notes: metap: added ben's cmds; updated readme (issue #127)

README.md

@@ -115,6 +115,8 @@ Note that the workflow will create additional output files not necessarily requi
 
 This workflow creates various summary files, plots and an HTML report for a sample using the output of the main workflow.
 
+Note: How the metaP peptide/protein reports were generated from raw metaP data is described in `notes/gdb_metap.md`.
+
 - config:
   - sample configs used for the main workflow
 - workflow: `workflow_report/`
@@ -141,10 +143,11 @@ snakemake -s workflow_figures/Snakefile --cores 1 --configfile config/fig.yaml -
 
 # Notes
 
-Notes about manual analyses done using the generated data.
+Notes for manual/additional analyses done using the generated data.
 
+- `gdb_metap.md`: how the metaP reports were generated
 - `gdb_mmseqs2_highconf.md`: sample GDB, "high-confidence" proteins and protein clusters (assembly intersection and metaT cov.)
 - `gdb_rgi_aro3004454_flye.md`: sample GDB, an RGI example for diff. between SR/Hy and LR, and metaT coverage
-- ~~`gdb_mmseqs2_uniq_metat.md`: sample GDB, unique genes and their metaT coverage~~
-- ~~`gdb_rgi_other.md`: sample GDB, other RGI examples for diff. between SR/Hy and LR, and metaT coverage~~
-- ~~`gdb_barrnap_metat.md`: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)~~
\ No newline at end of file
+- `gdb_mmseqs2_uniq_metat.md`: sample GDB, unique genes and their metaT coverage
+- `gdb_rgi_other.md`: sample GDB, other RGI examples for diff. between SR/Hy and LR, and metaT coverage
+- `gdb_barrnap_metat.md`: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)
\ No newline at end of file

notes/gdb_metap.md

+Code used to generate metaP reports which are included in the report workflow.
+
+The reports were generated for
+- proteins from each assembly separately
+- all proteins from all assemblies together
+
+```bash
+##Generate parameters file
+java-cp SearchGUI-3.3.20.jar eu.isas.searchgui.cmd.IdentificationParametersCLI \
+    -out "params.par" \
+    -db "database.fasta" \
+    -prec_tol 10 \
+    -prec_ppm 1 \
+    -frag_tol 15 \
+    -frag_ppm 1 \
+    -digestion 0 \
+    -enzyme "Trypsin" \
+    -specificity 0 \
+    -mc 2 \
+    -fixed_mods "Carbamidomethylation of C" \
+    -variable_mods "Oxidation of M" \
+    -min_charge 2 \
+    -max_charge 4 \
+    -fi "b" \
+    -ri "y" \
+    -min_isotope 0 \
+    -max_isotope 1 \
+    -import_peptide_length_min 7 \
+    -import_peptide_length_max 60 \
+    -xtandem_noise_suppr 0 \
+    -xtandem_quick_acetyl 1 \
+    -xtandem_quick_pyro 1 \
+    -xtandem_refine 1 \
+    -msgf_instrument 1 \
+    -msgf_fragmentation 1 \
+    -msgf_protocol 0 \
+    -msgf_min_pep_length 7 \
+    -msgf_max_pep_length 60 \
+    -msgf_num_ptms 2 \
+    -comet_num_ptms 2
+#SearchGUI search
+java -cp SearchGUI-3.3.20.jar eu.isas.searchgui.cmd.SearchCLI \
+    -spectrum_files "MGF_DIR" \
+    -output_folder "OUT_DIR" \
+    -id_params "params.par" \
+    -xtandem 1 \
+    -msgf 1 \
+    -comet 1 \
+    -andromeda 0 \
+    -output_default_name "Sample_Name" \
+    -output_option 0 \
+    -output_data 1 \
+    -output_date 1 
+#PeptideShaker analysis
+java -cp PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI \
+    -experiment "Sample_Name" \
+    -sample "1" \
+    -replicate "1" \
+    -identification_files "SearchGUI_Outpit" \
+    -out "Sample_Name.cpsx" \
+    -zip "Sample_Name.cpsx.zip" 
+    
+#PeptideShaker reports.
+java -cp PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.ReportCLI \
+    -in "Sample_Name.cpsx.zip" \
+    -out_reports "OUT_DIR" \
+    -reports 6,9 
+    
+#Mzid Generation
+java -cp PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.MzidCLI \
+    -in "Sample_Name.cpsx.zip" \
+    -output_file "Sample_Name.mzid" \
+    -contact_first_name Benoit \
+    -contact_last_name Kunath \
+    -contact_email benoit.j.kunath@gmail.com \
+    -contact_address avenue de l’Université 7 Belval Luxembourg \
+    -organization_name LCSB \
+    -organization_email benoit.kunath@uni.lu \
+    -organization_address avenue de l’Université 7 Belval Luxembourg
+```
\ No newline at end of file