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

        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)

       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

   standardarguments:-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: ('|', '=', ','))

   pairingarguments:--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)

   outputfiles:
              pair-pass

              successfully paired reads with modified annotations.

              pair-fail

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

   outputannotationfields:
              <user defined>

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

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