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https://github.com/jimhester/fasta_utilities

A collection of scripts developed to interact with fasta, fastq and sam/bam files.
https://github.com/jimhester/fasta_utilities

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A collection of scripts developed to interact with fasta, fastq and sam/bam files.

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# Fasta Utilities #



A collection of scripts developed to interact with FASTA, FASTQ and SAM files.

All the scripts use the ReadFastx module I wrote, which reads either a FASTA

or FASTQ file by record.  It also uses the FileBar module, which gives

a terminal progress bar on a file as it is processed.  ReadSam is the SAM

equivalent.



## Conversion ##

* 2big.pl                 -  takes a bed, SAM, or wiggle file and creates a big

  version of it to upload to ucsc

* fastq2fasta.pl          -  converts FASTQ to FASTA

* sam2fastq.pl            -  Converts a SAM format to FASTQ format

* mate_pair2paired_end.pl -  converts mate pair reads to paired end orientation



## Reformatting ##

* fix_headers.pl       -  fixes the FASTQ header by removing spaces and

  optionally appending a suffix

* remap_file.pl        -  takes a file with tab delimited mappings and

  substitutes each of the first terms for each of the second terms

* standardize_names.pl -  renames FASTA files from ncbi into uscs nomenclature

  chr##

* unique_headers.pl    -  reads a FASTA file and ensures all of the names are

  unique

* wrap.pl              -  limits FASTA lines to 80 characters



## Modification ##

* bisulfite_convert.pl  -  bisulfite converts the sequences given to it

* merge_records.pl      -  merges all the input records into one record, by

  default uses the name of the first record, but can be changed with -name

* reverse_complement.pl -  takes sequences and reverse complements them

* trim_fasta.pl         -  trims a fastx file to x bp

* pairs_sorted.pl       -  takes two files of reads sorted by header, and

  outputs two files containing those reads which have pairs

* pairs_unsorted.pl     -  gets the pairs of the files in the first file from

  the second file, pairs are matched by header name

* regex_fasta.pl        -  applies the given regex to the FASTA headers or

  sequence

* remove_ambiguous.pl   -  removes ambiguity codes from FASTA files

* splice.pl             -  splice a FASTA file given a gff file

* split_fasta.pl        -  splits a multi FASTA file into multiple files, can

  split in different ways

* subset_fasta.pl       -  subsets a FASTA file

* trans_fasta.pl        -  translate a FASTA cDNA to protein

* generate_fasta.pl     -  create a random FASTA file

* consensus.pl          -  generate a consensus FASTA file from a bam file



## Filtering ##

* filter_align.pl -  filters alignments from a bam or SAM file

* filter_reads.pl -  filters aligned reads from a file by mapping with bowtie2

* get_fasta.pl    -  selects FASTA records which match or don't match a pattern

* in_list.pl      -  reads a list of headers, and a fastx file and outputs

  records which are in the list

* size_select.pl  -  returns the sequences with lengths between the values

  specified by -low and -high

* sort.pl         -  sorts a FASTA file using gnu sort, can sort by header,

  sequence, length ect.



## Information ##

* avg_coverage.pl -  gets the average coverage per sequence from a bam file

* lengths.pl      -  length of each record

* calcN.pl        -  takes a file of FASTA lengths, or a FASTA or FASTQ file

  directly, and calculates the nX of the file, by default N50

* CpG_count.pl    -  counts the number of CpGs in a FASTA file

* distances.pl    -  get the within group bitscore distance of all the records

  in a FASTA file using blast

* fasta_head.pl   -  emulates unix head for FASTA and FASTQ files

* fasta_tail.pl   -  emulates unix tail for FASTA and FASTQ files

* percent_GC.pl   -  calculates percent GC for each FASTA record in a file, as

  well as the total GC content

* sam_lengths.pl  -  gets the sequence lengths from a SAM file

* size.pl         -  gets the total size of a FASTA file and the number of

  sequences



## Bed scripts ##

* absolute_coordinates.pl -  takes a file with the chromosome and location and

  a file of chromosome sizes, and converts the coordinates to an absolute scale

  for plotting

* bed2igv.pl              -  converts a bed file to a igv snapshot script

* combine_bed.pl          -  Combine bed files

* gff2bed.pl              -  converts a gff file to a bed file



## Miscellaneous ##

* align_progress.pl    -  given the input filename and the output filename,

  figures out the last line using tail, then greps for that header in the

  input, and works out the percentage that way

* blast_information.pl -  gets sequence information from gi numbers from

  a blast results file

* fetch_entrez.pl      -  Download a number of sequences from an entrez query

* fetch_gi.pl          -  download FASTA files from NCBI and outputs a FASTA file

* fetch_sra.pl         -  downloads the sra sequences from NCBI using aspera

  and outputs a FASTQ file

* generate_map.pl      -  remaps FASTA sequences from the first file to FASTA

  sequences from the second file, matches by hashing the sequence

* mpileup_counts.pl    -  parses a mpileup file and gets the base counts

* rename_script.pl     -  Rename a file, changing any references to the old

  name in the file to the new name



## Installation ##

Install with optional prefix, omit the prefix if you want to install

system-wide.

```bash

perl Makefile.PL PREFIX=$HOME

make

make install

```