NCBI Blast error - with Pipe symbols in fasta header

I am running NCBI blast version 2.2.28 for my analysis.  I encountered an error while making database for my local blast.

Error:

$ ~/Documents/Blast/makeblastdb -in HSA_GRCh37.p13_EnsGenes.fasta -dbtype nucl -out HSA_GRCh37.p13_EnsGenes.BlastDB -parse_seqids

Building a new DB, current time: 08/05/2016 11:11:15
New DB name:   HSA_GRCh37.p13_EnsGenes.BlastDB
New DB title:  HSA_GRCh37.p13_EnsGenes.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B

No volumes were created because no sequences were found.

Error: NCBI C++ Exception:
    "/am/ncbiapdata/release/blast/src/2.2.25/Linux64-Suse-icc/c++/ICC1010-ReleaseMT64--Linux64-Suse-icc/../src/objects/seq/../seqloc/Seq_id.cpp", line 1637: Error: ncbi::objects::CSeq_id::x_Init() - Unsupported ID type ENSG00000003137

Fasta file was okay but the header is the problem. It contained pipe symbol "|". So replaced all the pipes with an underscore "_"

$ sed -i 's/|/_/g' HSA_GRCh37.p13_EnsGenes.fasta

Database was created succesfully.

$ ~/Documents/Blast/makeblastdb -in HSA_GRCh37.p13_EnsGenes.fasta -dbtype nucl -out HSA_GRCh37.p13_EnsGenes.BlastDB -parse_seqids

Building a new DB, current time: 08/05/2016 11:12:05
New DB name:   HSA_GRCh37.p13_EnsGenes.BlastDB
New DB title:  HSA_GRCh37.p13_EnsGenes.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 215647 sequences in 15.894 seconds.

Reverse complement fastq to fastq/a

When dealing with long insert mate pairs, some tools like Reapr might need the reads to be reverse complemented fastq in order to run the tool. So, I started searching for some softwares which can actually do what I wanted that.

One of the tool, I most of the times used was fastx_toolkit. It has a utility called fastx_reverse_complement by which I could convert all fastq to rc fastq files.

FASTQ to REV-COMP FASTQ:

$ fastx_reverse_complement -i sample.fastq -o rc_sample_fastx_tk.fastq

FASTQ to REV-COMP FASTA:

Sometimes, we might have to reverse complement fastq and need to convert to fasta file. This could be achieved by running revseq tool in EMBOSS with the following command:

$ revseq -sequence sample.fastq -outseq rc_sample.fasta -notag

* If there is a following error

fastx_reverse_complement: Invalid quality score value (char '0' ord 48 quality value -16) on line 4

Try pasting "-Q33" (without quotes) after fastx_reverse_complement.

Rename the fasta file with the first sequence header

Suppose there are multiple fasta files with single sequence. We want to rename the fasta file with the header of the single sequence present in the fasta file. We can run the following command.

Place all the fasta files you want to change the file names in one directory and run the following command.

for i in *; do if [ ! -f $i ]; then echo "skipping $i"; else newname=`head -1 $i | sed 's/^\s*\([a-zA-Z0-9]\+\).*$/\1/'`; [ -n "$newname" ] ; mv -i $i $newname.fasta || echo "error at: $i"; fi; done | rename s/ // *.fasta