGGCTG
+80,yes,no,ATCCAGGAGGTCTAGGAACC
+81,yes,no,ATCCTAGAAAAGGCGAAGGC
+82,yes,no,ATGCCATGACGACAACTAGC
+83,yes,no,ATGCTAGCTGGAACTATCGG
+84,no,yes,ATTAGGATTGCGAGCGACAC
+85,no,yes,ATTAGTACACTCCGTGAGCG
+86,no,yes,ATTCAAGGGTTGGACGACTC
+87,no,yes,ATTCTCACGACGCAAGATGG
+88,no,yes,ATTGACGGGAACTACACTCG
+89,no,yes,CACTCGATAGGTACAACCGG
+90,no,yes,CAGACCTACGGATCTTAGCG
+91,no,yes,CCACGAGATAAGAGGATGGC
+92,no,yes,CCAGAGCTTAGGGGACATAC
+93,no,yes,CCCGAGGGGAGAAATATACC
+94,no,yes,CCGAGGGAACCATGATACAG
+95,no,yes,CCGGGAGGAAGATATAGCAC
+96,no,yes,CCGGTTGTACCTATCGAGTG
+97,no,yes,CCGTGCGACAAGATTTCAAG
+98,no,yes,CCTTTAACAGGACATGCAGC
+99,no,yes,CGAACGCAAAAGTCCTCAAG
+100,no,yes,CGATAGAACGACCAGGTAGC
+101,no,yes,CGGATCGAACTTAGGTAGCC
+102,no,yes,CGGGAGGAAGTCTTTAGACC
+103,no,yes,CTAATATCCCTGAGCGACGG
+104,no,yes,CTAGGGAACCAGGCTTAACG
+105,no,yes,CTAGGGGATGGTCCAATACG
+106,no,yes,CTATAGAATCCGGGCTGGTC
+107,no,yes,CTGCTAGGGGCTACTTATCG
+108,no,yes,GAAAAGTCCCAATGAGTGCC
+109,no,yes,GAAGTGGTTTGCCTAAACGC
+110,no,yes,GACCATGCAAGGAGAGGTAC
+111,no,yes,GATACATAGACTTGGCCCCG
+112,no,yes,GCACGCAAAAGGACATAACC
+113,no,yes,GCAGCGTTTTAGCCTACAAG
+114,no,yes,GCATAAAGTTGACAGGCCAG
+115,no,yes,GCTAAATAGAGGGAAGCCCC
+116,no,yes,GGAAAACTAAGACAAGGCGC
+117,no,yes,GGAAACAATAACCATCGGCG
+118,no,yes,GGGCACCGATTAAGAAATGC
+119,no,yes,GGGTTGTCTCCTCTGATAGC
+120,no,yes,GTACTCAGAGATTGCCGGAG
+121,no,yes,GTATAAGATCAGCCGGACCC
+122,no,yes,GTATGTCGGCTCTCGTATCG
+123,no,yes,GTTCAGAGGTACGAACCCTC
+124,no,yes,GTTGCATCTAAGCCAAGTGC
+125,no,yes,TAAAGAGAGGGCGTCCAATC
+126,no,yes,TAACGACGTGCCGAACTTAG
+127,no,yes,TAAGATAGCACCACGGATGG
+128,no,yes,TAAGGATTCATCAGGTGCGC
+129,no,yes,TAAGGGACGATGCTTAACCC
+130,no,yes,TACCACGAAATGCACAGGAG
+131,no,yes,TACTGATAATTCGGACGCCC
+132,no,yes,TACTTGAATACCACGTGGCC
+133,no,yes,TAGCCAGGCAAAAGAGATCC
+134,no,yes,TAGCTCGATAATCAAGGGGC
+135,no,yes,TAGTGACCTAATGCCATGGG
+136,no,yes,TAGTTGAGAACACGAACCCG
+137,no,yes,TATAACAGGCTGCTGAGACC
+138,no,yes,TATACTGAAGAACGGCCCAG
+139,no,yes,TATCAATCCGGAACCAGTGC
+140,no,yes,TATCACGGAAGGACTCAACG
+141,no,yes,TCAAAGGAGCACGAACCTAC
+142,no,yes,TCAAGGTCCGTTATGGAACC
+143,no,yes,TCACATAGAAGGACATGGCG
+144,no,yes,TCACTTGGTATCGAGAACGG
+145,no,yes,TCAGCCTTTCATTGATTGCG
+146,no,yes,TCATCGACAAGATACAGGCG
+147,no,yes,TCCAATTATACGGAGCAGGC
+148,no,yes,TCGAATATGCTGTAACCCCG
+149,no,yes,TCGACCAGGTTATCATGAGC
+150,no,yes,TCGAGACAAGAACGATTCCC
+151,no,yes,TCTAGGACTATCACCGGAGG
+152,no,yes,TCTTCATAAGCCAGAGTGCC
+153,no,yes,TCTTGCGATAGACACAAGCC
+154,no,yes,TGAGCCATAAAAGCAAAGCG
+155,no,yes,TGAGCGCAGAACTATCAGAC
+156,no,yes,TGCATAGTATCCCAACAGGG
+157,no,yes,TGCCAAAGGGTAGAGACATC
+158,no,yes,TGCTGAATGAGAAACCTCGG
+159,no,yes,TGGGGACGACTTATAATGCC
+160,no,yes,TGTGGACCCTATCAAACGAG
+161,no,yes,TTAGCTCAGGTCCAAAGTCC
+162,no,yes,TTAGTAGGCAAGCATACCCG
+163,no,yes,TTCGGGAGCGGATTATACAC
+164,no,yes,TTCTGGGACTGGATAACACG
+165,no,yes,TTGACAGACAATCCGTAGGC
+universal,no,yes,CTTCTCCTTTACTAGTGAATTC

ogilo/data/handles/raw/winston2022.csv

@@ -0,0 +1,20 @@
+# https://doi.org/10.1021/acssynbio.1c00482
+pcr_handle_id,is_forward,to_reverse_complement,sequence
+FP1,yes,no,CTATCTGGCCTCAAAGCACT
+FP2,yes,no,TCTGGCAGCACGAAGATAAG
+FP3,yes,no,AGGAGACAAGTAACGTGTGC
+FP4,yes,no,TAAGAAAGGCATCGTCACCG
+FP5,yes,no,GTCACGTCACCAGGTAACAA
+FP6,yes,no,TTTCCGATAGTTGAGGCAGG
+FP7,yes,no,TGGTGAAACTACCGACTTCC
+FP8,yes,no,AGTTGGTGACTATCCGTCCT
+FP9,yes,no,CACATAGGCAAAGCGGAGTA
+RP1,no,no,TTGACTCCTCCTCTTGCCTA
+RP2,no,no,CGACTCAATTCTGCTCCTGT
+RP3,no,no,GTCGAGCACTGATTGTGGAA
+RP4,no,no,GTACTGCTCGGCCACTTATT
+RP5,no,no,GCGTTGTCTCTAGCGAAAGA
+RP6,no,no,TCATTTCTCCGACAGGCTTG
+RP7,no,no,CCTCTCTTCGCGTTGATCTT
+RP8,no,no,GCAAGACAATAGGCTTCGGT
+RP9,no,no,CGCTGCTGGTAATTTAACCG

ogilo/data/handles/scripts/compile-table.sh

@@ -0,0 +1,63 @@
+#!/usr/bin/env bash
+
+sort_table () {
+    local sep=${3:-,}
+    local field=$(get_column_number "$1" $2)
+    cat <(head -n1 "$1") <(tail -n+2 "$1" | sort -k"$field" -t"$sep")
+}
+
+set -e
+set -x
+
+script_dir="$(dirname $0)"
+inputs=("$script_dir"/../raw/*.csv)
+output_dir="$script_dir"/..
+temp_dir="$script_dir"/../temp
+
+mkdir -p "$temp_dir"
+
+for inp in "${inputs[@]}"
+do
+    inp_id=$(basename "$inp" .csv)
+    this_output_file="$output_dir"/"$inp_id"-pcr-handles.csv
+    pp_seq_file="$temp_dir"/"$inp_id"-preprocessed.csv
+    fw_seq_file="$temp_dir"/"$inp_id"-fw.csv
+    rv_seq_file="$temp_dir"/"$inp_id"-rv.csv
+
+    cat "$inp" | sed '1s/^\xEF\xBB\xBF//' | tr -d $'\r' | grep -v '^#' > "$pp_seq_file"
+    cat \
+        <(paste -d, \
+            <(head -n1 "$pp_seq_file") \
+            <(echo "reverse_complement")) \
+        <(paste -d, \
+            <(tail -n+2 "$pp_seq_file") \
+            <(tail -n+2 "$pp_seq_file" | cut -d, -f4 | tr ATCG TAGC | rev)) \
+    > "$pp_seq_file".temp && mv "$pp_seq_file".temp "$pp_seq_file"
+
+    awk -F, -v OFS=, \
+        'NR == 1 { print $0 } (NR > 1 && $3 == "yes") { $(NF-1)=$NF; print $0 } (NR > 1 && $3 == "no") { print $0 }' \
+        "$pp_seq_file" \
+    | awk -F, -v OFS=, \
+        '{ print "__join__",$1,$2,$(NF-1) }' \
+    >> "$pp_seq_file".temp && mv "$pp_seq_file".temp "$pp_seq_file"
+
+    awk -F, -v OFS=, \
+        'NR == 1 { print $1,$2,"pcr_handle_f" } (NR > 1 && $3 == "yes") { print $1,$2,$NF }' \
+        "$pp_seq_file" \
+    > "$fw_seq_file"
+
+    awk -F, -v OFS=, \
+        'NR == 1 { print $1,$2,"pcr_handle_r" } (NR > 1 && $3 == "no") { print $1,$2,$NF }' \
+        "$pp_seq_file" \
+    > "$rv_seq_file"
+
+    join --header -1 1 -2 1 -t, \
+        "$fw_seq_file" "$rv_seq_file" \
+    | cut -d, -f2- \
+    | awk -F, -v OFS=, -v inp_id="$inp_id" \
+        'NR == 1 { print $1,$2,$4 } NR > 1 { print inp_id"-"$1"."$3,$2,$4 }' \
+    > "$this_output_file"
+
+done
+
+rm -r "$temp_dir"