thys

bin/bash/Progenio

@@ -126,10 +126,10 @@ if [ ! -d $outdir/jbrowse ] ; then
     # not needed  #mq_strains2ref_peptides.py $config $outdir  || ( rm -rf $outdir/jbrowse ; exit 1 )
     mq_strains2ref.py $config $outdir      || ( rm -rf $outdir/jbrowse ; exit 1 )	
     mq_reference_features.py $config $outdir
+    mq_peptide_features.py $config $outdir
+    mq_jbrowse_upload_script.py $config $outdir || ( rm -rf $outdir/jbrowse_ ; exit 1 )
 fi
 
-mq_peptide_features.py $config $outdir
-mq_jbrowse_upload_script.py $config $outdir || ( rm -rf $outdir/jbrowse_ ; exit 1 )
 
 
 #exit 0

bin/python/mq_peptide_to_protein.py

@@ -272,7 +272,7 @@ def peptide_list_blast(peptides, targets, features):
 
     #pg = pg.head(10)
 
-    combined = pg
+    combined = pg.copy()
 
 
     for row in combined.iterrows():

bin/python/mq_reference_features.py

@@ -85,6 +85,10 @@ def load_gff3(file):
 
 
 for ref in config['reference']:
+    proteome_id = config['reference'][ref]['proteome_id']
+    with open(output + '/blast/orfs2proteins/{}_mapping.json'.format(proteome_id), 'r') as f:
+        orf2protein = json.load(f)
+
     assembly_id = config['reference'][ref]['assembly_id']
     for strain in config['strains']:
 
@@ -142,23 +146,28 @@ def load_gff3(file):
         rows = ['##gff-version 3']
         feature_rows = ['##gff-version 3']
         seen = []
-
-        for orf, group in peptide_annotations.groupby('ORF_id'):
-           #orf = group['ORF_id'].values[0]
-
+
+
+        #for orf, group in peptide_annotations.groupby('ORF_id'):
+        for orf_id in list(set(ref_orfs['ORF_id'].tolist())):
+
+           group = peptide_annotations[peptide_annotations['ORF_id'].apply(lambda x:x.split('|')[1] == orf_id)]
+           assert len(group['ORF_id'].unique()) <= 1 
            #var_start = group['PeptidePosition'].min()
 
            #var_peps = peptide_annotations[peptide_annotations['ORF_id'] == orf]
            #var_pe
 
 
-           blastp_list  = group['BLASTP'].values
-           assert len(set(blastp_list)) == 1
-           blastp = blastp_list[0]
+           try:
+               blastp = orf2protein[orf_id][0]
+           except:
+               blastp = 'None'
+           #orf_id = orf.split('|')[1]
 
-           orf_id = orf.split('|')[1]
            #print(group) 
            orf_filt = ref_orfs[ref_orfs['ORF_id'] == orf_id]
+
            if len(orf_filt) == 0:
                continue
            feat_id = orf_filt['ID'].values[0]
@@ -194,6 +203,7 @@ def load_gff3(file):
                orf_peptides = [] 
                # iterate through the proteoform peptides
                for row in group.iterrows():
+                   orf = row[1]['ORF_id']
                    var_id = row[1]['VarId']
 
                    if isinstance(var_id, str):