XspecT 0.1.0__py3-none-any.whl → 0.1.3__py3-none-any.whl

xspect/train_filter/README_XspecT_Erweiterung.md

@@ -0,0 +1,119 @@
+# XspecT-Erweiterung
+
+Expands XspecT, so new filter for a genus can automatically be trained. It's main 
+script is XspecT_trainer.py. The rest of the scripts are inside the python module 
+train_filter. 
+
+## Training new filter
+
+XspecT_trainer.py uses command line arguments. The examples for using XspecT_trainer.py
+are using Salmonella since this genus only has two defined species in the NCBI 
+databases.
+
+### Jellyfish
+
+The program jellyfish is used to count distinct k-meres in the assemblies. For XspecT_
+trainer.py to work jellyfish needs to be installed. It can be installed using bioconda:
+
+`
+conda install -c bioconda jellyfish
+`
+
+### Training examples
+
+New filters with assemblies from NCBI RefSeq can be trained with the following line. The 
+python libraries from [requirements.txt](..%2Frequirements.txt) need to be installed.
+
+`
+python XspecT_trainer.py Salmonella 1
+`
+
+Training filters with custom data can be done using the following line.
+
+`
+python XspecT_trainer.py Salmonella 2 -bf /path/to/concate_assemblies -svm 
+/path/to/assemblies
+`
+
+All command line arguments are explained using the following line.
+
+`
+python XspecT_trainer.py -h
+`
+
+# Explanation of the scripts
+
+## backup_filter.py
+
+Creates a backup of all files needed for the species assignment by XspecT for a specific
+genus. The backup will be done, if new filters will be created for a genus which 
+already has trained filters.
+
+## create_svm.py
+
+Downloads the needed assemblies and trains a support-vector-machine for the genus.
+
+## extract_and_concatenate.py
+
+Unzips the downloaded assemblies. Concatenates assemblies per species that will be used 
+to train the bloomfilters.
+
+## get_paths.py
+
+Functions that get specific paths.
+
+## html_scrap.py
+
+Updates a list of all NCBI RefSeq assembly accessions that have a taxonomy check result
+of OK. The taxonomy check from NCBI RefSeq uses the ANI (average-nucleotide-
+identity) to compute a result.
+
+## interface_XspecT.py
+
+Mostly functions that train new bloomfilters automatically. The functions were 
+originally writen for XspecT in a non-automatic way and were updated.
+
+## k_mer_count.py
+
+Uses jellyfish to count distinct k-meres in every concatenated assembly. The highest
+count will be used to compute the size of the bloomfilters.
+
+## ncbi_api
+
+A module which makes requests to the NCBI Datasets API.
+
+### download_assemblies.py
+
+The specific function that downloads assemblies from NCBI RefSeq using NCBI 
+datasets.
+
+### ncbi_assembly_metadata.py
+
+Takes a dictionary with species and their taxon ID and asks NCBI for assemblies of
+the species. Saves the collected accessions of the found and selected assemblies.
+
+### ncbi_children_tree.py
+
+Takes the name or ID of a genus and gives a list with all its species.
+
+### ncbi_taxon_metadata.py
+
+Takes a list with taxon and collects metadata like their scientific name and rank.
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+

xspect/train_filter/create_svm.py

@@ -127,7 +127,7 @@ def perform_lookup(bloomfilter, files, file_paths, accessions, names, spacing):
             # Dominik: changed sample size to var
             for j in range(0, len(sequence.seq) - BF.k, spacing):
                 BF.number_of_kmeres += 1
-                BF.lookup(str(sequence.seq[j : j + BF.k]))
+                BF.lookup_canonical(str(sequence.seq[j : j + BF.k]))
 
         score = BF.get_score()
         score = [str(x) for x in score]

XspecT-0.1.0.dist-info/RECORD

@@ -1,31 +0,0 @@
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-xspect/WebApp.py,sha256=eo1EJOMjW5grCZyvX5g1J4ppwyZb_M9lYGCNuJidM0Q,25224
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-xspect/train_filter/extract_and_concatenate.py,sha256=kXGqCrOk3TbOkKLJV8nKC6nL8Zg0TWKDCJu2gq8K_cw,5239
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-xspect/train_filter/html_scrap.py,sha256=iQXREhG37SNUx7gHoP8eqayMEIH00QLFMTNmIMogb_M,3799
-xspect/train_filter/interface_XspecT.py,sha256=HVCwVHqtvJ1EA9u6GByeKCve-6sADK5AceB5itPV62k,6735
-xspect/train_filter/k_mer_count.py,sha256=0yHCxzsOH8LhO6tD35O7BjWodfE5lJDKWYzzcCrr0JE,5226
-xspect/train_filter/ncbi_api/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-xspect/train_filter/ncbi_api/download_assemblies.py,sha256=iX1qK8R6p2b3RiHPfqVsLp-dV_7iZZv0AxY1xQ-Ad48,1171
-xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py,sha256=RhHvxKiQ8HJgoSb6njYEgO_vPioBqEMPvT3lE2lHXp0,3766
-xspect/train_filter/ncbi_api/ncbi_children_tree.py,sha256=pmzg6-fDGLinNSXNbBRv0v62lRgHxW4aXZ0uV1TJhOE,1793
-xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py,sha256=uhBBGffgL4mcJpyp9KxVyOGUh8FxUTAI4xKzoLDav_Y,1577
-XspecT-0.1.0.dist-info/LICENSE,sha256=bhBGDKIRUVwYIHGOGO5hshzuVHyqFJajvSOA3XXOLKI,1094
-XspecT-0.1.0.dist-info/METADATA,sha256=z0sd9RECNiNoQPrLPDzHf-VmgWI4B1qDnvy1a8X2kuQ,5475
-XspecT-0.1.0.dist-info/WHEEL,sha256=oiQVh_5PnQM0E3gPdiz09WCNmwiHDMaGer_elqB3coM,92
-XspecT-0.1.0.dist-info/entry_points.txt,sha256=L7qliX3pIuwupQxpuOSsrBJCSHYPOPNEzH8KZKQGGUw,43
-XspecT-0.1.0.dist-info/top_level.txt,sha256=hdoa4cnBv6OVzpyhMmyxpJxEydH5n2lDciy8urc1paE,7
-XspecT-0.1.0.dist-info/RECORD,,