Merge pull request #8 from ttubb/v0.9.1

re0.9.1

examples/01_samples_reads_assembly_bins_mags.yaml

@@ -50,7 +50,7 @@ PAIRED_END_READS:
   RELATED_SAMPLE_TITLE: "idx00_main digester sample"                          # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
   ADDITIONAL_MANIFEST_FIELDS:                                                 # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_e01_coassembly"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
+  ASSEMBLY_NAME: "idx00_e01_coasm"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/02_samples_reads_assembly_bins.yaml

@@ -31,7 +31,7 @@ SINGLE_READS:
   RELATED_SAMPLE_TITLE: 'idx00_example02_sample01'                                                    # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
   ADDITIONAL_MANIFEST_FIELDS:                                                                         # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: 'idx00_e02_assembly'                                                                 # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: 'idx00_e02_asm'                                                                 # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   ASSEMBLY_SOFTWARE: 'metaSPAdes'                                                                     # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: 'ant fungus garden'                                                               # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                                                   # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/03_samples_reads_assembly.yaml

@@ -68,7 +68,7 @@ PAIRED_END_READS:
   RELATED_SAMPLE_TITLE: "idx00_main digester sample"                          # The title of the sample that these reads originate from >>EXAMPLE: "Bioreactor_2_sample"
   ADDITIONAL_MANIFEST_FIELDS:                                                 # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_e01_coassembly"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
+  ASSEMBLY_NAME: "idx00_e03_coasm"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/04_reads_assembly_bins_mags.yaml

@@ -21,7 +21,7 @@ SINGLE_READS:
   RELATED_SAMPLE_ACCESSION: 'SAMEA113417017'                                  # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
   ADDITIONAL_MANIFEST_FIELDS:                                                 # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_e01_coassembly"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
+  ASSEMBLY_NAME: "idx00_e04_coasm"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/05_reads_assembly_bins.yaml

@@ -32,7 +32,7 @@ PAIRED_END_READS:
   RELATED_SAMPLE_ACCESSION: 'SAMEA113417018'                                  # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
   ADDITIONAL_MANIFEST_FIELDS:                                                 # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_e01_coassembly"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
+  ASSEMBLY_NAME: "idx00_e05_coasm"                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "SGMA project mg"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/06_reads_assembly.yaml

@@ -30,7 +30,7 @@ PAIRED_END_READS:
   RELATED_SAMPLE_ACCESSION: 'SAMEA113417017'                                                # The accession of the sample that these reads originate from >>EXAMPLE: "ERS15898933"
   ADDITIONAL_MANIFEST_FIELDS:                                                               # You can add additional fields that will be written to the manifest
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: 'idx00_e06_assembly'                                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: 'idx00_e06_asm'                                                       # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   ASSEMBLY_SOFTWARE: 'metaSPAdes'                                                           # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: 'ant fungus garden'                                                     # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                                         # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/07_assembly_bins_mags.yaml

@@ -13,7 +13,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            #
 PROJECT_NAME: "idx00_AgRFex 2 Survey"                                         # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
 SAMPLE_ACCESSIONS: ['SAMEA113417017']                                         # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex07_assembly"                                              # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex07_asm"                                              # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/08_assembly_bins.yaml

@@ -11,7 +11,7 @@ METAGENOME_TAXID: "718289"                                                    #
 SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            # One of https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#platform >>EXAMPLE: ["ILLUMINA","OXFORD_NANOPORE"]
 SAMPLE_ACCESSIONS: ['SAMEA113417017']                                         # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex08_assembly"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex08_asm"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/09_assembly.yaml

@@ -10,7 +10,7 @@ METAGENOME_TAXID: "718289"                                                    #
 SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            # One of https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#platform >>EXAMPLE: ["ILLUMINA","OXFORD_NANOPORE"]
 SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018']                        # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex09_assembly"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex09_asm"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"
   ISOLATION_SOURCE: "biogas plant anaerobic digester"                         # Describe where your sample was taken from >>EXAMPLE: "biogas plant anaerobic digester"
   FASTA_FILE: "data/assembly.fasta"                                           # Path to the fasta file >>EXAMPLE: "/mnt/data/assembly.fasta.gz"

examples/10_bins_mags.yaml

@@ -11,7 +11,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            #
 PROJECT_NAME: "Project ex10 idx00"                                            # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
 SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018']                        # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex10_assembly"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex10_asm"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   EXISTING_ASSEMBLY_ANALYSIS_ACCESSION:                                       # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
   EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION: 'SAMEA114745644'                     # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"

examples/11_bins.yaml

@@ -11,7 +11,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            #
 PROJECT_NAME: "Project ex11 idx00"                                            # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
 SAMPLE_ACCESSIONS: ["SAMEA113417017"]                                         # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex11_assembly"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex11_asm"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   EXISTING_ASSEMBLY_ANALYSIS_ACCESSION: "ERZ21942150"                         # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
   EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION:                                      # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"

examples/12_mags.yaml

@@ -12,7 +12,7 @@ SEQUENCING_PLATFORMS: ["ILLUMINA"]                                            #
 PROJECT_NAME: "idx00_ex12_proj"                                               # Name of the project within which the sequencing was organized >>EXAMPLE: "AgRFex 2 Biogas Survey"
 SAMPLE_ACCESSIONS: ['SAMEA113417017','SAMEA113417018']                        # These samples exist in ENA. Your assembly is based on them. >>EXAMPLE: ["ERS15898933","ERS15898932"]
 ASSEMBLY:                                         
-  ASSEMBLY_NAME: "idx00_ex12_assembly"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
+  ASSEMBLY_NAME: "idx00_ex12_asm"                                        # Choose a name, even if your assembly has been uploaded already. Will only be used for naming assembly and bins/MAGs. >>EXAMPLE: "Northern Germany biogas digester metagenome"
   EXISTING_ASSEMBLY_ANALYSIS_ACCESSION:                                       # The accession of the assembly analysis that all bins/MAGs originate from >>EXAMPLE: "GCA_012552665"
   EXISTING_CO_ASSEMBLY_SAMPLE_ACCESSION: 'SAMEA114745644'                     # The accession of the virtual sample of the co-assembly which all bins/MAGs originate from >>EXAMPLE: "ERZ21942150"
   ASSEMBLY_SOFTWARE: "MEGAHIT"                                                # Software used to generate the assembly >>EXAMPLE: "MEGAHIT"

setup.py

@@ -10,7 +10,7 @@ def run(self):
 
 setup(
     name='synum',
-    version='0.9.0',
+    version='0.9.1',
     packages=find_packages(),
     install_requires=[
         'pysam>=0.19.1',