start structure for strainphlan tools

tools/strainphlan/extract_markers/README.md

+# extract_markers.py for strainphlan
+
+This step will extract the markers of selected species from MetaPhlAn database.
+
+### Help section
+
+```
+usage: extract_markers.py [-h] [-d DATABASE] [-c CLADE] [-o OUTPUT_DIR]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -d DATABASE, --database DATABASE
+                        The input MetaPhlAn dtabase
+  -c CLADE, --clade CLADE
+                        The clades to investigate
+  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        The output directory
+```

tools/strainphlan/strainphlan/README.md

+# extract_markers.py for strainphlan
+
+This step will build the multiple sequence alignment and the phylogenetic tree for each species.
+
+### Help section
+
+```
+usage: strainphlan [-h] [-d DATABASE] [-m CLADE_MARKERS]
+                   [-s SAMPLES [SAMPLES ...]] [-r REFERENCES [REFERENCES ...]]
+                   [-c CLADE] [-o OUTPUT_DIR] [-n NPROCS]
+                   [--secondary_samples SECONDARY_SAMPLES [SECONDARY_SAMPLES ...]]
+                   [--secondary_references SECONDARY_REFERENCES [SECONDARY_REFERENCES ...]]
+                   [--trim_sequences TRIM_SEQUENCES]
+                   [--marker_in_n_samples MARKER_IN_N_SAMPLES]
+                   [--sample_with_n_markers SAMPLE_WITH_N_MARKERS]
+                   [--secondary_sample_with_n_markers SECONDARY_SAMPLE_WITH_N_MARKERS]
+                   [--phylophlan_mode {accurate,fast}]
+                   [--phylophlan_configuration PHYLOPHLAN_CONFIGURATION]
+                   [--mutation_rates] [--print_clades_only]
+
+optional arguments:
+  -h, --help            show this help message and exit
+  -d DATABASE, --database DATABASE
+                        The input MetaPhlAn 3.0 database (default: /pasteur/so
+                        nic/homes/kehillio/miniconda3/envs/mpa/lib/python3.7/s
+                        ite-packages/metaphlan/metaphlan_databases/mpa_v30_CHO
+                        COPhlAn_201901.pkl)
+  -m CLADE_MARKERS, --clade_markers CLADE_MARKERS
+                        The clade markers as FASTA file (default: None)
+  -s SAMPLES [SAMPLES ...], --samples SAMPLES [SAMPLES ...]
+                        The reconstructed markers for each sample (default:
+                        [])
+  -r REFERENCES [REFERENCES ...], --references REFERENCES [REFERENCES ...]
+                        The reference genomes (default: [])
+  -c CLADE, --clade CLADE
+                        The clade to investigate (default: None)
+  -o OUTPUT_DIR, --output_dir OUTPUT_DIR
+                        The output directory (default: None)
+  -n NPROCS, --nprocs NPROCS
+                        The number of threads to use (default: 1)
+  --secondary_samples SECONDARY_SAMPLES [SECONDARY_SAMPLES ...]
+                        The reconstructed markers for each secondary sample
+                        (default: [])
+  --secondary_references SECONDARY_REFERENCES [SECONDARY_REFERENCES ...]
+                        The secondary reference genomes (default: [])
+  --trim_sequences TRIM_SEQUENCES
+                        The number of bases to remove from both ends when
+                        trimming markers (default: 50)
+  --marker_in_n_samples MARKER_IN_N_SAMPLES
+                        Theshold defining the minimum percentage of samples to
+                        keep a marker (default: 80)
+  --sample_with_n_markers SAMPLE_WITH_N_MARKERS
+                        Threshold defining the minimun number of markers to
+                        keep a sample (default: 20)
+  --secondary_sample_with_n_markers SECONDARY_SAMPLE_WITH_N_MARKERS
+                        Threshold defining the minimun number of markers to
+                        keep a secondary sample (default: 20)
+  --phylophlan_mode {accurate,fast}
+                        The presets for fast or accurate phylogenetic analysis
+                        (default: accurate)
+  --phylophlan_configuration PHYLOPHLAN_CONFIGURATION
+                        The PhyloPhlAn configuration file (default: None)
+  --mutation_rates      If specified will produced a mutation rates table for
+                        each of the aligned markers and a summary table for
+                        the concatenated MSA. This operation can take long
+                        time to finish (default: False)
+  --print_clades_only   If specified only print the potential clades and stop
+                        without building any tree (default: False)
+```