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Clarify filename requirements for --primerTarget (disallow hyphens) #18

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Clarify filename requirements for --primerTarget (disallow hyphens) #18

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6 changes: 4 additions & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,8 @@ Options:
Input filenames must meet these conditions:
- Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
- Contain the string "cds" after the unique identifier;
- End with the extension .fna (PUPpy automatically only uses such files in the given folder).
- End with the extension .fna (PUPpy automatically only uses such files in the given folder);
- Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
-nt, --nonTarget Directory with CDS files of non-targets in the defined microbial community, for specificity checks.
-o, --outdir Relative path to the output folder. Default: Align_OUT.
Expand Down Expand Up @@ -277,7 +278,8 @@ Options:
Input filenames must meet these conditions:
- Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
- Contain the string "cds" after the unique identifier;
- End with the extension .fna (PUPpy automatically only uses such files in the given folder).
- End with the extension .fna (PUPpy automatically only uses such files in the given folder);
- Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
-i, --input Input file (ResultDB.tsv) from `puppy-align` or UniqueGenesList.tsv. Required.
-o, --outdir Output directory for primer design files. Default: 'Primer3_output'.
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3 changes: 2 additions & 1 deletion scripts/puppy-align
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Expand Up @@ -68,7 +68,8 @@ Options:
Input filenames must meet these conditions:
- Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
- Contain the string "cds" after the unique identifier;
- End with the extension .fna (PUPpy automatically only uses such files in the given folder).
- End with the extension .fna (PUPpy automatically only uses such files in the given folder);
- Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
-nt, --nonTarget Directory with CDS files of non-targets in the defined microbial community, for specificity checks.
-o, --outdir Relative path to the output folder. Default: Align_OUT.
Expand Down
3 changes: 2 additions & 1 deletion scripts/puppy-primers
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Expand Up @@ -77,7 +77,8 @@ Options:
Input filenames must meet these conditions:
- Contain a unique identifier at the beginning of the name (e.g. EcoliBW25113);
- Contain the string "cds" after the unique identifier;
- End with the extension .fna (PUPpy automatically only uses such files in the given folder).
- End with the extension .fna (PUPpy automatically only uses such files in the given folder);
- Must NOT contain hyphens (-) in the filename as they cause unintended behavior.
A filename example is: "EcoliBW25113_cds.fna". For more detailed instructions, please refer to the PUPpy GitHub documentation.
-i, --input Input file (ResultDB.tsv) from `puppy-align` or UniqueGenesList.tsv. Required.
-o, --outdir Output directory for primer design files. Default: 'Primer3_output'.
Expand Down