Commit 483ccfb9 authored by Jorge Navarro Muñoz's avatar Jorge Navarro Muñoz
Browse files

Small fixes in README's formatting

parent d129fa41
......@@ -39,8 +39,8 @@ There are some options to re-run BiG-SCAPE and skip some of the most time-consum
* Writes list of sequences per domain (.fasta)
* Writes list of domains per BGC (.pfs)
* Writes selected information from domtable files per BGC (.pfd)
* Saves dictionary with list of specific domains per BGC (<output dir>/BGCs.dict)
* When using the `seqdist` distance method, calculates multiple alignments using MAFFT (.algn) for domains represented by more than one sequence. Saves alignment information in <output dir>/DMS.dict
* Saves dictionary with list of specific domains per BGC (`<output dir>/BGCs.dict`)
* When using the `seqdist` distance method, calculates multiple alignments using MAFFT (.algn) for domains represented by more than one sequence. Saves alignment information in `<output dir>/DMS.dict`
* Calculates distance between BGCs
* Generates network files
......@@ -55,7 +55,7 @@ There are some options to re-run BiG-SCAPE and skip some of the most time-consum
### What it does
Skips domain prediction using `hmmscan` and extraction of information, but recalculates everything else:
* When using the `seqdist` distance method, calculates multiple alignments using MAFFT (.algn) for domains represented by more than one sequence. Saves alignment information in <output dir>/DMS.dict
* When using the `seqdist` distance method, calculates multiple alignments using MAFFT (.algn) for domains represented by more than one sequence. Saves alignment information in `<output dir>/DMS.dict`
* Calculates distance between BGCs
* Generates network files
......@@ -68,8 +68,8 @@ Skips domain prediction using `hmmscan` and extraction of information, but recal
* The original .gbk files. These are necessary to rebuild the original structure
* The list of domains per BGC (.pfs files). These are necessary for distance calculations
* The output from `hmmscan` (.domtable files). These are necesary to see whether a particular .gbk file had no predicted domains (in which case it will be taken out of the analysis)
* If using the `seqdist` method, the fasta sequence files per domain (<output dir>/domains/). These are necessary for the alignments
* The BGCs dictionary (<output dir>/BGCs.dict). This contains a list of domains per BGC (and for each of these domains, a list of all predicted locations within the BGC). Needed for distance calculations
* If using the `seqdist` method, the fasta sequence files per domain (`<output dir>/domains/`). These are necessary for the alignments
* The BGCs dictionary (`<output dir>/BGCs.dict`). This contains a list of domains per BGC (and for each of these domains, a list of all predicted locations within the BGC). Needed for distance calculations
## Parameter `--skip_mafft`
......@@ -90,8 +90,8 @@ Skips domain prediction usnig `hmmscan`, extraction of sequences and domain sequ
* The original .gbk files. These are necessary to rebuild the original structure
* The list of domains per BGC (.pfs files). These are necessary for distance calculations
* The output from `hmmscan` (.domtable files). These are necesary to see whether a particular .gbk file had no predicted domains (in which case will be taken out of the analysis
* The BGCs dictionary (<output dir>/BGCs.dict). This contains a list of domains per BGC (and for each of these domains, a list of all predicted locations within the BGC). Needed for distance calculations
* The DMS dictionary (<output dir>/DMS.dict). This contains information from the sequence alignment
* The BGCs dictionary (`<output dir>/BGCs.dict`). This contains a list of domains per BGC (and for each of these domains, a list of all predicted locations within the BGC). Needed for distance calculations
* The DMS dictionary (`<output dir>/DMS.dict`). This contains information from the sequence alignment
## Parameter `--skip_all`
......
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