2 Bugs Fixed

[HaoranPeng21]

grep: /scratch/p312334/project/3--BCG/test_FunOMIC/003_V1/tmp/003_V1.30.c80.list: No such file or directory
[E::hts_open_format] Failed to open file --threads
samtools idxstats: failed to open "--threads": No such file or directory
/scratch/p312334/database/FunOMIC/get_pwy_abundance_v1.py:68: DtypeWarning: Columns (3) have mixed types. Specify dtype option on import or set low_memory=False.
  jgi_ann=pd.read_csv(ann_path,delimiter='\t',names=column_names,index_col=False,dtype={'fourth_column': 'str'})
/scratch/p312334/database/FunOMIC/get_pwy_abundance_v1.py:70: DtypeWarning: Columns (1) have mixed types. Specify dtype option on import or set low_memory=False.
  rid_to_uniprot_species=pd.read_csv(uniprot_catalog,delimiter='\t',names=["rid","uniprotId","speciesID"],dtype={'first_column': 'str', 'second_column': 'str'},index_col=False)
Traceback (most recent call last):
  File "/scratch/p312334/database/FunOMIC/get_pwy_abundance_v1.py", line 109, in <module>
    pwy_counts=pwy_counts.append(inter,ignore_index = True,sort=False)
  File "/scratch/p312334/database/conda/envs/FunOMIC/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in __getattr__
    return object.__getattribute__(self, name)
AttributeError: 'DataFrame' object has no attribute 'append'

Here are the bugs I encountered.

1. grep -f $outdir/tmp/${prefix}.30.c80.list: No such file or directory
   This bug is related to coverageFilter.py
   q30sam=pd.read_csv(q30reads,delimiter='\t', error_bad_lines=False,names=["QNAME","FLAG","RNAME","POS","MAPQ","CIGAR","RNEXT","PNEXT","TLEN","SEQ","QUAL","BT1","BT2","BT3","BT4","BT5","BT6","BT7","BT8","BT9","BT10","BT11"]) ---->>
   q30sam=pd.read_csv(q30reads,delimiter='\t', on_bad_lines='skip',names=["QNAME","FLAG","RNAME","POS","MAPQ","CIGAR","RNEXT","PNEXT","TLEN","SEQ","QUAL","BT1","BT2","BT3","BT4","BT5","BT6","BT7","BT8","BT9","BT10","BT11"])

2. samtools idxstats: failed to open "--threads": No such file or directory
   This bug is in FunOMIC.sh
   samtools idxstats --threads $threads $outdir/tmp/${prefix}.30.c80.bam > $outdir/tmp/${prefix}.idxstats.txt
   ---->>>
   samtools idxstats $outdir/tmp/${prefix}.30.c80.bam > $outdir/tmp/${prefix}.idxstats.txt

3. File "/scratch/p312334/database/FunOMIC/buglist.py", line 62, in
   new=pd.concat([kingdom_counts.kingdom.append(phylum_counts.combined).append(class_counts.combined).append(order_counts.combined).append(family_counts.combined).append(genus_counts.combined).append(species_counts.combined),kingdom_counts.Abundance.append(phylum_counts.Abundance).append(class_counts.Abundance).append(order_counts.Abundance).append(family_counts.Abundance).append(genus_counts.Abundance).append(species_counts.Abundance)],axis=1)
   File "/scratch/p312334/database/conda/envs/FunOMIC/lib/python3.8/site-packages/pandas/core/generic.py", line 5989, in getattr
   return object.getattribute(self, name)
   AttributeError: 'Series' object has no attribute 'append'

This bug is related to buglist.py

new=pd.concat([kingdom_counts.kingdom.append(phylum_counts.combined).append(class_counts.combined).append(order_counts.combined).append(family_counts.combined).append(genus_counts.combined).append(species_counts.combined),kingdom_counts.Abundance.append(phylum_counts.Abundance).append(class_counts.Abundance).append(order_cou$
---->
pd.concat([kingdom_counts.kingdom,phylum_counts.combined,class_counts.combined,order_counts.combined,family_counts.combined,genus_counts.combined,species_counts.combined]),pd.concat([kingdom_counts.Abundance,phylum_counts.Abundance,class_counts.Abundance,order_counts.Abundance,family_counts.Abundance,genus_counts.Abundance,species_counts.Abundance])], axis=1)