add blast max version

refactor version matching, add test for blast max version, update readme

readme.md

@@ -91,6 +91,9 @@ For correct function the rboAnalyze needs a copy of RFAM database.
 
 There are 2 ways:
 1. Run rboAnalyzer with `--download_rfam` flag.
+    ```shell
+    rboAnalyzer --download_rfam
+    ```
 This will download RFAM covariance models to default directory
 (`[INSTALL_LOCATION]/rna_blast_analyze/3rd_party_source/rfam`).
 
@@ -230,25 +233,24 @@ rboAnalyzer -in MS1_BLAST_output -q MS1_query.fasta -db genomes.fasta.bdb -html
 ```
 
 ## Solving issues:
-1. One or more records not found.
-
-  Reason: the blastdbcmd was not able to find sequence(s) with respective id(s) in provided database. This is due to inconsistency between the sequence accessions and the BLAST database.
-
-  The inconsistency may rise from
-  1. sequence is not in the database
-    Solution: Provide correct blast database (update current or create new with `genomes_from_blast`).
-  2. capturing regexp does not capture the accession number
-    Solution: Provide capturing regular expression (python 3 syntax) for capturing the sequence id from the fasta header (it must match the id to the BLAST database used)
-  3. the BLAST database was created without the `-parse_seqids` flag
-    Solution: Create new database from the sequences used to create new one, this time with `-parse_seqids` flag.
+- __One or more records not found__
+  Reason: the blastdbcmd was not able to find sequence(s) with respective id(s) in provided database.
+  This is due to inconsistency between the sequence accessions and the BLAST database.
+  The inconsistency may rise from:
+    1. __sequence is not in the database__
+      Solution: Provide correct blast database (update current or create new with `genomes_from_blast`).
+    2. __capturing regexp does not capture the accession number__
+      Solution: Provide capturing regular expression (python 3 syntax) for capturing the sequence id from the fasta header (it must match the id to the BLAST database used)
+    3. __the BLAST database was created without the `-parse_seqids` flag__
+      Solution: Create new database from the sequences used to create new one, this time with `-parse_seqids` flag.
 
   Another option is to call pipeline with `--skip_missing` flag.
   This will skip the missing sequences.
 
   Note that no HSP for the missing sequence will be included in pipeline output
   and some prediction methods may be influenced by the missing sequence.
 
-2. The `genomes_from_blast` failed
+- __The `genomes_from_blast` failed__
   The `genomes_from_blast` script has build in handling of failed downloads,
   but by default it tries only 10 times. If you are on instable connection
   you might get better results by setting the `--retry` to some larger number.

rna_blast_analyze/BR_core/BA_verify.py

@@ -2,14 +2,15 @@
 import os
 import re
 import sys
+import operator
 from subprocess import check_output, STDOUT, CalledProcessError
 
 from rna_blast_analyze.BR_core import cmalign
 from rna_blast_analyze.BR_core.config import CONFIG
 from rna_blast_analyze.BR_core.tools_versions import blast_minimal_version, locarna_minimal_version, \
     infernal_minimal_version, vrna_minimal_version, clustalo_minimal_version, muscle_minimal_version, \
     centroid_homfold_minimal_version, turbofold_minimal_version,\
-    mfold_minimal_version, method_required_tools
+    mfold_minimal_version, method_required_tools, blast_maximal_version
 
 ml = logging.getLogger(__name__)
 
@@ -40,10 +41,10 @@ def verify_query_blast(blast, query):
     return
 
 
-def verify_blastdbcmd(minimal_version):
+def verify_blastdbcmd(minimal_version, maximal_version):
     """verify if blastdbcmd is present in supported version
     """
-    msgversion = 'blastcmd not installed in required version, required version is {}.{}.{}'.format(*minimal_version)
+    msgversion = 'blastcmd not installed in required version, required version is between {}.{}.{} and {}.{}.{}'.format(*minimal_version + maximal_version)
     msgpath = '{}blastcmd could not be located (not in PATH)'.format(CONFIG.blast_path)
     msgsuccess = 'blastcmd is installed in required version'
     try:
@@ -58,15 +59,12 @@ def verify_blastdbcmd(minimal_version):
         if r:
             ver = r.group().split('.')
             ver = [int(i) for i in ver]
-            for v, minv in zip(ver, minimal_version):
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            bb_min = version_check(ver, minimal_version, msgsuccess, msgversion)
+            bb_max = version_check(ver, maximal_version, msgsuccess, msgversion, op=operator.le)
+            if bb_min and bb_max:
+                return True
+            else:
+                return False
         else:
             ml.warning(msgversion)
             return False
@@ -88,17 +86,8 @@ def verify_locarna(minimal_version):
         )
         a = a.decode()
         if a.startswith('LocARNA'):
-            r = re.finditer('[0-9]+', a)
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', a)]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -123,15 +112,7 @@ def verify_infernal(program, minimal_version):
             r = re.search('(?<=# INFERNAL )[0-9.]+', a)
             ver = r.group().split('.')
             ver = [int(i) for i in ver]
-            for v, minv in zip(ver, minimal_version):
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            return version_check(ver, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -153,16 +134,8 @@ def verify_viennarna_program(program, minimal_version):
         )
         a = a.decode()
         if a.startswith(program):
-            ver = a.split()[1].split('.')
-            for v, minv in zip(ver, minimal_version):
-                if int(v) > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif int(v) < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            ver = [int(i) for i in a.split()[1].split('.')]
+            return version_check(ver, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -217,17 +190,8 @@ def verify_clustalo(minimal_version):
         )
         a = a.decode()
         if a:
-            r = re.finditer('[0-9]+', a)
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', a)]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -249,17 +213,8 @@ def verify_muscle(minimal_version):
         )
         a = a.decode()
         if a.startswith('MUSCLE'):
-            r = re.finditer('[0-9]+', a)
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', a)]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -288,17 +243,8 @@ def verify_centroid_homfold(minimal_version):
         a = a.decode()
         b = a.split()
         if b[0] == 'CentroidHomfold':
-            r = re.finditer('[0-9]+', b[1])
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', b[1])]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -326,17 +272,8 @@ def verify_turbofold(minimal_version):
         a = a.decode()
         b = a.split()
         if b[0] == 'TurboFold:':
-            r = re.finditer('[0-9]+', b[2])
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', b[2])]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -374,17 +311,8 @@ def verify_mfold(minimal_version):
         a = a.decode()
         b = a.split()
         if b[0] == 'hybrid-ss-min':
-            r = re.finditer('[0-9]+', b[2])
-            for match, minv in zip(r, minimal_version):
-                v = int(match.group())
-                if v > minv:
-                    ml.info(msgsuccess)
-                    return True
-                elif v < minv:
-                    ml.warning(msgversion)
-                    return False
-            ml.info(msgsuccess)
-            return True
+            r = [int(m.group()) for m in re.finditer('[0-9]+', b[2])]
+            return version_check(r, minimal_version, msgsuccess, msgversion)
         else:
             ml.warning(msgversion)
             return False
@@ -393,9 +321,21 @@ def verify_mfold(minimal_version):
         return False
 
 
+def version_check(r, minimal_version, msgsuccess, msgversion, op=operator.ge):
+    for v, minv in zip(r, minimal_version):
+        if op(v, minv):
+            ml.info(msgsuccess)
+            return True
+        elif op(minv, v):
+            ml.warning(msgversion)
+            return False
+    ml.info(msgsuccess)
+    return True
+
+
 def check_3rd_party_tools():
     installed = set()
-    if verify_blastdbcmd(blast_minimal_version):
+    if verify_blastdbcmd(blast_minimal_version, blast_maximal_version):
         installed.add('blastdbcmd')
 
     if verify_locarna(locarna_minimal_version):

rna_blast_analyze/BR_core/tools_versions.py

@@ -1,4 +1,5 @@
 blast_minimal_version = [2, 6, 0]
+blast_maximal_version = [2, 8, 0]
 locarna_minimal_version = [1, 9, 2]
 infernal_minimal_version = [1, 1, 2]
 vrna_minimal_version = [2, 3, 5]

test_func/test_verify_version.py

@@ -0,0 +1,25 @@
+import unittest
+import operator
+from rna_blast_analyze.BR_core.BA_verify import version_check
+
+
+class TestBlastParser(unittest.TestCase):
+    def test_less(self):
+        self.assertTrue(
+            version_check([2, 1, 0], [2, 0, 0], '', '')
+        )
+
+    def test_greater(self):
+        self.assertTrue(
+            version_check([2, 0, 0], [2, 1, 0], '', '', op=operator.le)
+        )
+
+    def test_equal(self):
+        self.assertTrue(
+            version_check([1, 1, 1], [1, 1, 1], '', '')
+        )
+
+    def test_equal2(self):
+        self.assertTrue(
+            version_check([1, 1, 1], [1, 1, 1], '', '', op=operator.le)
+        )