MVesuviusC/primerTree

Primer-Blast parameter ORGANISM is not recognised

rogeriobioinfo opened this issue · 4 comments

rogeriobioinfo commented

Hi again, kkkkkk

I would like to restrict the search blast to a specific organism, it is possible in primer-blast ncbi interface.
However, in primertree, an error is reported when I used that param.

script:
result <- search_primer_pair('CTTGGTCATTTAGAGGAAGTAA','TCCTCCGCTTATTGATATGC',num_aligns = 1000,num_permutations = 25, TOTAL_MISMATCH_IGNORE = 1, ORGANISM = 'Fungi', clustal_options=c(exec="D:/prjPrimers/clustal-omega-1.2.2-win64/clustal-omega-1.2.2-win64/clustalo.exe"))

output:
BLASTing 1 primer combinations
name type defval
1 SEQFILE file
2 PRIMER5_START text
3 PRIMER5_END text
4 PRIMER3_START text
5 PRIMER3_END text
6 PRIMER_LEFT_INPUT text
7 PRIMER_RIGHT_INPUT text
8 PRIMER_PRODUCT_MIN text 70
9 PRIMER_PRODUCT_MAX text 1000
10 PRIMER_NUM_RETURN text 10
11 PRIMER_MIN_TM text 57.0
12 PRIMER_OPT_TM text 60.0
13 PRIMER_MAX_TM text 63.0
14 PRIMER_MAX_DIFF_TM text 3
15 PRIMER_ON_SPLICE_SITE dropdown 0
16 SPLICE_SITE_OVERLAP_5END text 7
17 SPLICE_SITE_OVERLAP_3END text 4
18 SPLICE_SITE_OVERLAP_3END_MAX text 8
19 SPAN_INTRON checkbox
20 MIN_INTRON_SIZE text 1000
21 MAX_INTRON_SIZE text 1000000
22 SEARCH_SPECIFIC_PRIMER checkbox on
23 SEARCHMODE dropdown 0
24 PRIMER_SPECIFICITY_DATABASE dropdown refseq_mrna
25 CUSTOMSEQFILE file
26 EXCLUDE_XM checkbox
27 EXCLUDE_ENV checkbox
28 ORGANISM text Homo sapiens
31 slctOrg text
32 AddOrg button
33 ENTREZ_QUERY text
34 TOTAL_PRIMER_SPECIFICITY_MISMATCH dropdown 1
35 PRIMER_3END_SPECIFICITY_MISMATCH dropdown 1
36 MISMATCH_REGION_LENGTH dropdown 5
37 TOTAL_MISMATCH_IGNORE dropdown 6
38 MAX_TARGET_SIZE dropdown 4000
39 ALLOW_TRANSCRIPT_VARIANTS checkbox
40 NEWWIN checkbox
41 SHOW_SVIEWER checkbox on
42 HITSIZE dropdown 50000
44 EVALUE dropdown 30000
45 WORD_SIZE dropdown 7
46 MAX_CANDIDATE_PRIMER dropdown 500
47 NUM_TARGETS text 20
48 NUM_TARGETS_WITH_PRIMERS text 1000
49 MAX_TARGET_PER_TEMPLATE text 100
50 PRODUCT_MIN_TM text
51 PRODUCT_OPT_TM text
52 PRODUCT_MAX_TM text
53 PRIMER_MIN_SIZE text 15
54 PRIMER_OPT_SIZE text 20
55 PRIMER_MAX_SIZE text 25
56 PRIMER_MIN_GC text 20.0
57 PRIMER_MAX_GC text 80.0
58 GC_CLAMP text 0
59 POLYX text 5
60 PRIMER_MAX_END_STABILITY text 9
61 PRIMER_MAX_END_GC text 5
62 TH_OLOGO_ALIGNMENT checkbox
63 TH_TEMPLATE_ALIGNMENT checkbox
64 PRIMER_MAX_TEMPLATE_MISPRIMING_TH text 40.00
65 PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH text 70.00
66 PRIMER_MAX_SELF_ANY_TH text 45.0
67 PRIMER_MAX_SELF_END_TH text 35.0
68 PRIMER_PAIR_MAX_COMPL_ANY_TH text 45.0
69 PRIMER_PAIR_MAX_COMPL_END_TH text 35.0
70 PRIMER_MAX_HAIRPIN_TH text 24.0
71 PRIMER_MAX_TEMPLATE_MISPRIMING text 12.00
72 PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING text 24.00
73 SELF_ANY text 8.00
74 SELF_END text 3.00
75 PRIMER_PAIR_MAX_COMPL_ANY text 8.00
76 PRIMER_PAIR_MAX_COMPL_END text 3.00
77 EXCLUDED_REGIONS text
78 OVERLAP text
79 OVERLAP_5END text 7
80 OVERLAP_3END text 4
81 MONO_CATIONS text 50.0
82 DIVA_CATIONS text 1.5
83 CON_DNTPS text 0.6
84 SALT_FORMULAR dropdown 1
85 TM_METHOD dropdown 1
86 CON_ANEAL_OLIGO text 50.0
87 NO_SNP checkbox
88 PRIMER_MISPRIMING_LIBRARY dropdown AUTO
89 LOW_COMPLEXITY_FILTER checkbox on
90 PICK_HYB_PROBE checkbox
91 PRIMER_INTERNAL_OLIGO_MIN_SIZE text 18
92 PRIMER_INTERNAL_OLIGO_OPT_SIZE text 20
93 PRIMER_INTERNAL_OLIGO_MAX_SIZE text 27
94 PRIMER_INTERNAL_OLIGO_MIN_TM text 57.0
95 PRIMER_INTERNAL_OLIGO_OPT_TM text 60.0
96 PRIMER_INTERNAL_OLIGO_MAX_TM text 63.0
97 PRIMER_INTERNAL_OLIGO_MIN_GC text 20.0
98 PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT text 50
99 PRIMER_INTERNAL_OLIGO_MAX_GC text 80.0
100 NEWWIN checkbox
101 SHOW_SVIEWER checkbox on

Error in BLAST_primer(row$forward, row$reverse, num_targets_with_primers = max(num_aligns%/%nrow(primers), :
ORGANISM not valid option

MVesuviusC commented

I don't know that it will work that way, but in the past I've used "organism" instead of "ORGANISM" and it works.

julianponsford commented

I'm having a similar problem. Is there documentation that describes what all these options accept as input or what they correspond to on the Primer BLAST website?

Gabriel-Kirchgraber commented

I also got it to work by setting the options lowercase eg.
primer_specificity_database = "refseq_mrna"
If you "inspect element" via your Browser on the Primer Blast site you can see what it's name is and it will correpond to an entry in the list in the first post.

elOscatron commented

Hi again, kkkkkk

I would like to restrict the search blast to a specific organism, it is possible in primer-blast ncbi interface. However, in primertree, an error is reported when I used that param.

script: result <- search_primer_pair('CTTGGTCATTTAGAGGAAGTAA','TCCTCCGCTTATTGATATGC',num_aligns = 1000,num_permutations = 25, TOTAL_MISMATCH_IGNORE = 1, ORGANISM = 'Fungi', clustal_options=c(exec="D:/prjPrimers/clustal-omega-1.2.2-win64/clustal-omega-1.2.2-win64/clustalo.exe"))

output: BLASTing 1 primer combinations name type defval 1 SEQFILE file 2 PRIMER5_START text 3 PRIMER5_END text 4 PRIMER3_START text 5 PRIMER3_END text 6 PRIMER_LEFT_INPUT text 7 PRIMER_RIGHT_INPUT text 8 PRIMER_PRODUCT_MIN text 70 9 PRIMER_PRODUCT_MAX text 1000 10 PRIMER_NUM_RETURN text 10 11 PRIMER_MIN_TM text 57.0 12 PRIMER_OPT_TM text 60.0 13 PRIMER_MAX_TM text 63.0 14 PRIMER_MAX_DIFF_TM text 3 15 PRIMER_ON_SPLICE_SITE dropdown 0 16 SPLICE_SITE_OVERLAP_5END text 7 17 SPLICE_SITE_OVERLAP_3END text 4 18 SPLICE_SITE_OVERLAP_3END_MAX text 8 19 SPAN_INTRON checkbox 20 MIN_INTRON_SIZE text 1000 21 MAX_INTRON_SIZE text 1000000 22 SEARCH_SPECIFIC_PRIMER checkbox on 23 SEARCHMODE dropdown 0 24 PRIMER_SPECIFICITY_DATABASE dropdown refseq_mrna 25 CUSTOMSEQFILE file 26 EXCLUDE_XM checkbox 27 EXCLUDE_ENV checkbox 28 ORGANISM text Homo sapiens 31 slctOrg text 32 AddOrg button 33 ENTREZ_QUERY text 34 TOTAL_PRIMER_SPECIFICITY_MISMATCH dropdown 1 35 PRIMER_3END_SPECIFICITY_MISMATCH dropdown 1 36 MISMATCH_REGION_LENGTH dropdown 5 37 TOTAL_MISMATCH_IGNORE dropdown 6 38 MAX_TARGET_SIZE dropdown 4000 39 ALLOW_TRANSCRIPT_VARIANTS checkbox 40 NEWWIN checkbox 41 SHOW_SVIEWER checkbox on 42 HITSIZE dropdown 50000 44 EVALUE dropdown 30000 45 WORD_SIZE dropdown 7 46 MAX_CANDIDATE_PRIMER dropdown 500 47 NUM_TARGETS text 20 48 NUM_TARGETS_WITH_PRIMERS text 1000 49 MAX_TARGET_PER_TEMPLATE text 100 50 PRODUCT_MIN_TM text 51 PRODUCT_OPT_TM text 52 PRODUCT_MAX_TM text 53 PRIMER_MIN_SIZE text 15 54 PRIMER_OPT_SIZE text 20 55 PRIMER_MAX_SIZE text 25 56 PRIMER_MIN_GC text 20.0 57 PRIMER_MAX_GC text 80.0 58 GC_CLAMP text 0 59 POLYX text 5 60 PRIMER_MAX_END_STABILITY text 9 61 PRIMER_MAX_END_GC text 5 62 TH_OLOGO_ALIGNMENT checkbox 63 TH_TEMPLATE_ALIGNMENT checkbox 64 PRIMER_MAX_TEMPLATE_MISPRIMING_TH text 40.00 65 PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING_TH text 70.00 66 PRIMER_MAX_SELF_ANY_TH text 45.0 67 PRIMER_MAX_SELF_END_TH text 35.0 68 PRIMER_PAIR_MAX_COMPL_ANY_TH text 45.0 69 PRIMER_PAIR_MAX_COMPL_END_TH text 35.0 70 PRIMER_MAX_HAIRPIN_TH text 24.0 71 PRIMER_MAX_TEMPLATE_MISPRIMING text 12.00 72 PRIMER_PAIR_MAX_TEMPLATE_MISPRIMING text 24.00 73 SELF_ANY text 8.00 74 SELF_END text 3.00 75 PRIMER_PAIR_MAX_COMPL_ANY text 8.00 76 PRIMER_PAIR_MAX_COMPL_END text 3.00 77 EXCLUDED_REGIONS text 78 OVERLAP text 79 OVERLAP_5END text 7 80 OVERLAP_3END text 4 81 MONO_CATIONS text 50.0 82 DIVA_CATIONS text 1.5 83 CON_DNTPS text 0.6 84 SALT_FORMULAR dropdown 1 85 TM_METHOD dropdown 1 86 CON_ANEAL_OLIGO text 50.0 87 NO_SNP checkbox 88 PRIMER_MISPRIMING_LIBRARY dropdown AUTO 89 LOW_COMPLEXITY_FILTER checkbox on 90 PICK_HYB_PROBE checkbox 91 PRIMER_INTERNAL_OLIGO_MIN_SIZE text 18 92 PRIMER_INTERNAL_OLIGO_OPT_SIZE text 20 93 PRIMER_INTERNAL_OLIGO_MAX_SIZE text 27 94 PRIMER_INTERNAL_OLIGO_MIN_TM text 57.0 95 PRIMER_INTERNAL_OLIGO_OPT_TM text 60.0 96 PRIMER_INTERNAL_OLIGO_MAX_TM text 63.0 97 PRIMER_INTERNAL_OLIGO_MIN_GC text 20.0 98 PRIMER_INTERNAL_OLIGO_OPT_GC_PERCENT text 50 99 PRIMER_INTERNAL_OLIGO_MAX_GC text 80.0 100 NEWWIN checkbox 101 SHOW_SVIEWER checkbox on

Error in BLAST_primer(row$forward, row$reverse, num_targets_with_primers = max(num_aligns%/%nrow(primers), : ORGANISM not valid option

Hello,

I would like to ask, how can I know which are the possible arguments to enter? I mean, I've been a long time until I discovered that you put "primer_specificity_database" instead of "database" or "subject_database". In my case, I don't even see that report with the options (only the ones I have put).

For example, I would like to be able to specify the "Optimize for" options, putting "More dissimilar sequences (discontiguous megablast)" or "Somewhat similar sequences (blastn)"... but I don't even know the name of the option or how to write the algorithms.