NAME

       PairSeq.py - Sorts and matches sequence records with matching coordinates across files

DESCRIPTION

       usage: PairSeq.py [--version] [-h] -1 SEQ_FILES_1 [SEQ_FILES_1 ...] -2

              SEQ_FILES_2  [SEQ_FILES_2  ...]  [--outdir  OUT_DIR]  [--outname  OUT_NAME]  [--failed]  [--fasta]
              [--delim DELIMITER DELIMITER DELIMITER] [--1f FIELDS_1 [FIELDS_1 ...]]  [--2f  FIELDS_2  [FIELDS_2
              ...]] [--act {min,max,sum,set,cat}] [--coord {illumina,solexa,sra,454,presto}]

       Sorts and matches sequence records with matching coordinates across files

   help:
       --version
              show program's version number and exit

       -h, --help
              show this help message and exit

   standard arguments:
       -1 SEQ_FILES_1 [SEQ_FILES_1 ...]
              An ordered list of FASTA/FASTQ files containing head/primary sequences. (default: None)

       -2 SEQ_FILES_2 [SEQ_FILES_2 ...]
              An ordered list of FASTA/FASTQ files containing tail/secondary sequences. (default: None)

       --outdir OUT_DIR
              Specify  to  changes  the  output directory to the location specified. The input file directory is
              used if this is not specified. (default: None)

       --outname OUT_NAME
              Changes the prefix of the successfully processed output file to the string specified. May  not  be
              specified with multiple input files. (default: None)

       --failed
              If specified create files containing records that fail processing. (default: False)

       --fasta
              Specify to force output as FASTA rather than FASTQ.  (default: None)

       --delim DELIMITER DELIMITER DELIMITER
              A list of the three delimiters that separate annotation blocks, field names and values, and values
              within a field, respectively. (default: ('|', '=', ','))

   pairing arguments:
       --1f FIELDS_1 [FIELDS_1 ...]
              The  annotation  fields  to  copy  from file 1 records into file 2 records. If a copied annotation
              already exists in a file 2 record, then the annotations copied from file 1 will be  added  to  the
              front of the existing annotation. (default: None)

       --2f FIELDS_2 [FIELDS_2 ...]
              The  annotation  fields  to  copy  from file 2 records into file 1 records. If a copied annotation
              already exists in a file 1 record, then the annotations copied from file 2 will be  added  to  the
              end of the existing annotation. (default: None)

       --act {min,max,sum,set,cat}
              The collapse actions to take on all fields copied between files to combine duplicate fields into a
              single  value. The actions "min", "max", "sum" perform the corresponding mathematical operation on
              numeric annotations. The action "set" collapses annotations into a comma delimited list of  unique
              values.  The  action  "cat" concatenates the values together into a single string. Only applies if
              the field already exists in the header before being copying from the other file. (default: None)

       --coord {illumina,solexa,sra,454,presto}
              The format of the sequence identifier which defines  shared  coordinate  information  across  mate
              pairs.  (default: presto)

   output files:
              pair-pass

              successfully paired reads with modified annotations.

              pair-fail

              raw reads that could not be assigned to a mate-pair.

   output annotation fields:
              <user defined>

              annotation fields specified by the --1f or --2f arguments.

AUTHOR

        This manpage was written by Andreas Tille for the Debian distribution and
        can be used for any other usage of the program.

PairSeq.py 0.6.0                                    May 2020                                       PAIRSEQ.PY(1)