fxtools

light-weight processing tool for FASTA, FASTQ and BAM format data

Installation

git clone https://github.com/yangao07/fxtools.git --recursive
cd fxtools; make

Commands and options

Program: fxtools (light-weight processing tool for FASTA, FASTQ and BAM format data)
Usage:   fxtools <command> [options]

Command: 
         filter (fl)           filter fa/fq sequences with specified length boundary.
         filter-name (fn)      filter fa/fq sequences with specified name.
         filter-bam (fb)       filter bam/sam records with specified read length boundary.
         filter-bam-name (fbn) filter bam/sam records with specified read name.
         split-fx (sx)         split fa/fq file into multipule files.
         fq2fa (qa)            convert FASTQ format data to FASTA format data.
         fa2fq (aq)            convert FASTA format data to FASTQ format data.
         bam2bed (bb)          convert BAM file to BED file. seperated exon regions for spliced BAM
         re-co (rc)            convert DNA sequence(fa/fq) to its reverse-complementary sequence.
         seq-display (sd)      display a specified region of FASTA/FASTQ file.
         cigar-parse (cp)      parse the given cigar(stdout).
         length-parse (lp)     parse the length of sequences in fa/fq file.
         merge-fa (mf)         merge the reads with same read name in fasta/fastq file.
         merge-filter-fa (mff) merge and filter the reads with same read name in fasta file.
         duplicate-fa (df)     duplicate the read sequence with specific copy number.
         error-parse (ep)      parse indel and mismatch error based on CIGAR and NM in bam file.
         dna2rna (dr)          convert DNA fa/fq to RNA fa/fq.
         rna2dna (rd)          convert RNA fa/fq to DNA fa/fq.
         trim (tr)             trim poly A tail(poly T head).
         trimF (tf)            trim and filter with poly A tail(poly T head). Only poly A contained reads will be kept.