| Previous changeset 12:ee28ec28140d (2025-05-23) |
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Commit message:
planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae |
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modified:
get_DB_data.xml get_db_info.py output.html output.json test-data/test_missing_input.csv testMock.py |
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added:
test-data/2-step-golden_gate_plan.csv |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 get_DB_data.xml --- a/get_DB_data.xml Fri May 23 12:45:20 2025 +0000 +++ b/get_DB_data.xml Fri May 23 13:47:21 2025 +0000 |
| b |
| @@ -37,31 +37,71 @@ <tests> <!--python get_db_info.py -input 'test-data/test_input.csv' -sequence_column 'sequence' -annotation_column 'annotation' -db_uri 'postgresql://postgres:RK17@localhost:5432/test_fragments_db' -table 'sample' -fragment_column 'fragment' -output 'test-data/output'--> <test> - <param name="input" value="test_input.csv" /> + <param name="input" value="2-step-golden_gate_plan.csv" /> <param name="table" value="sample" /> <param name="sequence_column" value="sequence" /> <param name="annotation_columns" value="annotation" /> <param name="fragment_column" value="fragment" /> <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" /> - <output_collection name="output_gb" type="list" count="4"> - <element name="ACP10001AaCbbBS"> + <output_collection name="output_gb" type="list" count="12"> + <element name="part_A"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_B"> <assert_contents> - <has_n_lines min="3" /> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_C"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_D"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_E"> + <assert_contents> + <has_n_lines min="10" /> </assert_contents> </element> - <element name="CFP10002AaCbbBS"> + <element name="part_F"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_G"> <assert_contents> - <has_n_lines min="3" /> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_H"> + <assert_contents> + <has_n_lines min="10" /> </assert_contents> </element> - <element name="QWE10004AaCbbBS"> + <element name="part_I"> <assert_contents> - <has_n_lines min="3" /> + <has_n_lines min="10" /> </assert_contents> </element> - <element name="XYZ10003AaCbbBS"> + <element name="part_J"> + <assert_contents> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_K"> <assert_contents> - <has_n_lines min="3" /> + <has_n_lines min="10" /> + </assert_contents> + </element> + <element name="part_L"> + <assert_contents> + <has_n_lines min="10" /> </assert_contents> </element> </output_collection> |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 get_db_info.py --- a/get_db_info.py Fri May 23 12:45:20 2025 +0000 +++ b/get_db_info.py Fri May 23 13:47:21 2025 +0000 |
| [ |
| @@ -106,17 +106,18 @@ # Compare fragments between CSV and DB csv_fragments = set() - all_ids = set(df[0]) + all_ids = set(df[0].dropna().astype(str)) for _, row in df.iterrows(): for col in df.columns: - if col != 0: # Skip the first column + if col != 0: fragment = row[col] - if fragment not in all_ids: - csv_fragments.add(fragment) + if pd.notna(fragment): + fragment_str = str(fragment) + if fragment_str not in all_ids: + csv_fragments.add(fragment_str) db_fragments = set(fragment_map.keys()) missing_fragments = sorted(list(csv_fragments - db_fragments)) - if missing_fragments: raise ValueError( f" Missing fragments in DB: {', '.join(missing_fragments)}" @@ -128,6 +129,8 @@ for col in df.columns: if col != 0: fragment = row[col] + if fragment not in csv_fragments: + continue db_row = fragment_map.get(fragment) if db_row: |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 output.html --- a/output.html Fri May 23 12:45:20 2025 +0000 +++ b/output.html Fri May 23 13:47:21 2025 +0000 |
| b |
| @@ -285,7 +285,7 @@ var md = window.markdownit({ html: true, }); - target.innerHTML = md.render(atob('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')); + target.innerHTML = md.render(atob('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')); </script> </body> </html> \ No newline at end of file |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 output.json --- a/output.json Fri May 23 12:45:20 2025 +0000 +++ b/output.json Fri May 23 13:47:21 2025 +0000 |
| [ |
| b'@@ -13,29 +13,29 @@\n "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db",\n "fragment_column": "fragment",\n "input": {\n- "id": "21ac64467e79a23d",\n+ "id": "3e55d5e4bd660a72",\n "src": "hda"\n },\n "sequence_column": "sequence",\n "table": "sample"\n },\n "job": {\n- "command_line": "mkdir \'outdir\' && python \'/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py\' --input \'/tmp/tmp20abmio8/files/0/0/5/dataset_00567b2f-5032-43b8-a612-c16e8ac097ca.dat\' --sequence_column \'sequence\' --annotation_columns \'annotation\' --db_uri \'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\' --table \'sample\' --fragment_column \'fragment\' --output \'outdir\'",\n+ "command_line": "mkdir \'outdir\' && python \'/home/rkhaled/galaxytools/tools/get_db_data/get_db_info.py\' --input \'/tmp/tmpkx9eg1ax/files/b/7/5/dataset_b7584f2c-5438-48d4-823c-b2c3f4274df3.dat\' --sequence_column \'sequence\' --annotation_columns \'annotation\' --db_uri \'postgresql://postgres:RK17__at__localhost:5432/test_fragments_db\' --table \'sample\' --fragment_column \'fragment\' --output \'outdir\'",\n "command_version": null,\n "copied_from_job_id": null,\n- "create_time": "2025-05-23T12:44:22.666476",\n+ "create_time": "2025-05-23T13:46:12.315974",\n "dependencies": [],\n "exit_code": 0,\n- "external_id": "196443",\n+ "external_id": "224853",\n "galaxy_version": "24.2",\n "handler": null,\n- "history_id": "21ac64467e79a23d",\n- "id": "16392a867bb52b96",\n+ "history_id": "3e55d5e4bd660a72",\n+ "id": "024baef40a002eb4",\n "inputs": {\n "input": {\n- "id": "21ac64467e79a23d",\n+ "id": "3e55d5e4bd660a72",\n "src": "hda",\n- "uuid": "00567b2f-5032-43b8-a612-c16e8ac097ca"\n+ "uuid": "b7584f2c-5438-48d4-823c-b2c3f4274df3"\n }\n },\n "job_messages": [],\n@@ -46,36 +46,76 @@\n "model_class": "Job",\n "output_collections": {\n "output_gb": {\n- "id": "21ac64467e79a23d",\n+ "id": "3e55d5e4bd660a72",\n "src": "hdca"\n }\n },\n "outputs": {\n- "__new_primary_file_output_gb|ACP10001AaCbbBS__": {\n- "id": "16392a867bb52b96",\n+ "__new_primary_file_output_gb|part_A__": {\n+ "id": "024baef40a002eb4",\n "src": "hda",\n- "uuid": "f6166465-8329-42d3-8b8d-634164cb00d1"\n+ "uuid": "93fbeb5d-074d-48e6-9eec-fd7445ec81dd"\n+ },\n+ "__new_primary_file_output_gb|part_B__": {\n+ "id": "26cae1ed3aa61beb",\n+ "src": "hda",\n+ "uuid": "d9595d0c-e479-4529-8c8f-92910ba304e2"\n+ },\n+ "__new_primary_file_output_gb|part_C__": {\n+ "id": "63a16c870de58b5c",\n+ "src": "hda",\n+ "uuid": "f7f751b7-bc0a-496e-999f-a1eaded9db2c"\n },\n- "__new_primary_file_output_gb|CFP10002AaCbbBS__": {\n- "id"'..b' },\n+ "__new_primary_file_output_gb|part_E__": {\n+ "id": "a522ff593fd68eb0",\n+ "src": "hda",\n+ "uuid": "42671fc1-73de-4a25-b090-242c9c233349"\n+ },\n+ "__new_primary_file_output_gb|part_F__": {\n+ "id": "4790cce11de15e49",\n+ "src": "hda",\n+ "uuid": "28fa25eb-6a6f-422b-b18f-cc27335d0057"\n },\n- "__new_primary_file_output_gb|QWE10004AaCbbBS__": {\n- "id": "c5caf62a8c51ce22",\n+ "__new_primary_file_output_gb|part_G__": {\n+ "id": "fd0d5f6f6b618b2e",\n "src": "hda",\n- "uuid": "79161280-74b3-4786-9d94-d5e616a85047"\n+ "uuid": "2f9a4438-cc15-4157-8d4e-76e265f001e5"\n+ },\n+ "__new_primary_file_output_gb|part_H__": {\n+ "id": "55923ec0abca33c6",\n+ "src": "hda",\n+ "uuid": "ec95f6c6-83ce-4908-a438-4b75b70f300b"\n+ },\n+ "__new_primary_file_output_gb|part_I__": {\n+ "id": "a7c1ac8dd0e0cd88",\n+ "src": "hda",\n+ "uuid": "ae511dd8-952c-4402-9520-d158966dd7f2"\n },\n- "__new_primary_file_output_gb|XYZ10003AaCbbBS__": {\n- "id": "33cdc5f5dcf09503",\n+ "__new_primary_file_output_gb|part_J__": {\n+ "id": "03ce4e2872cac014",\n "src": "hda",\n- "uuid": "3cc67d62-a001-42bf-9628-c508daf0934c"\n+ "uuid": "143078c2-aa8d-4f30-858a-dcc96d854582"\n+ },\n+ "__new_primary_file_output_gb|part_K__": {\n+ "id": "7036040c587c5933",\n+ "src": "hda",\n+ "uuid": "6287af7a-a2ad-4348-a4d8-9bc78969a188"\n+ },\n+ "__new_primary_file_output_gb|part_L__": {\n+ "id": "bf44ed04fc51b238",\n+ "src": "hda",\n+ "uuid": "a32e4a55-fb89-434c-a222-506576b7fc34"\n }\n },\n "params": {\n "__input_ext": "\\"input\\"",\n "annotation_columns": "\\"annotation\\"",\n- "chromInfo": "\\"/tmp/tmp20abmio8/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\\"",\n+ "chromInfo": "\\"/tmp/tmpkx9eg1ax/galaxy-dev/tool-data/shared/ucsc/chrom/?.len\\"",\n "db_uri": "\\"postgresql://postgres:RK17@localhost:5432/test_fragments_db\\"",\n "dbkey": "\\"?\\"",\n "fragment_column": "\\"fragment\\"",\n@@ -88,13 +128,13 @@\n "tool_id": "get_DB_data",\n "tool_stderr": "",\n "tool_stdout": "Container \'test_fragments_db\' is already running.\\nConnected to database.\\n",\n- "update_time": "2025-05-23T12:44:29.552502",\n+ "update_time": "2025-05-23T13:46:18.962770",\n "user_email": "planemo@galaxyproject.org",\n- "user_id": "21ac64467e79a23d"\n+ "user_id": "3e55d5e4bd660a72"\n },\n "status": "success",\n "test_index": 0,\n- "time_seconds": 17.09453797340393,\n+ "time_seconds": 16.930965185165405,\n "tool_id": "get_DB_data",\n "tool_version": "0.1.0+galaxy0"\n },\n' |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 test-data/2-step-golden_gate_plan.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/2-step-golden_gate_plan.csv Fri May 23 13:47:21 2025 +0000 |
| b |
| @@ -0,0 +1,4 @@ +construct_3,construct_1,part_L,part_J,part_K,, +construct_4,construct_2,part_L,part_J,part_K,, +construct_1,part_A,part_B,part_C,part_D,part_E,part_F +construct_2,part_A,part_G,part_H,part_I,part_F, |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 test-data/test_missing_input.csv --- a/test-data/test_missing_input.csv Fri May 23 12:45:20 2025 +0000 +++ b/test-data/test_missing_input.csv Fri May 23 13:47:21 2025 +0000 |
| b |
| @@ -1,5 +1,4 @@ -ID,Frag1,Frag2,Frag3 Sample-1,ACP10001AaCbbBS,NEW20001BbDccKT,XYZ10003AaCbbBS Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,ALT30005CcEddLM Sample-3,XYZ10003AaCbbBS,ALT30005CcEddLM,ACP10001AaCbbBS -Sample-4,QWE10004AaCbbBS,NEW20001BbDccKT,CFP10002AaCbbBS \ No newline at end of file +Sample-4,QWE10004AaCbbBS,NEW20001BbDccKT,CFP10002AaCbbBS |
| b |
| diff -r ee28ec28140d -r 5b16f2911491 testMock.py --- a/testMock.py Fri May 23 12:45:20 2025 +0000 +++ b/testMock.py Fri May 23 13:47:21 2025 +0000 |
| [ |
| b"@@ -58,74 +58,1289 @@\n VALUES (%s, %s, %s, %s, %s);\n ''', [\n (\n- 'ACP10001AaCbbBS',\n+ 'part_A',\n '''ORIGIN\n-1 atggccattg taatgggccg ctgaaagggt gcccggatca ctttcgctgt ttcgacgttg\n-61 gcttggtccc agcggcggca ccgagctggg tagcggtcag gagctgcttc gcgtgagcgg\n-121 ctgccagggc agctgacgcc gctgcgcgca gctgcgcatg\n+ 1 tcacaggatg gtccaacgaa actaggcttt agacgaggga tgaatgaccg acccccactc\n+ 61 gtggcactaa cggacagact tccctgacgg ttattcgacc attaaagtca gacatgcggg\n+ 121 ggtgaataaa ttagccaaat tgtgtcgaag aaaagacgtg cggctggcac ataaggcagt\n+ 181 cttgatccta gtcttgcagg gatgcacgta agtcgcctca attaactgca gccgagctcc\n+ 241 aggttaccaa agaccctagt atgccagggc ctaacggttg gagtatatta tgggtacgca\n+ 301 atagtgcgga agttaacctg ggcaacatcc aggtgagagg ttggacggaa gcgacagtaa\n+ 361 gtggccatag actgccgagt cgtgttaatg aatcgctata cgcccatgga gttgtggggt\n+ 421 cgttttatcc gagtaggggc ccgctgacta cttcgtccag acaatatgcc gtcttcaata\n+ 481 gtctacctga gagtcatgcc ggcatttccg acgctgagtg aaacccgcgt agccaggcga\n+ 541 aatttgcatc ttgaaatacc actgcagatc agccagtaag gcccatataa gggcgctggt\n+ 601 gttctggcga cagataaagt gttatctaat gtaacccgcg gacttttaga ggatacttga\n+ 661 atgcgggcat atcgtcccac cagcgtcacg tggtcgggct agcggcagac aaactctgcc\n+ 721 gatgtttttc tttgccgcga tagcgggcta gtcaattcac tatccggcga tgaagcatag\n+ 781 attgttatcg cgcttatgcg gaggataatc aagtcttggc agaacctgct cgctcatgca\n+ 841 ctggtgaggc gtggttatcc taacaaccgc ctaggacgaa gaatgggctc ggtagggaca\n+ 901 gttcgtgcgt ttagcttcgt cccatcttaa tgctgtctgg agggaggcta catgcgaaca\n+ 961 gaagccgtgg gcgaaagttg ttgatccggg tctaacacgg ataagggcca tggtgaacgc\n+ 1021 atcatgcgat acttcttggt agttcttcta acatgaccgt gccatagccc ttaccctttg\n+ 1081 aagaagttaa cctatctgcc gtctcctgca cgaatagcga ctggactcgg gtattttgga\n+ 1141 tacctcacga aagcacttcg atcggccgaa gcatggatat ttcgccggac gggcccgaat\n+ 1201 agagagcctt gtatgtcggt tagtacaacg cagtcctgga gacatctacg cggatgggcc\n+ 1261 taggggctgg acttaacatt gggtaacgta cctggtccaa agtgaatgca aagcactttt\n+ 1321 acaaagcgcg ggtccccgtg ggtgtttagg gtagaagatt ggcggatgct acgaacgatc\n+ 1381 ccgctttgaa actatcatta catcgtgtaa aagagacact taacaaaggc caataaactg\n+ 1441 ccagtaagaa tcgctcagtg cggtgctggg gacgctaagt aggggcaaca gccagtgaag\n+ 1501 gacgtgaccg acctttctca gataagatat gctggcgtct atctaataag catagtgaaa\n+ 1561 aaccaaccat ttcacttaca cgaagtacat ttgcattgct agtaaagacg cctaaacaga\n+ 1621 agtgcccttg catgctgtat gtctatagtc cttagggaag catcagccct tctacttatt\n+ 1681 cgaggtctga gaaaccctgg acaagctccg aattattcaa tgtgcctgtc tccgaggtta\n+ 1741 gatagcgcta tgctcttaag agttgcacag aatgaccatc ctggaatgtc cctggagggg\n+ 1801 tctaggtatg ctgatcgaag ggtgctctaa ggacttgacg tgcgtccgag gagggtgctg\n+ 1861 cctccttcgc ctttagatcc aacgcggatc acatgcgcgt gagctaatag gatcaccttc\n+ 1921 tgctccgatt tttaccctcc tgggtcactt ccgaatgagg tagcgggcga aatataatgt\n+ 1981 ctccactcgt aggtgttccc tgtatgtgaa gctctatagt ggacaaaggt ttgatgaact\n+ 2041 agcccccgta tacgctctca ccgacggacg cgggggtctg ttatttgaag catcatacat\n+ 2101 gcgaaggtgc cttctcagca acgaaaggta gtgggagtgt acaagttcaa tgcgccgcca\n+ 2161 taggtctgag tatacaaggg gatgccccca tccacaacgg gattggctac ccggagagct\n+ 2221 ggctccgctc caacaaataa ttatattaac ctattggaat tccacctgca tatcagagga\n+ 2281 gagagacctt tacggctatt ctgtttaccg gatccatcgg taccaaggat cagaaagtga\n+ 2341 cacggtttga acgggttgtt gtaatacttt gagtatacct ctgacgctga gcgtgtcgtc\n+ 2401 ctgagcgcag actcaataac atagcagtcc gacatcgccg tgatatgtaa atgcaacgaa\n+ 2461 tttaggtctt gactcggtct accatgtcaa aagggtagcc agatttcagc gcgaaattga\n+ 2521 actttgtgtt tagtgtgggg tcctcggtta caaaatagga tcagacatgt gtgattttgg\n+ 2581 taacctagtc tggcagtccg acagacttcg ctatgatttg atggggccgg cctataattg\n+ 2641 gcttgcgcaa cccgctcatc tcgggcgtgt tttacttcct gcggtcccca cgccctattt\n+ 2701 tcgggccagc tgtaggtgct agagtgaatg ctggcgaata agattccccg ctatttggcg\n+ 2761 cctcgccaca gctctggcac tatgggggga gtttctctgt tccttaaaca gcacccgttt\n+ 2821 ttgaggtgta ttggtttcgg ttctgcatta ggcaattcgt "..b'tgcaga ccgtagagaa ataccggcta\n+ 481 aggcagtcgc tcaatgcaca ccagcatcgc cgagacatat aaagccataa acattaattg\n+ 541 gaatgctagt cacagcgtgt tgactggacg cttaaaagtt tctacaaaag gtatagtttt\n+ 601 aacatttctc tgagttagcg ctatcgggtc gactgacatc tagaattgac acgttactca\n+ 661 cctggatcct agtcacactc cgggaaccgc tcgcttagtg gcagtagcgg ggggcgtccc\n+ 721 taggatagct gcgcaaagcg tggtttatct aatcgtggct tgtgtggaca tgatgctgtt\n+ 781 caggcgcatc tgtggccgcc acagcattac caagctaatc agaaaccgcg gcatgtcccc\n+ 841 gcgatgcgag aggcatctgt tagagccaaa gagtggaggt ctgtaatatc gctagcggag\n+ 901 attttctaag gggcgtggga ctttatcccg atatggctga acgatccaac ggcaaatggt\n+ 961 tctgccattg aactttaacc atgaatagac tccaggcgag ggataatgga aataatagca\n+ 1021 ggaaatgaca atctactagg tgcgcactat caagattgta tgtttgcgta tcgtagttct\n+ 1081 aatggtcttg tgtcccgtat tgggtcggac ggtgctgttc ctgatcgtag caatgcccgg\n+ 1141 ttagaatcac gcatcggagc gatcatttcg ggcgatacgc gttcgttctg tccactcttg\n+ 1201 tgggagtccg acgtatgcct gctcggtatt gttttattca ggcgacagta cctcccattc\n+ 1261 aaatatacag ggttatacta cacaccacga gtaataaaga cttgtgttgt gccaattcct\n+ 1321 cgtgggactg ccacgctcgt gagcttcgcg gttacatacc cctatgtccc caactgttgg\n+ 1381 tggcaaatcc ctaatctaat ctattgtatc acagtcggtc aacgactgaa attggggcaa\n+ 1441 caccaacagt gctcttacga tattcgtctg tgtctaacaa tccaacaaaa agctgttatt\n+ 1501 atgatggagg atcttggatt gcgtcagtac tacggtgttg tacgagaatt gcatgatgat\n+ 1561 tcctcgatgt cgagtccttg caagatcgtg atctatagcc aagctgctgc tgtagatcaa\n+ 1621 cctcaccggg gcgggggtcc cattactatg ggcggcatta gagtaccata gatgaacgcg\n+ 1681 agcagagaca tgtcaatgta tcccagtcct gcagtactac gtcagtctct gctcctgggg\n+ 1741 ccaatgcacg cctgtagaat agggccgtgt tcccatgaga aatttgaggg acttacgatt\n+ 1801 agatggcctt ggcaggggac tccgcgtacg tgtggggatg aaccggcacc ggccttggcc\n+ 1861 ctgagtaaat gtaagcgata tcaacttcgc tattcatgat cagtggtatt cgtgtaggca\n+ 1921 ccgaaagtcc cttggcgaaa gtagagacat acgatacgga ccgcaagcga gcagaatttc\n+ 1981 agcacatgac agttattagc ttttttctaa tggtgctccc attatgattg tcaagtcccg\n+ 2041 actgctagct gtaggatgaa acacatccac acacgtgtta ccatactgat tttgacacta\n+ 2101 cttcctaacc gggccgaatg gtatctgctg cgatgcttag ttacgtaaca gccgaatgtc\n+ 2161 acgccactgc atattgtggt tctggaattc cacctgcata tgtcacgcta gagaccgtat\n+ 2221 gaggtgggcg gatagtggtg acttcaaacc catatgcagg tgctgca\n+\'\'\',\n+ \'\'\'LOCUS part_L 2267 bp ds-DNA circular UNK 28-OCT-2019\n+DEFINITION .\n+ACCESSION part_L\n+VERSION part_L\n+KEYWORDS "creator:SynthSys Center" "marker:KanR".\n+SOURCE .\n+ ORGANISM .\n+ .\n+FEATURES Location/Qualifiers\n+ misc_feature join(2263..2267,1)\n+ /label="feature"\n+ /ApEinfo_fwdcolor="#84b0dc"\n+ terminator 2..59\n+ /label="another feature"\n+ /ApEinfo_fwdcolor="#c6c9d1"\n+ CDS complement(1140..1955)\n+ /label="yet another feature"\n+ /ApEinfo_fwdcolor="#b7e6d7"\n+ misc_feature 2206..2209\n+ /label="feature"\n+ /ApEinfo_fwdcolor="#ff0000"\n+ misc_feature 2202..2205\n+ /label="another feature"\n+ /ApEinfo_fwdcolor="#faac61"\n+ terminator 2139..2182\n+ /label="yet another feature"\n+ /ApEinfo_fwdcolor="#c6c9d1"\n+ rep_origin complement(254..842)\n+ /label="feature"\n+ /ApEinfo_fwdcolor="#ffef86"\n+ misc_feature 2248..2251\n+ /label="another feature"\n+ /ApEinfo_fwdcolor="#ff0000"\n+ misc_feature 2185..2190\n+ /label="yet another feature"\n+ /ApEinfo_fwdcolor="#84b0dc"\n+ terminator 1025..1119\n+ /label="feature"\n+ /ApEinfo_fwdcolor="#c6c9d1"\n+\'\'\',\n+ \'Metadata1 for part_L\', \'Metadata2 for part_L\'\n )\n ])\n \n' |