fix path to refspec fa; add amino to hmmbuild

Author: trvinh

fdog/checkData.py

@@ -127,50 +127,13 @@ def write_faChecked(fa_file):
 
 def check_fasta(args):
     """ Check fasta file in searchTaxa_dir and coreTaxa_dir """
-    # taxon_list = []
-    # for fd in general_fn.read_dir(checkDir):
-    #     taxon = fd
-    #     check_valid_folder_name('%s/%s' % (checkDir, taxon))
-    #     for file in listdir('%s/%s' % (checkDir, taxon)):
-    #         if file.endswith('.fa'):
-    #             fa_file = '%s/%s/%s' % (checkDir, taxon, file)
-    #             if os.path.islink(fa_file):
-    #                 fa_file = os.path.realpath(fa_file)
-    #             general_fn.check_file_exist(fa_file)
-    #             checkfa_file = check_valid_fasta(fa_file)
-    #             taxon_list.append(taxon)
-    #             if not os.path.exists('%s.checked' % fa_file):
-    #                 print(taxon)
-    #                 if list(checkfa_file.keys())[0] == 'notFasta':
-    #                     sys.exit('*** ERROR: %s does not look like a fasta file!' % fa_file)
-    #                 elif list(checkfa_file.keys())[0] == 'longHeader':
-    #                     sys.exit('*** ERROR: %s contains long headers! E.g. %s' % (fa_file, list(checkfa_file.values())[0]))
-    #                 elif list(checkfa_file.keys())[0] == 'space':
-    #                     sys.exit('*** ERROR: %s contains spaces/tabs!' % fa_file)
-    #                 elif list(checkfa_file.keys())[0] == 'multiLine':
-    #                     if not concat:
-    #                         print('*** ERROR: %s contains multiple-line sequences!' % fa_file)
-    #                         sys.exit('Please use "--concat" with "--replace" or "--delete" to join them into single lines')
-    #                     else:
-    #                         rewrite_seqs(fa_file, replace, delete)
-    #                 elif list(checkfa_file.keys())[0] == 'ok':
-    #                     if not (delete or replace):
-    #                         check_valid_seqs(fa_file)
-    #                     else:
-    #                         rewrite_seqs(fa_file, replace, delete)
-    #                 write_faChecked(fa_file)
-    #             if not os.path.exists('%s.fai' % fa_file):
-    #                 fasta_fn.read_fasta(fa_file)
-    # return(taxon_list)
     (taxon, file, checkDir, replace, delete, concat) = args
     fa_file = '%s/%s/%s' % (checkDir, taxon, file)
     if os.path.islink(fa_file):
         fa_file = os.path.realpath(fa_file)
     general_fn.check_file_exist(fa_file)
     checkfa_file = check_valid_fasta(fa_file)
-    # taxon_list.append(taxon)
     if not os.path.exists('%s.checked' % fa_file):
-        print(taxon)
         if list(checkfa_file.keys())[0] == 'notFasta':
             sys.exit('*** ERROR: %s does not look like a fasta file!' % fa_file)
         elif list(checkfa_file.keys())[0] == 'longHeader':

fdog/libs/hmm.py

@@ -25,7 +25,7 @@
 
 def create_hmm(aln_file, out_file):
     """ Create hmm file for an alinment file """
-    hmmbuild_cmd = 'hmmbuild %s %s' % (out_file, aln_file)
+    hmmbuild_cmd = 'hmmbuild --amino %s %s' % (out_file, aln_file)
     try:
         subprocess.run(
             [hmmbuild_cmd], shell = True,

fdog/libs/orthosearch.py

@@ -46,7 +46,7 @@ def hamstr(args):
     ### (00) Parse input files
     hmm_file = '%s/%s/hmm_dir/%s.hmm' % (hmmpath, seqName, seqName)
     refspec_db = '%s/%s/%s' % (corepath, refspec, refspec)
-    refspec_fa = '%s/%s/%s.fa' % (searchpath, refspec, refspec)
+    refspec_fa = '%s/%s/%s.fa' % (corepath, refspec, refspec)
     search_fa = '%s/%s/%s.fa' % (searchpath, search_taxon, search_taxon)
     ### (000) Adapt parameters
     if rbh == True:
@@ -260,7 +260,7 @@ def run_hamstr(args):
                     hamstr_out = {**hamstr_out, **_}
 
     ### Get seed seq
-    refspec_fa = '%s/%s/%s.fa' % (searchpath, refspec, refspec)
+    refspec_fa = '%s/%s/%s.fa' % (corepath, refspec, refspec)
     refspec_seqs = fasta_fn.read_fasta(refspec_fa)
     seed_id_mod = '%s|%s|%s|1' % (seqName, refspec, seed_id)
     seed_seq = refspec_seqs.fetch(seed_id)

setup.py

@@ -9,7 +9,7 @@
 #  the Free Software Foundation, either version 3 of the License, or
 #  (at your option) any later version.
 #
-#  hamstr1s is distributed in the hope that it will be useful,
+#  fdog is distributed in the hope that it will be useful,
 #  but WITHOUT ANY WARRANTY; without even the implied warranty of
 #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 #  GNU General Public License for more details.